http://192.168.164.12:81/ricewiki/api.php?action=feedcontributions&feedformat=atom&user=LinaRiceWiki - User contributions [en]2026-05-24T06:02:38ZUser contributionsMediaWiki 1.30.0https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0271200&diff=183373Os04g02712002014-06-10T07:32:58Z<p>Lina: /* References */</p>
<hr />
<div>Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" /><br />
<br />
*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.<br />
<br />
*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" /> <br />
<br />
*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" /><br />
<br />
*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" /><br />
<br />
*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" /><br />
<br />
*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" /><br />
<br />
*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" /><br />
<br />
*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" /><br />
<br />
===Expression===<br />
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" /><br />
<br />
*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" /><br />
<br />
*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" /> <br />
<br />
*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" /><br />
<br />
*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" /><br />
<br />
*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" /><br />
<br />
[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]<br />
<br />Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated.<br /><br />
<br />
[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]<br />
<br />Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. <br /><br />
<br />
[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]<br />
<br />Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.<br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br />
===Evolution===<br />
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.<br />
<br />
*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" /><br />
<br />
*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />. <br />
<br />
*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" /><br />
<br />
*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" /><br />
[[File:F1.small.gif]]<br />
<br />Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.<br />
<br />
*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" /> <br />
<br />
*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" /><br />
<br />
==Labs working on this gene==<br />
<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)<br />
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)<br />
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)<br />
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.<br />
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China<br />
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of <br />
*Institute of Plant Biology, National Taiwan University, Taipei<br />
*University of Chinese Academy of Sciences, Beijing 100049, China<br />
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref><br />
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref><br />
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref><br />
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref><br />
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref><br />
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim<br />
Subcellular localization of rice histone deacetylases in organelles<br />
FEBS Lett., 583 (2009), pp. 2249–2254</ref><br />
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou<br />
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice<br />
Plant Physiol., 144 (2007), pp. 1508–1519</ref><br />
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu<br />
Cell signaling during cold, drought, and salt stress<br />
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref><br />
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref><br />
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref><br />
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref><br />
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref><br />
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref><br />
<ref name="ref14">Rhoads DM, Subbaiah CC (2007) Mitochondrial retrograde regulation in plants. Mitochondrion 7: 177–194 </ref><br />
<ref name="ref15"> Hartl M, Finkemeier I (2012) Plant mitochondrial retrograde signaling: post-translational modifications enter the stage. Front Plant Sci 3: 253</ref><br />
<ref name="ref16"> Newman JC, He W, Verdin E (2012) Mitochondrial protein acylation and intermediary metabolism: regulation by sirtuins and implications for metabolic disease. J Biol Chem 287: 42436–42443 </ref><br />
<ref name="ref17">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref><br />
<ref name="ref18">Finkemeier I, Laxa M, Miguet L, Howden AJ, Sweetlove LJ (2011) Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol 155: 1779–1790</ref><br />
<ref name="ref19">Hollender C, Liu Z (2008) Histone deacetylase genes in Arabidopsis development. J Integr Plant Biol 50: 875–885 </ref><br />
<ref name="ref20"> Sauve AA (2010) Sirtuins. Biochim Biophys Acta 1804: 1565–1566</ref><br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0271200|<br />
Description = Silent information regulator protein Sir2 family protein|<br />
Version = NM_001058879.1 GI:115457487 GeneID:4335343|<br />
Length = 2712 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0271200, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:11382902..11385613|<br />
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581<br>,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:11382902..11385613<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:11382902..11385613<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|<br />
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|<br />
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0271200&diff=183368Os04g02712002014-06-10T07:26:33Z<p>Lina: /* Evolution */</p>
<hr />
<div>Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" /><br />
<br />
*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.<br />
<br />
*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" /> <br />
<br />
*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" /><br />
<br />
*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" /><br />
<br />
*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" /><br />
<br />
*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" /><br />
<br />
*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" /><br />
<br />
*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" /><br />
<br />
===Expression===<br />
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" /><br />
<br />
*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" /><br />
<br />
*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" /> <br />
<br />
*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" /><br />
<br />
*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" /><br />
<br />
*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" /><br />
<br />
[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]<br />
<br />Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated.<br /><br />
<br />
[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]<br />
<br />Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. <br /><br />
<br />
[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]<br />
<br />Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.<br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br />
===Evolution===<br />
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.<br />
<br />
*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" /><br />
<br />
*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />. <br />
<br />
*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" /><br />
<br />
*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" /><br />
[[File:F1.small.gif]]<br />
<br />Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.<br />
<br />
*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression,<ref name="ref14" /> posttranslational modifications of proteins are thought to be essential for the regulation of central metabolic pathways and thus determine the plasticity of plant metabolism.<ref name="ref15" /> In mammalian mitochondria, the regulation of metabolic functions by posttranslational Lys acetylation of proteins was recently discovered to be of great importance.<ref name="ref16" /> Lys acetylation can have a strong impact on the biochemical function of proteins as the transfer of the acetyl group to Lys masks the positive charge, which is known to be important in many catalytic centers of enzymes, as well as for protein-protein and protein-DNA interactions. In plants, Lys acetylation was, until recently, mainly thought to occur on histone proteins as regulatory mechanism for transcription and chromatin functions.<ref name="ref17" />However, several central metabolic enzymes of diverse subcellular compartments were recently discovered to be Lys acetylated in Arabidopsis (Arabidopsis thaliana), and in vitro deacetylation tests confirmed that Lys acetylation affects enzyme activities and protein functions.<ref name="ref18" /> <br />
<br />
*Generally, protein acetyltransferases and deacetylases are known to catalyze the reversible modification of the εN-group of Lys. In addition to the classical family of histone deacetylases, a second family of protein deacetylases exists, namely the sirtuins, which are conserved across bacteria, yeast (Saccharomyces cerevisiae), plants, and animals.<ref name="ref19" /> Sirtuins catalyze an NAD+-dependent deacetylation of acetyl-Lys in proteins and thereby produce a deacetylated Lys, as well as the metabolites nicotinamide and 2′-O-acetyl-ADP-ribose. Sirtuins have recently emerged as key regulators of life span, cell survival, apoptosis, and metabolism in different heterotrophic organisms.<ref name="ref20" /><br />
<br />
==Labs working on this gene==<br />
<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)<br />
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)<br />
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)<br />
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.<br />
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China<br />
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of <br />
*Institute of Plant Biology, National Taiwan University, Taipei<br />
*University of Chinese Academy of Sciences, Beijing 100049, China<br />
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref><br />
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref><br />
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref><br />
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref><br />
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref><br />
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim<br />
Subcellular localization of rice histone deacetylases in organelles<br />
FEBS Lett., 583 (2009), pp. 2249–2254</ref><br />
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou<br />
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice<br />
Plant Physiol., 144 (2007), pp. 1508–1519</ref><br />
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu<br />
Cell signaling during cold, drought, and salt stress<br />
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref><br />
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref><br />
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref><br />
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref><br />
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref><br />
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref><br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0271200|<br />
Description = Silent information regulator protein Sir2 family protein|<br />
Version = NM_001058879.1 GI:115457487 GeneID:4335343|<br />
Length = 2712 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0271200, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:11382902..11385613|<br />
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581<br>,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:11382902..11385613<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:11382902..11385613<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|<br />
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|<br />
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0271200&diff=183362Os04g02712002014-06-10T07:20:28Z<p>Lina: /* Evolution */</p>
<hr />
<div>Os04g0271200 is reported as '''SRT701'''and '''SRT702'''.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Histone modifications including acetylation, methylation, phosphorylation, ubiquitination and others are shown to play an important role in chromatin function and gene regulation. The homeostatic balance of nucleosomal histone acetylation is maintained by antagonistic action of histone acetyltransferases (HAT) and histone deacetylases (HDAC). Plant HDAC can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.<ref name="ref1" /><br />
<br />
*The SILENT INFORMATION REGULATOR2 (SIR2) family proteins are NAD +-dependent histone deacetylases. Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions<ref name="ref1" />.<br />
<br />
*The SIR2 family has two members in rice: SRT701 and SRT702.<ref name="ref2" /> <br />
<br />
*The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref1" />, whereas SRT702 is recently shown to be localized in the mitochondria.<ref name="ref3" /><br />
<br />
*SRT701 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of SRT701 enhanced tolerance to oxidative stress. Transcript microarray analysis revealed that the transcription of many transposons and retrotransposons in addition to genes related to hypersensitive response and/or programmed cell death was activated. Chromatin immunoprecipitation assays showed that SRT701 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by SRT701. Rice SIR2-like gene is required for safeguard against genome instability and cell damage to ensure plant cell growth.<ref name="ref1" /><br />
<br />
*SRT702 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport.SRT702 is important in fine-tuning mitochondrial energy metabolism.<ref name="ref4" /><br />
<br />
*Sir2 silences chromatin, enables DNA repair, and is involved in chromosome fidelity during meiosis (Blander and Guarente 2004). Sir2 promotes longevity by suppressing the formation of toxic extrachromosomal rDNA circles (ERCs) in yeast.<ref name="ref10" /><br />
<br />
*The Caenorhabditis elegans ortholog sir-2.1 also extends worm lifespan, but by a distinct mechanism.Sir-2.1 requires the worm forkhead protein DAF-16 for lifespan extension .<ref name="ref11" /><br />
<br />
*While earlier models suggested sir-2.1 might function by down-regulating insulin signaling, more recent findings show that sir-2.1 binds to DAF-16, activating it directly. Moreover, sir-2.1 does not respond to changes in insulin signaling, but, rather, is activated by stress treatments, such as heat shock and oxidative damage <ref name="ref12" /><br />
<br />
===Expression===<br />
*Several genes were found to have a specific expression pattern. For instance, HDA710 was more expressed in germinating and young seedlings as well as in stamens, whereas HDA703 was highly expressed in calli and in imbibed seeds. HAD714 and HDA706 were found to be mainly expressed in shoots and leaves, whereas HDA716 showed a strong expression in developing endosperm and germinating seeds. The leaf/shoot specificity of HDA714 is consistent with its protein localization in chloroplasts and mitochondria <ref name="ref6" /> , suggesting that this HDAC may play a role in plant specific functions. Three groups of closely related genes (group 1: HDA705, HDA702, HDA709, HDA710 and HDA711; group 2: HDA704 and HDA713; group 3: HDT701 and HDT702) showed a very similar expression pattern with a relatively high level in developing panicles and calli. However, the expression patterns of the two members of the Sir2-like HDACs, SRT701 and SRT702 were found to be different. The two proteins are likely to have distinct functions, as SRT701 (OsSRT1) is nuclear localized and is shown to be involved in histone H3K9 deacetlyation required for transposon repression in rice<ref name="ref7" />, whereas SRT702 is recently shown to be localized in the mitochondria. <ref name="ref6" /><br />
<br />
*Two genes (HDA703 and HDA710) are induced, while nine others (i.e. HDA701, HDA702, HDA704, HDA705, HDA706, HDA712, HDA714, HDA716, HDT701 and HDT702) are clearly repressed by drought and salt,Two additional genes (HDA709 and SRT702) are induced by drought, but repressed by salt. However, cold treatment seemed to have less impact on rice HDAC gene expression. Abscisic acid (ABA) is the major plant hormone in water stress signaling and regulates water balance and osmotic stress tolerance.<ref name="ref8" /><br />
<br />
*SRT701 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues.<ref name="ref3" /> <br />
<br />
*It has highest levels in active cell dividing organs/tissues. Down-regulation of SRT701 by RNAi induced lesion mimic cell death and precocious senescence, whereas overexpression showed tolerance to oxidative stress. <ref name="ref3" /><br />
<br />
*Cell death was induced in OsSRT1 RNAi plants. Cell death in the SRT701 RNAi plants also resembled hypersensitive response-mediated PCD. Either both types of PCD were induced by SRT701 down-regulation, or different triggers of PCD may be interdependent in plants and the downstream effectors of PCD may be shared among different pathways.<ref name="ref3" /><br />
<br />
*Western-blot analysis of enriched histone fractions detected a decrease of H3K9 acetylation in overexpression plants (Fig. 6B). The overexpression plants showed no particular visible or morphological phenotype. However, when treated with paraquat (1,1′-dimethyl-4,4′-bipyridylium), an herbicide that induces oxidative stresses in plants, the overexpression plants showed an enhanced tolerance compared to the wild type, as demonstrated by fewer and smaller lesions observed on the overexpression plants than the wild type.<ref name="ref1" /><br />
<br />
[[File:F1.medium.gif|right|thumb|360px|F1.medium.''<ref name="ref5" />'']]<br />
<br />Neighbor-joining tree of SIR2-related proteins from eukaryotes. Abbreviations are as follows (in parentheses): Arabidopsis (at), Caenorhabditis elegans (ce), Drosophila melanogaster (dm), Homo sapiens (hs), rice (os), Saccharomyces cerevisiae (sc), Schizosaccharomyces pombe (sp), wheat (ta), and maize (zm). Four subclasses are indicated.<br /><br />
<br />
[[File:F6.small.gif|left|thumb|360px|F6.small.''<ref name="ref1" />'']]<br />
<br />Overexpression of OsSRT1 conferred tolerance to paraquat treatment. A, Northern-blot analysis of OsSRT1 overexpression in different transgenic lines compared to the wild type. The 18S ribosomal RNA levels were revealed as controls. B, Western-blot analysis of enriched histone fractions from pooled samples of the overexpression plants with antibodies against acetylated histone H3K9. C, Comparison of overexpression plants with wild-type ones challenged by 10 μM paraquat. D, Comparison of leaves from overexpression and wild type treated with or without 10 μM paraquat. <br /><br />
<br />
[[File:1-s2.0-S0006291X09015459-gr1.jpg|left|thumb|360px|1-s2.0-S0006291X09015459-gr1.''<ref name="ref2" />'']]<br />
<br />Expression analysis of the rice HDAC genes. Upper: A hierarchical cluster display of relative expression levels of the rice HDAC genes in 33 samples representing different organs or tissues at different developmental stages of the Minghui 63 cultivar. 1–5: Calli at different induction stages from cultured embryos. 6: Plumule at 48 h after emergence in the dark. 7: Plumule at 48 h after emergence in the light. 8: Radical at 48 h after emergence in the dark. 9: Radical at 48 h after emergence in the light. 10: 72 h imbibed seed. 11: Embryo and radicle after germination. 12: Seedling leaves and roots at three-leaf stage. 13: Shoots of seedlings with two tillers. 14: Roots of seedlings with two tillers. 15: Stem at day 5 before heading. 16: Stems at heading stage. 17: Leaves from plants at young panicle stage 3. 18: Leaves at young panicle stage 7. 19: Flag leaves at day 5 before heading. 20: Flag leaf at day 14 after heading. 21: Sheaths at young panicle stage 3. 22: Sheaths at young panicle stage 7. 23 : Hulls one day before flowering. 24: Stamens one day before flowering. 25: Young panicle at stage 3. 26: Young panicles at stage 4. 27: Young panicles at stage 5. 28: Panicles at stage 7. 29: Panicles at heading stage. 30: Spikelets, 3 days after pollination. 31: Endosperm, 7 days after pollination. 32: Endosperm, 14 days after pollination. 33: Endosperm, 21 days after pollination. Lower: Expression changes of HDAC genes responding to abiotic stresses including drought, salt and cold in seven-day-old light-grown seedlings. Color bar at the base represents log2 expression values: green, representing low expression; black, medium expression; red, high expression.<br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br /><br />
<br />
===Evolution===<br />
*Silent information regulator (Sir) proteins regulate lifespan in multiple model organisms. In yeast, an extra copy of the SIR2 gene extends replicative lifespan by 50%, while deleting Sir2 shortens lifespan<ref name="ref9" />.<br />
<br />
*Plant histone deacetylases (HDAC)can be grouped into four classes. Among them, three have primary homology to three yeast HDAC groups: RDP3, HDA1 and SIR2.During the last years, HDAC function has been most studied in Arabidopsis.<ref name="ref2" /><br />
<br />
*The function of SIR2 family HDACs was first been investigated in Arabidopsis. The Arabidopsis genome encodes two SIR2 family HDACs: SRT1 and SRT2. SRT2 resides predominantly at the inner mitochondrial membrane and interacts with a small number of protein complexes mainly involved in energy metabolism and metabolite transport<ref name="ref3" />. <br />
<br />
*SRT701(OsSRT1), one of the two SIR2-related genes found in rice, has been studied in Huang et al and proved its' function<ref name="ref1" />, while SRT702's function has been studied in Arabidopsis.<ref name="ref4" /><br />
<br />
*Mechanistically, ADP-ribosylation and deacetylation reactions by sirtuins are similar because they cleave NAD in each reaction cycle.<ref name="ref13" /><br />
[[File:F1.small.gif]]<br />
<br />Sirtuin deacetylation and ADP-ribosylation reactions. Both deacetylation and ADP-ribosylation occur via cleavage of NAD to release nicotinamide.<br />
<br />
*Mitochondria are central hubs of energy metabolism in plants and animals. In addition to a fine-tuned mitochondria-to-nuclear signaling that regulates transcription of nuclear gene expression.<ref name="ref14" /><br />
<br />
==Labs working on this gene==<br />
<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China (L.H., Q.S., F.Q., C.L., Y.Z.)<br />
*Department of Quartermaster,Military Economy Academy, Wuhan 430035, China (L.H.)<br />
*Institut de Biotechnologie des Plantes, Universite´ Paris Sud 11, 91405 Orsay, France (D.-X.Z.)<br />
*Department I of Biology, Ludwig Maximilians University Munich, Grosshaderner Strasse 2, 82152 Martinsried, Germany.<br />
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China<br />
*Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of <br />
*Institute of Plant Biology, National Taiwan University, Taipei<br />
*University of Chinese Academy of Sciences, Beijing 100049, China<br />
*Institut de biotechnologie des Plantes, Université Paris sud 11, 91405 Orsay, France<br />
<br />
==References==<br />
<references><br />
<ref name="ref1">Huang, L., et al., Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiol, 2007. 144(3): p. 1508-19.</ref><br />
<ref name="ref2">Hu, Y., et al., Rice histone deacetylase genes display specific expression patterns and developmental functions. Biochem Biophys Res Commun, 2009. 388(2): p. 266-71.</ref><br />
<ref name="ref3">Liu, X., et al., Transcriptional repression by histone deacetylases in plants. Mol Plant, 2014. 7(5): p. 764-72.</ref><br />
<ref name="ref4">Konig, A.C., et al., The Arabidopsis Class II Sirtuin Is a Lysine Deacetylase and Interacts with Mitochondrial Energy Metabolism. Plant Physiology, 2014. 164(3): p. 1401-1414.</ref><br />
<ref name="ref5">Pandey R, Muller A, Napoli CA, Selinger DA, Pikaard CS, Richards EJ, Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res 30: 5036–5055</ref><br />
<ref name="ref6">P.J. Chung, Y.S. Kim, S.H. Park, B.H. Nahm, J.K. Kim<br />
Subcellular localization of rice histone deacetylases in organelles<br />
FEBS Lett., 583 (2009), pp. 2249–2254</ref><br />
<ref name="ref7">L. Huang, Q. Sun, F. Qin, C. Li, Y. Zhao, D.X. Zhou<br />
Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice<br />
Plant Physiol., 144 (2007), pp. 1508–1519</ref><br />
<ref name="ref8">L. Xiong, K.S. Schumaker, J.K. Zhu<br />
Cell signaling during cold, drought, and salt stress<br />
Plant Cell, 14 (Suppl.) (2002), pp. S165–S183</ref><br />
<ref name="ref9">Haigis M.C., Guarente L.P. (2006). Mammalian sirtuins: emerging roles in physiology, aging, and calorie restriction. Genes Dev. 20, 2913–2921.</ref><br />
<ref name="ref10">Sinclair, D.A., Guarente, L.(1997) Extrachromosomal rDNA circles—A cause of aging in yeast. Cell 91:1033–1042.</ref><br />
<ref name="ref11">Tissenbaum, H.A., Guarente, L.(2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans Nature 410:227–230. </ref><br />
<ref name="ref12">Berdichevsky, A., Viswanathan, M., Horvitz, H.R., Guarente, L.(2006) C. elegans SIR-2.1 interacts with 14–3–3 proteins to activate DAF-16 and extend life span. Cell 125:1165–1177.</ref><br />
<ref name="ref13">Grubisha, O., Smith, B.C., Denu, J.M.(2005) Small molecule regulation of Sir2 protein deacetylases. FEBS J. 272:4607–4616.</ref><br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0271200|<br />
Description = Silent information regulator protein Sir2 family protein|<br />
Version = NM_001058879.1 GI:115457487 GeneID:4335343|<br />
Length = 2712 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0271200, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:11382902..11385613|<br />
CDS = 11382931..11383001,11383087..11383198,11383743..11383761,11384020..11384108,11384528..11384581<br>,11384732..11384802,11384906..11384987,11385087..11385183,11385304..11385374<br>|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:11382902..11385613<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:11382902..11385613<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatgggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggagattcttcatgggcttgtaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagagacacattcacatatccttgttacttccttggtcataagctggtccatcactgagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataa</cdnaseq>|<br />
AA = <aaseq>MAGVGSAVRRLYLSVYNWAVFFGWAQVLYYAVTTLLESGHEAVY AAVERPLQFAQTAAFLEILHGLVGLVRSPVSATLPQIGSRLFLTWGILWSFPETHSHI LVTSLVISWSITEIIRYSFFGMKEAFGFAPSWLLWLRYSTFMVLYPTGISSEVGLIYI ALPYMKASEKYCLRMPNKWNFSFDFFYASILSLAIYVPGSPHMFTYMLAQRKKALAKA KAA</aaseq>|<br />
DNA = <dnaseqindica>30..100#186..297#842..860#1119..1207#1627..1680#1831..1901#2005..2086#2186..2282#2403..2473#ccttgttagctactgctgagtgctcggcgatggcgggcgtcgggtcggcggtgcggcggctctacctctccgtttacaactgggccgtcttcttcggatggtactctgccgcctcgcgccaccgcctgctggcgtttggatccttgttttcttggcttgatttgggggtttcttggatcttgcagggcgcaggtgctgtactacgcggtcacgacgctgctggagagcggccatgaggccgtctacgccgccgtcgagcggccgctgcagttcgcgcagaccgccgccttcttggaggtctggtttttctgctattctgtgcgctctgacttatttttgaattttaatcgcagtaaaactgtagattttagcgcaagcttgtataatttgggcagctctgacttaattttgaatttttcgtctacccaattagggttgctggtgttgagcaatggcacagaggaaaaaaatttatccccttttgcgttctaaaaatcaaccaaacatttagcctgagagaaatattaccagtgttatagcaaaatatactgcaattaattcaacttcaatgttattatgtttctgctgcctgatcctctcccccgataattctgctaaaaagaaaagaaaaatttctgctgccctatactttgtgttaaattccttgtagttccctggataaggaagcatttatattctttgcacggagcagctgaacgagtctgcggtgaacacagaatgaacgagtattccatgtttatttcatttctttgcaaattgtgttttgtgaggtactgaacatttttgtgtttgtttggcgatggcgttgctggtggctcagattcttcatgggcttgtaggtaagaagttgttcttctcttctacttatgttattttcactatccttgtcatcatttggaatcgtacggtttctgtctatagcgtgccgcttgcaaactgcatggaaatagactttcttgttagaaagcacgtcaaagacacatttcaatttacaggaagtgtcctgttagattatgaaaataattgtacttaataagttcacttttacggcactttcatttttttcacctgtataacatgctgactttgttttaaaggtttggtgaggtctccagtctctgcaactcttccacaaattggatcgaggttgtttcttacctggggcatcctgtggagctttccagaggtatcatcgactatcactaacaagtgttgatgtgctatgttcatgagatttggaaattttcttctttagttagacacttctcctaagcgcttactgtttctccgagacattgaaacatgacataattttggggtttaaaaccattgtctaaataggaaatatggattatatgatttgatttttatatgaggacaggacactaggtagtttgtctgttttatatctggttgtggatcaagtaaataatggtgatgattgtacaagttactaaatggcataactactggtactgatatgcaaatgcagtgcctttacttttgcatccctagttttctgttagttgcatacttgtagtgtagcttaacacctggtttcttgacatatatattgattgacccctttgtacatttgtcttgcagacacattcacatatccttgttacttccttggtcataagctggtccatcactgaggtatattttaaagacttgcttcttaaagagacactgtattttccaaattctaattttgatttttcctgtgctaagcttattcacaccaatatttaaaatattgtgaatttgatagcataacgtgatggaaatatttgtggttccttgcagatcattagatattccttctttggcatgaaggaggcattcggatttgctccttcctggctcttatggctgaggttagtaaagaagatatatcattatttaggacaaatttagagggaatgattttctttttctttcataactttttttcttaaacctggtgctgattttgtacaggtatagcacctttatggtattgtatcctactggtatcagcagtgaggtcggtttaatctacattgccttgccttacatgaaggtaacaagaatgaacttcagaaatgaagatctccacgttgttcattgcataatgcataatgcgtaatttaactgctcctttcttgtgactactatgcaggcatcagagaaatactgccttaggatgcccaacaaatggaacttctcctttgatttcttctatgcatccatcctttctctcgccatctacgtgcccggtatcccctcctgccttgcagtcatcctttattcagtggttgaaattaaaactagaattgcaatgttgttttttagtagctgggattaagataggatctgacaagaacactgcgttgcaggatcgcctcacatgttcacctacatgcttgcccaacggaagaaggcattggcaaaggctaaggctgcataatggtgatgctcaagagctttcttgaatttttcatgtgtggcttaaggatctgcctaaatagctcatatttgctactcttttagtacaagtctgtagatgaggaaatgttggaaagaactactatcttaatcccagcatttgttgtaactgtagtaactgcccatcatttgttgtaactgtagtcttctaccaagaattgtatgatattttacctggttaaattattgaatgattgatcc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001058879.1 RefSeq:Os04g0271200]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0445900&diff=183360Os05g04459002014-06-10T07:14:12Z<p>Lina: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. As well, there are some proteins coded for DNA demethylation. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation are DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3). Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1orthologs and twoDML3orthologs, but no DME orthologs.<br />
<br />
1.It has been demonstrated that rice ROS1a protein is a bi-functional DNA glycosylase/lyase for 5-meC DNA demethylation, although biochemical characterization of the ROS1a enzyme remains to be performed to confirm this.Rice ROS1a is toxic to E. coli containing 5-meC in its genome. When ROS1a cDNA was expressed under the control of an IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible promoter, ROS1a was toxic to an E. coli dcm+ strain containing 5-meC in an IPTG-dependent manner, and was less toxic to a dcm− mutant without 5-meC.<br />
<br />
[[File:TPJ_5009_f2.gif]]<br />
<br />
2. ROS1a is the most abundantly expressed gene in tissues. It was recently reported that null mutants of ROS1c, which encodes a 5-meC DNA glycosylase/lyase, show no effects on transmission of the null alleles and produce a small portion of wrinkled seeds.And the null mutation, ros1a-GUS1, was hardly ever transmitted to progeny.Even in the presence of the wild-type paternal ROS1a allele, the maternal nullros1a-GUS1allele caused failure of early stage endosperm development, indicating non-equivalent contribution of maternal and paternal ROS1a to endosperm development.<br />
<br />
[[File:TPJ_5009_f4.gif]]<br />
<br />
<br />
Figure. Histochemical GUS staining patterns in ROS1a/ros1a-GUS1 plants. (a) Longitudinal section through basal shoot meristem region of mature plants. Insets are magnified views of shoot apical and lateral (upper) and inflorescence (lower) meristems. (b) Flowers. (c) Anthers. Approximately half of the pollen present showed GUS staining (see also Figure S7b). The inset is a magnified view. (d) Pistils. Insets are ovules before pollination exposed by removing the carpel. The upper and lower insets show a GUS-stained ovule and its sibling, which displayed no GUS staining, respectively. Before pollination, ovules containing gametes with the wild-type ROS1a allele were morphologically indistinguishable from those with ros1a-GUS1 allele. (e) Schematic representation of a rice female gametophyte enclosed by the maternal tissues of the ovule: ovary tissue (light brown), integument (dark brown), and nucellus (gray). The haploid female gametophyte consists of the egg apparatus (green), including the egg cell and two synergids, the central cell (white), which contains large vacuoles and thin lines of cytoplasm (pink), and antipodals (blue). (f,g) Differential interference contrast micrographs of GUS-stained female gametophytes of ROS1a/ros1a-GUS1 plants. To make the borders of different tissues clear, white lines are drawn on the image in (f), which corresponds to the area enclosed by the red line in (e). (h) Differential interference contrast micrograph of a sibling female gametophyte displaying no GUS staining. Arrows indicate GUS-stained meristems (a), pollen (b) and the probable egg apparatus (d). In (b), the arrowhead indicates the GUS-stained lodicule. AP, antipodals; PN, polar nuclei. The images in (g,h) correspond to the area enclosed by the blue line in (e). Scale bars = 1 mm [a,b, inset in (a)], 500 μm [c,d], 100 μm [inset in (d)] and 50 μm [inset in (c) and f-h].<br />
<br />
3.Rare transmission of the ros1a-GUS1 allele to progeny.To obtain homozygous knock-in plants, we self-pollinated the isolated T0 plants. Of the 250 fully grown seeds selected, 232 germinated, and the resulting T1 seedlings were genotyped by PCR analysis. Surprisingly, only two were ROS1a/ros1a-GUS1 plants, and the remaining 230 seedlings were homozygous for the wild-type allele (ROS1a/ROS1a) (Table 1). Moreover, the ros1a-GUS1 allele in the two heterozygous T1 plants was not transmitted to progeny, confirming that the ros1a-GUS1 allele is rarely transmittable to progeny. Close inspection revealed that the T0 panicles comprised three types of grain: empty grains with only infertile flower remnants , grains with normal-shaped seeds , and grains with deformed seeds containing severely under-developed and non-starch-producing endosperm . Approximately equal numbers of normal-shaped and deformed seeds were observed (54:56, 1:1, χ2 = 0.036, P > 0.8; Table 2). Embryos in the deformed seeds always displayed GUS-positive staining, but none of the normal-shaped seeds showed GUS-positive patterns, indicating that the ros1a-GUS1 allele co-segregated with the deformed seed phenotype and that the normal-shaped seeds were ROS1a/ROS1a (Table 2 and Figure 5b,d). In the analysis of the segregation ratio of ros1a-GUS1 in seedlings (Table 1), deformed seeds bearing the ros1a-GUS1 allele were probably excluded from the analysis because only fully grown seeds were used.<br />
<br />
[[File:360截图20140610120515955.jpg]]<br />
<br />
===Expression===<br />
Rice contains four ROS1 orthologs and two DML3 orthologs tentatively named ROS1a–d and DML3a and DML3b, that contain characteristic DNA glycosylase domains flanked by conserved domains of unknown functions. Of these, ROS1ais the longest gene, comprising 17 exons that encode a protein with 1952 amino acids, and 5¢ and 3¢ UTRs of 73 and 607 bp, respectively.RT-PCR analysis revealed thatROS1awas expressed in all vegetative and reproductive tissues tested . Quantitative RT-PCR analysis revealed that ROS1ais the most extensively expressed gene among the four genes(ROS1a, ROS1c, ROS1d and DML3a) expressed in five selected tissues examined, including anthers and pistils,whereas ROS1b and DML3bare scarcely expressed in these tissues. Interestingly, moderate levels of transcripts for ROS1c, ROS1dandDML3awere detected in pistils and immature seeds 2 days after pollination.<br />
[[File:TPJ_5009_f1.gif]]<br />
<br />
<br />
<br />
<br />
<br />
===Evolution===<br />
Phylogenetic analysis revealed that the rice (Oryza sativa) genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1 orthologs and two DML3 orthologs, but no DME orthologs (Zemach et al., 2010). Rice endosperm DNA is hypomethylated in all sequence contexts, implying that hypomethylation in rice endosperm relies on some of these DNA glycosylases or alternative biochemical mechanisms (Zemach et al., 2010). In this study, to characterize the function of one of the four rice ROS1 orthologs, tentatively named ROS1a (LOC_Os01g11900.1), that resides on chromosome 1, we used homologous recombination-promoted knock-in targeting with positive/negative selection (Yamauchi et al., 2009) to obtain a mutant that disrupts ROS1a by fusion of its endogenous promoter with the GUS reporter gene encoding β-glucuronidase. We reproducibly obtained T0 plants with the null knock-in allele, ros1a-GUS1, in the heterozygous condition, and detected GUS expression in the T0 plants in the shoot apical, lateral and inflorescence meristems, as well as in both female and male gametophytes before fertilization. The ros1a-GUS1 allele was hardly transmitted to the next generation; neither the maternal nor the paternal ros1a-GUS1 allele was virtually found in the progeny. The results indicate that ROS1a, presumably through DNA demethylation, is indispensable in both gametophytes, and that the null allele of ROS1a is difficult to isolate by conventional mutagenesis techniques, in which mutants are usually obtained as segregants in the progeny population. <br />
<br />
<br />
[[File:pnas.1009695107fig05.jpg]]<br />
<br />
===summary===<br />
<br />
DME is preferentially expressed in the homodiploid central cell of the female gametophyte before fertilization, and promotes maternal allele-specific global hypomethylation, leading to maternal allele-specific expression of imprinted genes in the endosperm, including the Polycomb Repressive Complex 2 (PRC2) genes MEDEA (MEA) and FERTILIZATION INDEPENDENT SEED 2 , and to maternal allele-specific expression of transposons in the endosperm. Expression of these imprinted genes is prerequisite for normal endosperm development. mea and fis2 mutants exhibited characteristic maternal defects in the endosperm similar to the dme mutant, because PRC2 represses autonomous growth of unfertilized endosperm and overgrowth of fertilized endosperm . In rice, GUS staining was detected in the central cells of ROS1a/ros1a-GUS1 plants , indicating that ROS1a is expressed in the central cell of the female gametophyte. Although many maternally expressed imprinted genes were identified in the rice endosperm, very few were in common with those in Arabidopsis . Expression of FERTILIZATION INDEPENDENT ENDOSPERM 1 (FIE1) (LOC_Os08g04290), one such imprinted gene encoding a component of PRC2 in rice, appears to correlate with DNA demethylation at its 5′ region, but an fie1 disruptant showed no defects in endosperm development . The results imply that certain roles of PRC2 in rice endosperm development differ from those of Arabidopsis. Although we could not demonstrate ROS1a-promoted DNA demethylation, ROS1a is postulated to activate the imprinted genes through DNA demethylation in order to facilitate normal endosperm development. GUS staining was also detected in the antipodals and the egg apparatus comprising two synergids and an egg cell whose genetic information is transmittable to progeny (Figure 4f,g). The molecular mechanisms of ROS1a function in these cells remain to be elucidated.<br />
<br />
Although DME in Arabidopsis is predominantly expressed in the central cell of the female gametophyte, and is only marginally expressed to demethylate some imprinted genes and transposons in the vegetative cell of the male gametophyte , comparable amounts of ROS1a were expressed in both the female and male gametophytes , and the paternal ros1a-GUS1 allele could not be transmitted to progeny . Although the molecular mechanisms for the inability to transmit the paternal ros1a-GUS1 allele are unknown, ros1a-GUS1 pollen germinated less efficiently than did ROS1a pollen. Reduced germination and transmission of dme pollen were also observed in certain Arabidopsis ecotypes (Col-gl and Col-0) . The vegetative nucleus in pollen supports the sperm cell before fertilization and shows reduced DNA methylation in Arabidopsis, resulting in transient reactivation of diverse transposons and generation of small interfering RNAs that may ensure the genomic integrity of sperm cells by silencing transposons in the sperm cells . Whether similar DNA demethylation occurs in the vegetative nucleus in rice pollen, and whether the ROS1a protein promotes such demethylation, remain to be determined. If such DNA demethylation occurs in the vegetative nucleus, it will be interesting to determine whether such demethylation directly correlates with the intransmittable nature of the paternal ros1a-GUS1 allele .<br />
<br />
Quantitative RT-PCR analysis revealed that ROS1a, ROS1c, ROS1d and DML3a are expressed in five selected tissues tested, including anthers and pistils, and ROS1a is the most abundantly expressed gene in these tissues . The same analysis showed that ROS1c, ROS1d and DML3a are moderately expressed in both pistils and immature seeds 2 days after pollination. It was recently reported that null mutants of ROS1c, which encodes a 5-meC DNA glycosylase/lyase, show no effects on transmission of the null alleles and produce a small portion of wrinkled seeds . Their results are in sharp contrast to those for the null allele of ROS1a described here, and indicate that moderate expression of ROS1c, ROS1d and DML3a in pistils could not compensate for the loss of ROS1a. It would be interesting to determine whether ROS1a and any of the other three genes are expressed simultaneously in the same cells in the pistil. If ROS1a and ROS1c are expressed in the same cells, it would then be interesting to determine whether the different transmittability of their null alleles may be explained simply by their expression levels or whether it is due to intrinsic differences in their molecular functions.<br />
<br />
The null ros1a-GUS1 allele was not transmitted to progeny . In conventional mutagenesis procedures, mutants are usually identified and isolated as segregants in the progeny population. Such procedures would not have enabled isolation of the ros1a-GUS1 allele. In contrast, our homologous recombination-promoted gene targeting procedure allowed T0 transgenic plants to be reproducibly obtained with the exactly anticipated structure of the targeted gene in the heterozygous condition. Moreover, the knock-in targeting strategy allowed detection of spatio-temporal ROS1a expression and tracking of the transmitted ros1a allele. However, because GUS staining was necessary to detect ROS1a expression, it was difficult to analyze in vivo and/or to isolate viable tissues that express GUS for detailed examination. Utilization of other markers such as green fluorescent protein, in combination with other techniques including laser micro-dissection and/or fluorescence-activated cell sorting, would facilitate further characterization of ROS1a function in endosperm development and pollen gametophytic transmission.<br />
<br />
==Labs working on this gene==<br />
1.National Institute for Basic Biology, Okazaki 444-8585, Japan<br />
<br />
2.Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan<br />
<br />
3.Graduate School of Nutritional and Environmental Sciences, Graduate School of Pharmaceutical Sciences, and Global Center of Excellence Program, University of Shizuoka, Shizuoka 422-8526, Japan<br />
<br />
==References==<br />
1.A. Zemach et al., Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107, 18729 (Oct 26, 2010).<br />
<br />
2.A. Ono et al., A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny. Plant J 71, 564 (Aug, 2012).<br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0445900|<br />
Description = Similar to ROS1 (Fragment)|<br />
Version = NM_001062220.1 GI:115464170 GeneID:4338940|<br />
Length = 5779 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0445900, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:21889157..21894935|<br />
CDS = 21889581..21889708,21890545..21890583,21890664..21890778,21890883..21890948,21892020..21892159<br>,21892239..21892302,21892380..21892416,21892564..21893001,21893713..21893795<br>,21893897..21893933,21894150..21894218,21894322..21894413,21894487..21894571<br>,21894906..21894934|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>ttaagagatgttcctccagactcagcaaaggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtatgagttacattatcagatgattacttttggaaaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtttacgaacttccagattcacatcccctcatgcaacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggtctaacaactgaagaaatacagcactgcttctggagaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactga</cdnaseq>|<br />
AA = <aaseq>LRDVPPDSAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVG RICVRLGWVPIQPLPESLQLHLLELYPVLETIQKYLWPRLCKLDQQTLYELHYQMITF GKVFCTKSKPNCNACPMRSECRHFASAFASARLALPSPQDKRLVNLSNQFAFHNGTMP TPNSTPLPQLEGSIHARDVHANNTNPIIEEPASPREEECRELLENDIEDFDEDTDEIP IIKLNMEAFSQNLENCIKESNKDFQSDDITKALVAISNEAASIPVPKLKNVHRLRTEH YVYELPDSHPLMQQLALDQREPDDPSPYLLAIWTPDELKDTREAPKPCCNPQTEGGLC SNEMCHNCVSERENQYRYVRGTVLVPCRTAMRGSFPLNGTYFQVNEVFADHSSSHNPI NIPREQLWNLHRRMVYFGTSVPTIFKGLTTEEIQHCFWRGFVCVRGFNMETRAPRPLC PHFHLAASKLRRSSKKAATEQTH</aaseq>|<br />
DNA = <dnaseqindica>5228..5355#4353..4391#4158..4272#3988..4053#2777..2916#2634..2697#2520..2556#1935..2372#1141..1223#1003..1039#718..786#523..614#365..449#2..30#gttaagagatgttcctccagactcagcaaagtaagatactacacctgtattcaatatttacaaatcccattgccctgctgatgagatttttctagttctggaaatgataaatcaagtatcaaagaagtttgtgaaccaattaaatggagcaagctgatccaagaacttgccagttaatatctagaattaaatactatgagcaaagttctatgaaatgggcacgcagaacagaaaaggctgtataatgtatgacacatgatcgaagcagtgaaggaatttttttttaggaaagaaaattccatgaaccctatttatttcacaggcgagaagtatgtcaattacaatgtgttcgaattattttcagggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagtaagtttctgttggattaattctccttcacctgcagccaatttgaaatttacactacattgttgcaactcaggttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctgtaagaatgttgcattgtctactacagttgtataaatactctctgcaattttatacgatgatgtttcaatttgaatatattgattttgtttgtgccttcaaagataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtgagttataaccaattaaccatacccactcatagttgcccttcttattagtttttttttacgcaagcccttcttattagtttgtgtaacttctaggttatttctttttcatgcaaattacagtatttggaatcatgaataattaaggcaataaggagtaaataacataatttataactataaggaattattaacagagtttcatggttttcacaggtatgagttacattatcagatgattacttttggaaaggtacttcattagcattaaggagtttggtctcttcattagcatctaccgacgcatttgttctcttttgtttgagtaaagataaattatcataacaaatgcaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaaggtattatggcaagcagaaaatgggagccttctggctgcaaggagacttacaaaataaacactatttgcttcagtagtcacttttttccgataaaggaagctttattaaaactcagtcaaatacaccaagatgatacattctaactgagccactcccggcctctgcatgaaatgcacaccgccacaaaacaggatctaactagaccctcaacacaaaacaaataaattagtgactatcaagccgtagactatatcgccacccatgctccagggtaaaaaactcctgtgccacctgatagtgcacagcaaaaaccacgagaaggatgtgctttcgttggtggagagaccgaattagctccattaacataatatgaccactaagagcgcaaaatagtgcttttgaagaataaaagggaaaatatgctaggagaaaaatcaatatatggttctagtacaccgccatggcactttgtgtagtctctgtctgcaacaaaatatatttgccgctttcacttatcttacctgggaattttgttatcacgtatttcctcgttccactatctttcttgttttgtttgtgcgcgcgcgcatgcctgatatatcttgctctttcagttgaccttacctgggagccttcattttgcatatttcttcatttgttattttttccttattaactctgttatattttgtttgacttttttaaatgaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtgtaagtgttggactgatattttatttagcttgaacatgtacctgtttaaacttacatttattatagagcccaccatctaagtaattctatacatcctgaacaaaatattttttaatttctattactgacttaaggttctgctcgcagttacgaacttccagattcacatcccctcatgcaacaggtgagaccatgagaaattgtgccatctttctttaaaacacttcaagatattatttctgattgcaaatgatcttacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccaggcaagtgcatttttctttaaatttataactgtccgtgtgtgtgtgctggttttcgtcgagtcatgtggctactgtgcagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggtaaatcaaccaacattatgtagcaatcatcaacattgaagagctgaacctctgcattagtcagctagtaaacaaaatattcattataatccaaacattggaatgaattcaggaattcaagaaaatgttgaagataacttttaatgaaaactagtgcttacaaagtgccaagcaaagctattctgttgtctgtgtaatctcttttcttgcatgaaatagcccactgtcttcactttaaacaataagaatagcatagattttgggtttccggctatacaacacatcttaatatgaacttttgtggaagtctaaaagagaacctctctgaacctttaaactgtacactatttaaccaacaatcaaagccgatcacttctcaacgtcattctgaattagctttgggcgatgtttcttaaccaggagatgtggtctgagattttagattttttttttcatctcctttatattagtagacgacttaaaattttctggaataatcttacttcgctgtgaagtatttataacccagataaatcggtaagattgaagtaaagtattattgtcccacgaaatttagtgtgtgaaagtagacaacatttttttctactgtccgattaaactttatttaactctgccccattttatctaggctataaatggtgatttcttctaggctatacggtttttcaatccaattttaccttattttgctttaccaaatttgtcaacattataatactttgtagtgcaagtgagattttttttttcaattttgttatgtcatttactaattttaaaattgaaaacctggttcagccttgggccattttgccacattagggacacatagtccaaagccactttaaatttgagacaaggttgaaaagcgcatggttttgatacttcaggttctgggttgaattgtgtccagttttctgctttggggttgtctctggactaacagaaaagttcagtattgcaaaacagactgtttcctatacaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacggttactggaacatgaacaggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttgactttacgatttctggatttgtttttgcaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggttaccaccattcacccatacaatgactcaaagaaatcttatctgcaactttaccgacaactgttattttcattctttaggtctaacaactgaagaaatacagcactgcttctggagaggtattaacagtatttttttcactcgctgtttcagcgcattctcctctgggacatatcttgtttcctcatatgatcaaacaatttgcagaatgcagatgccatcatataatcacaatatgtttctacagttatatagcattcgtgtgattgtgtcaaggtgtccacacacttttcacaaaaacttactccccctgtcccataatataagggattttgagcttttgtttgcactgtttgaccattcgtcttattcaaaaaaatttagaattatattttttttctttgtgacttactttattatccaaaatactttaagcacaacttttcgttttttatatttgcacaaattttttgaataagacgagtggtcaaacattataatcaaaaaactcaaaatcccttgtattatgggacggagggagtagtattaagggtctaaaaggagcctgaatatttggttcagttagagtctatatctgagtccattttaattcctagtgctatggataaaggtgtcctccttcaataaataaataaaggtctctccagttattagtcaccagcatccaatataactgcctgataatatatgtggtaagttatatggtgccaaagaggcaaagatactgctaccatgactaaccccctttttttttctgagttaataagggtgttagcatacatatagcttccaaattggtttagttaggtggaaaaagtcgtcatttcaggatgcagatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactgatttcaacagggacatatcaattctataaaataatgttgatggtgattacatcagttctcgatctgtgcatgggtcatattagttcctgcaggacgatagccattcttctaggaaataaacagtggagttggaaacagttaactttaagatgtgggagccaattgggcacgagaaagcaccaatatttcatatgcacctctggggcaggtcggatgcggatcatcatcatcagttaacatgggcgtagaatatcattccgttttttttttctgtggctttggtgtatcttattcacttttcatttgttttatccattcaactagcttgccaagagaccttaccatctgttctcatgacatgttagtttttcagaacttatagcaggtagtaccttcatattgatgatatgactttgattttcatt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062220.1 RefSeq:Os05g0445900]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178637Os09g03078002014-06-06T00:56:47Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']]<br />
*Several plant SDGs have in vitro HMTase activities<ref name="ref8"/>. For instance, SDG714 in rice tends to choose core histones as preferred substrates , but ArabidopsisSDG8, SDG26, and SDG25 prefer to methylate oligonucleosomes<ref name="ref9"/> <ref name="ref10"/>. <br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*despite of their close chromosomal locations and high degree of similarity, SDG724 specifically affects H3K36me2/3 levels at the RFT1, but not the Hd3alocus. In addition, H3K36me2/3 levels at the Ehd1locus were also found to be unchanged in lvp1 plants, even though its expression was downregulated in lvp1 compared with wild-type plants (Figure 6). At all the loci examined, H3K4me3 levels were not significantly different be-tween lvp1 mutant and wild-type plants, which demonstrated aspecific relationship between SDG724 and H3K36 methylation.<ref name="ref1" />.<br />
<br />
*To provide further evidence that MADS50, Ehd1, Hd3a, and RFT1 were downstream targets of SDG724, we examined the expression levels of those genes at four developmental stages (30, 60, 90, and 120 d after germination [DAG]) in plants grown in Beijing under natural LD conditions. Leaf samples were collected 2 h after dawn, when transcription of the putative downstream genes was at a high level. The results showed that compared with the wild type, transcript levels of the downstream genes were lower in the lvp1 mutant and that transcript levels of the flowering time genes peaked at 60 DAG in wild-type plants These observations further supported the conclusion that under LD conditions, SDG724 activity promoted MADS50 transcription, which leads to upregulation of its downstream targets Ehd1 and FT-like genes. Also notably, MADS50 expression was only marginally changed in the controlled growth chamber under artificial LD conditions at 30 d but considerably changed under natural LD conditions at 60 DAG , when he lvp1 mutant and wild-type plants were all still vegetative.<ref name="ref1" />. <br />
<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
[[File:Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.jpg|300px|thumb|left|Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.''<ref name="ref1"/>'']]<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
<ref name="ref8"> Liu, C., Lu, F., Cui, X., and Cao, X.(2010). Histone methylation in higher plants. Annu. Rev. Plant Biol.61:395–420.</ref><br />
<ref name="ref9"> Berr, A., Xu, L., Gao, J., Cognat, V., Steinmetz, A., Dong, A., and Shen, W.H.(2009). SET DOMAIN GROUP25encodes a histone methyltransferase and is involved inFLOWERING LOCUS Cacti-vation and repression offlowering. Plant Physiol.151:1476–1485.</ref><br />
<ref name="ref10">Xu, L., Zhao, Z., Dong, A., Soubigou-Taconnat, L., Renou, J.P.,Steinmetz, A., and Shen, W.H.(2008). Di- and tri- but not mono-methylation on histone H3 lysine 36 marks active transcription of genes involved inflowering time regulation and other processes in Arabidopsis thaliana.Mol.Cell.Biol.28:1348–1360.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178634Os09g03078002014-06-06T00:53:06Z<p>Lina: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']]<br />
*Several plant SDGs have in vitro HMTase activities<ref name="ref8"/>. For instance, SDG714 in rice tends to choose core histones as preferred substrates , but ArabidopsisSDG8, SDG26, and SDG25 prefer to methylate oligonucleosomes<ref name="ref9"/> <ref name="ref10"/>. <br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*despite of their close chromosomal locations and high degree of similarity, SDG724 specifically affects H3K36me2/3 levels at the RFT1, but not the Hd3alocus. In addition, H3K36me2/3 levels at the Ehd1locus were also found to be unchanged in lvp1 plants, even though its expression was downregulated in lvp1 compared with wild-type plants (Figure 6). At all the loci examined, H3K4me3 levels were not significantly different be-tween lvp1 mutant and wild-type plants, which demonstrated aspecific relationship between SDG724 and H3K36 methylation.<ref name="ref1" />.<br />
<br />
*To provide further evidence that MADS50, Ehd1, Hd3a, and RFT1 were downstream targets of SDG724, we examined the expression levels of those genes at four developmental stages (30, 60, 90, and 120 d after germination [DAG]) in plants grown in Beijing under natural LD conditions. Leaf samples were collected 2 h after dawn, when transcription of the putative downstream genes was at a high level. The results showed that compared with the wild type, transcript levels of the downstream genes were lower in the lvp1 mutant and that transcript levels of the flowering time genes peaked at 60 DAG in wild-type plants These observations further supported the conclusion that under LD conditions, SDG724 activity promoted MADS50 transcription, which leads to upregulation of its downstream targets Ehd1 and FT-like genes. Also notably, MADS50 expression was only marginally changed in the controlled growth chamber under artificial LD conditions at 30 d but considerably changed under natural LD conditions at 60 DAG , when he lvp1 mutant and wild-type plants were all still vegetative.<ref name="ref1" />. <br />
<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
[[File:Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.jpg|300px|thumb|left|Figure 4.Proposed Model for theSDG724Flowering Pathway in Rice.''<ref name="ref1"/>'']]<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
<ref name="ref8"> Liu, C., Lu, F., Cui, X., and Cao, X.(2010). Histone methylation in higher plants. Annu. Rev. Plant Biol.61:395–420.</ref><br />
<ref name="ref9"> Berr, A., Xu, L., Gao, J., Cognat, V., Steinmetz, A., Dong, A., and Shen, W.H.(2009). SET DOMAIN GROUP25encodes a histone methyltransferase and is involved inFLOWERING LOCUS Cacti-vation and repression offlowering. Plant Physiol.151:1476–1485.</ref><br />
<ref name="ref10">Xu, L., Zhao, Z., Dong, A., Soubigou-Taconnat, L., Renou, J.P.,Steinmetz, A., and Shen, W.H.(2008). Di- and tri- but not mono-methylation on histone H3 lysine 36 marks active transcription of genes involved inflowering time regulation and other processes in Arabidopsis thaliana.Mol.Cell.Biol.28:1348–1360.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178273Os09g03078002014-06-05T11:30:42Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178272Os09g03078002014-06-05T11:30:08Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178271Os09g03078002014-06-05T11:28:56Z<p>Lina: /* Function */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178270Os09g03078002014-06-05T11:28:29Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178269Os09g03078002014-06-05T11:27:38Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178268Os09g03078002014-06-05T11:26:41Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178267Os09g03078002014-06-05T11:25:46Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178266Os09g03078002014-06-05T11:25:07Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178264Os09g03078002014-06-05T11:24:23Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178263Os09g03078002014-06-05T11:23:41Z<p>Lina: /* Expression */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178261Os09g03078002014-06-05T11:23:12Z<p>Lina: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=File:Figure_3.SDG724_Acts_as_a_SET_Domain%E2%80%93Containing_Histone_Methyltransferase.jpg&diff=178259File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg2014-06-05T11:20:23Z<p>Lina: </p>
<hr />
<div></div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178258Os09g03078002014-06-05T11:19:42Z<p>Lina: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1"/>'']]<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178254Os09g03078002014-06-05T11:17:34Z<p>Lina: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.''<ref name="ref1">'']]<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178253Os09g03078002014-06-05T11:14:54Z<p>Lina: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg]]<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0409600&diff=178251Os04g04096002014-06-05T11:14:21Z<p>Lina: /* References */</p>
<hr />
<div>OsSRT1 is one of the two SIR2-related genes found in rice.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions <ref name="ref1" />.''<br />
<br />
*OsSRT1 is one of the two SIR2-related genes found in rice<ref name="ref2" />.''<br />
<br />
*Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.''<br />
<br />
[[File:Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.jpg|right|thumb|360px|Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.''<ref name="ref1" />'']]<br />
<br />
<br />
*OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1<ref name="ref1" />.''<br />
<br />
<br />
*OsSRT1 is a histone acetylation enzyme, participating in acetylation of H3K9, inhibition of transposon and gene expression related to cell apoptosis. Rice SIR2 gene is important to maintain genomic stability and avoid DNA damage in the process of plant cell growth. OsSRT1 is involved in the safeguard against genome instability and/or oxidative stress, required for plant cell growth<ref name="ref2" />.''<br />
<br />
<br />
*Histone lysine acetylation is an important epigenetic modification for genome function and gene activity. Dynamic modulation of histone acetylation in plants has been shown to be involved in gene expression programs of plant development and responses to environmental conditions <ref name="ref13" />.''<ref name="ref14" />.''<br />
<br />
===Expression===<br />
*OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues<ref name="ref1" />.'' <br />
<br />
<br />
*Our data show that OsSRT1 was preferentially expressed in rapidly dividing young tissues/organs and the protein was nuclear localized. Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.'' <br />
<br />
<br />
[[File:Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_fragmentation.jpg|right|thumb|360px|Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_<br />
fragmentation.''<ref name="ref3" />'']]<br />
<br />
*OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress<ref name="ref3" />.'' <br />
<br />
<br />
*So far no physiological function has been assigned to plant Sir2-related proteins. As there are fewer SIR2-related genes found in plant genomes, important questions arise, such as whether plant Sir2-related proteins conserve similar functions as yeast and animal homologs. In this work, we studied the function of a rice (Oryza sativa) SIR2-like gene,by transgenic approaches OsSRT1 <ref name="ref5" />.'' <br />
<br />
<br />
<br />
*As H3K9 dimethylation is closely associated with H3K9 deacetylation <ref name="ref8" />.'' we also tested with antibodies against dimethylated H3K9. As shown in Figure 3C, the OsSRT1 RNAi had little effect on overall histone H3 acetylation. However, the acetylation of H3K9 was induced, whereas the dimethylation of H3K9 was reduced, in agreement with the antagonistic relationship between H3K9 acetylation<ref name="ref1" />.'' <br />
<br />
<br />
*The RNAi lines were selected for phenotype observation and further analysis. The RNAi plants at the two-leaf stage (about 14 d after germination) began to produce brown dots on leaves, which became larger at latter stages, leading to precocious leaf senescence. Only two of the three RNAi lines could produce seeds. The severest line died before getting into maturity. The transgenic lines showing no alteration of OsSRT1 expression or histonemodification did notmanifest the phenotype, suggesting that the lesion mimic phenotype was induced by OsSRT1 down-regulation. The lesions were reminiscent of cell death induced by hypersensitive responses during plant pathogen infections, suggesting that OsSRT1 RNAi might have induced programmed cell death (PCD). To test this hypothesis, young leaf sheaths (T1 generation) were incubated with 3,3#-diaminobenzidine (DAB) to detect H2O2 <ref name="ref12" />.'' <br />
<br />
<br />
[[File:Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment.jpg|right|thumb|360px|Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment. ''<ref name="ref3" />'']] <br />
<br />
*OsSRT1 was generally expressed in different tested rice tissues, but with higher transcript levels detected in tissues with high cell proliferation rates, such as buds, seedlings, and developing panicles HSR201 and APO, but not HSR203J, were found to be induced by OsSRT1 RNAi in the microarray data. Consistently, the RT-PCR results showed that HSR201 and APO, but not HSR203J, were activated early in 7-d-old RNAi plants. In contrast, HSR203J was repressed by OsSRT1 overexpression.<ref name="ref1" />.'' <br />
<br />
<br />
*We compared the expression of two hypersensitive response (HSR201 and HSR203J) marker genes <ref name="ref9" />.''and a cytochromeP450 gene (calledAPO) that is closely related to wheat (Triticum aestivum) CYP709C1 and CYP709C3v2, both of which are suggested to be involved in wheat defense to pathogens <ref name="ref10" />.''<ref name="ref11" />.''<br />
<br />
<br />
*Down-regulation of OsSRT1 by RNAi produces a lesion-mimic phenotype and induces H3K9 acetylation (H3K9ac) and expression of hypersensitive response-related genes in rice plants. In addition, the transcription of many transposable elements is activated in the RNAi plants, indicating that transposons and cell death-related genes might be among the primary targets of OsSRT1-mediated gene silencing.<ref name="ref15" />.'' <br />
<br />
<br />
<br />
[[File:Figure 4. Expression profiles of OsSRT1.jpg|right|thumb|360px|Figure 4. Expression profiles of OsSRT1.''<ref name="ref1" />'']]<br />
<br />
<br />
*Histone acetylation is catalyzed by histone acetyltransferases, whereas histone deacetylation is catalyzed by histone deacetylases (HDACs). Plant HDACs can be grouped into four subclasses. Three of them have primary homology to the three classes of HDACs (RDP3, HDA1, and SIR2) found in yeast and animal cells <ref name="ref5" />.'' The fourth class of plant HDACs (known as the HD2 class) is found only in plants <ref name="ref5" />.'' <ref name="ref6" />.''<br />
<br />
===Evolution===<br />
*Sir2 family proteins, known also as sirtuins, are NAD1-dependent protein deacetylases. They contain a 200-amino acid domain conserved from bacteria to humans<ref name="ref5" />.<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, Plant genomes seem to contain relatively fewer SIR2 homologs than the other eukaryotes<ref name="ref6" />.''<br />
<br />
*Sequence analysis of the rice genome revealed two SIR2-related genes, named OsSRT1 andOsSRT2.OsSRT1 and other plant SRT1 homologs are found in the same class (class IV), whereas OsSRT2 belongs to class II of the SIR2-related genes<ref name="ref5" />.''<br />
<br />
*Compared to other eukaryotes, plants have relatively fewer SIR2-related genes Plant predicted SRT1 proteins showed relatively high conservation. Only the N-terminal parts of the plant proteins were conserved with the animal homologs<ref name="ref5" />.''<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, in addition to the founding member. All of the yeast members belong to class I of the Sir2-related proteins.Mammalian cells have seven members of the SIR2 family (SIRT1–SIRT7), distributed into all four classes <ref name="ref4" />.''Three of the mammalian members are localized in the nucleus; the remaining members are either cytoplasmic or mitochondrial localized <ref name="ref7" />.''<br />
<br />
==Labs working on this gene==<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China<br />
<br />
*Department of Quartermaster, Military Economy Academy, Wuhan 430035, China<br />
<br />
*Institut de Biotechnologiedes Plantes, Universite´ Paris Sud 11, 91405 Orsay, France<br />
==References==<br />
<references><br />
<br />
<ref name="ref1" > Limin Huang2, Qianwen Sun2, Fujun Qin, Chen Li, Yu Zhao, and Dao-Xiu Zhou* Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol. Vol. 144, 2007</ref><br />
<br />
<ref name="ref2" > Blander G, Guarente L (2004) The Sir2 family of protein deacetylases.Annu Rev Biochem 73: 417–435</ref><br />
<br />
<ref name="ref3" > Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2in plants. H2O2accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref4" > Frye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793–798</ref><br />
<br />
<ref name="ref5" > PandeyR,Muller A, NapoliCA,Selinger DA,PikaardCS,Richards EJ,Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.</ref><br />
<br />
<ref name="ref6" > Lusser A, Brosch G, Loidl A, Haas H, Loidl P (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91</ref><br />
<br />
<ref name="ref7" > Haigis MC, Guarente LP (2006) Mammalian sirtuins—emerging roles in physiology, aging, and calorie restriction. Genes Dev 20: 2913–2921</ref><br />
<br />
<ref name="ref8" > Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45</ref><br />
<br />
<ref name="ref9" > Chu Z, Yuan M, Yao J, Ge X, Yuan B, Xu C, Li X, Fu B, Li Z, Bennetzen JL,et al (2006) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20: 1250–1255</ref><br />
<br />
<ref name="ref10"> Kandel S, Morant M, Benvenist I, Ble´e E, Werck-Reichhart D, Pinot F(2005) Cloning, functional expression, and characterization of CYP709C1, the first sub-terminal hydroxylase of long chain fatty acid in plants. J Biol Chem 280: 35881–35889</ref><br />
<br />
<ref name="ref11"> Kong L, Anderson JM, OhmHW(2005) Induction of wheat defense and stressrelated genes in response to Fusarium graminearum. Genome 48: 29–40</ref><br />
<br />
<ref name="ref12"> Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2 in plants. H2O2 accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref13">Servet C, Conde E, Silva N, Zhou D-X (2010) Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Molecular plant 3: 670–677</ref><br />
<br />
<ref name="ref14">Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochimica et Biophysica Acta 1769: 295–307.</ref><br />
<br />
<ref name="ref15">Huang L, Sun Q, Qin F, Li C, Zhao Y, et al. (2007) Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice. Plant Physiology 144: 1508–1519.</ref><br />
<br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0409600|<br />
Description = Similar to Histone deacetylase|<br />
Version = NM_001059260.1 GI:115458249 GeneID:4335765|<br />
Length = 5631 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0409600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:20272401..20278031|<br />
CDS = 20274537..20274646,20274795..20274884,20275077..20275140,20275863..20275955,20276034..20276142<br>,20276428..20276477,20276551..20276641,20276876..20276946,20277195..20277293<br>,20277457..20277523,20277723..20277808|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatgaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttga</cdnaseq>|<br />
AA = <aaseq>IIKHVILLSIGLVDXXXXXXXXXXXXXXXXXXXXXXXSFSIPCQ VLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINI PLKDGIDDSGFTRLFKTVIAKVVETYLPGAIVLQCGADSLARDRLGCFNLSIEGHAEC VKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLLDTELPNEIPDNEYIKYFAPDYT LKVSNVNMDNLNSKSYLSSIKVQVMESLRAIQHAPGVQMQEVPPDFYIPDIDEDELDP DERVDQHTQDKQIHRDDEYYEGDNDNDHEDGAR</aaseq>|<br />
DNA = <dnaseqindica>2137..2246#2395..2484#2677..2740#3463..3555#3634..3742#4028..4077#4151..4241#4476..4546#4795..4893#5057..5123#5323..5408#cggtgcctttctacagcggcgttccactcgggttggtctctcccccgaggcacggccgccgccgccgccgcgctcggtctaatcggaatctatttctcgacgcgactccgcttccccggctcccctctcacccttccgcgccgccgccgccgccgcttgtagtggttggggggcgagcggccgctcgagagcgaagcgatgctggagaaagacaggatagcctacttctacgatggtacgaccgcgcattcgctaagcccccctcatctcctctccattctccctaatcactggagcaaccctagctctagctctagatgatagagcgaaatcctacgccgtctcgatgttgtgtggcttaatttcgtcgaagaaggggcatgcaattagtacctaagctgatttctagtggtgttatatgattgtggaggttggagtggatgttacggttggacggcttatgagaaattccagaactatgaacttcccaggacttgttcaactaggatttgtggtatttcagttgccctagccctaggtgcatgacgcatgattcattatcagtcagtaacataaggtggggaagcaacccttgaatcaagatttgaattagaatcgttgatccctttatctgtttaagagggcgcagtcaggctagatttggttaacaagttcctatattctttagcgccagccattttctaaaaggtcaccaacgccagccatatgtggttatttcttagatcacacataaatttccatgataagttctctcacatattttgtactaggtggtttcatgacttgtgccctcattcacccatggtcctttacatctctgtttatagagagccactcattttgcagatgtgaaaggaagttttcattgttcaaaatgtgtaatttttattactcattttgttttgatcgtttacctttttactgtgtcaatgaacaattcaggcgatgtgggcaatgtctactttgggccaaatcacccgatgaaaccacatcgactttgtatgacacatcatcttgtgctttcatatgatcttcacaagaagatggagatatatgtcagtatgaactttatttattcccttcgtttgcacttgttaactgcctaaagttcctttcacctcttacttttcacacaacgatttatgcagaggccccacaaagcatatccaacagagctcgcacagttccattctgctgattatgtggaattcttgcatcggataactcctgacacccaacacctgtatgaaaatgaattacgtagatgtatgaattatgaaacttttctcctctatgaactagtactctgggatttgttaattttacaataaaatggttgtcacatatcttgctactcatgtttaaattattataaatttatttattaagttccttacctggatctaataagtagcttagatcttcatgtacagttaaactataaggaatctcatacacaacttaaggctaattagcttcacttacatgaatgctgtcaggtgtatattcacgatatgcctatttgacaattcaaggaaaatgagggcatgtttggtcccctttcaagctcaagcaacttcccatctaacgctgcctagatagcgttggtgtttagtacagcttagcaagtcattcttcataggatgtatatccttgcccattgaagcgcatcccttgtggtcaaggtttacatgatttggtgcactaaatagttttggatatctttacagtatttatatagtattagttgcactcttctaggacacatgtgcttattttacagtttcagggcaaaataactgaacacctaacctaagtagcagagtaatctggacaaaagatccaacttacccactcttagagcttttccccaattgaagttggtttccaacataatcctcatgccttttggagctttctaacttcatttatctggttccttcatatttgttcccagacaatcttggagaagactgcccagtctttgataatctgtttgagttttgccaaatatatgctggaggaactctaggtaatatgaaaattctgaatgcttctttctaaagtgaactcttaagttcttctttgctattttagatgcggctcgcagattgaatcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcttttttggattctgagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacaggttcatgctgtttccaataaagtcatggatatgtagttaatcatttattgctgccaatatttttccaatccaatttccatctctgtgcattttgtgaattttggtggtaccataatatttatactaattccagtctcgggcttttgattttgcagggtatactaatattgtatacttattttgattttgcagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaatattttttatgtactttttggtatgatgtggttggtgattggcccttctctgcattctgttttatccttacccttttcgcatgaagtgtgtgtgacatgcgtactctcatttgtgtgaaaaaagaagagacagattaaccaaagatggtccccagttgattttgtaatgcacaaaattgatagcacctgtaggtaattgtttatgagcagttaatcttgtttctttttagttctacccgccaagaggctgtaaatatgtaacatcatagagttgaactttggttttttttactggagattcttggcatgttattctatttaaatatcaaccattgtaattgggaattcaggtggttatgtatttgaaaaacgtcatactagaatgcatcataattcgtatacgcatgcttaattgtcatctgggctgacaaaaaaaaaacatgtgcacatatacgcccgtcatttgaatcttgtagtatgttaatttgttatgtatccactgtactactaggcaactttattaaataaaaatatcccaaataactggaaggtagagcaagtgtgctacaaaaagggcaaggttgaaaatgaacataaaacatgccatgttcttctcagtaacgatgatactttatatagcttcgttttaaatgattgtgctgcttcatattgatttacctgactctcatttgaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagtaagcccactttacattactttctcatctttcatgtcattgtttagtcttatcaagttatgcatgtctattatgtaggttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggttctgtacttcttaaatctgatgtgtacttgttgattcagcagaactgtgctctagatgtaaagttagtgaactgtgctgcatattcttggatgagctattagggttcaggcggtatcttcgagataatgtgaaaccttctctcaagtctcaattatttcttaccatagttttgagattgttattgcactaatagttctgacttattttgaaatttaaattttgtttctttgagctatacttagtgaatgatcttttaatacttgcatgtgtacttgcaaacaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtaaggacaaaccgttactgcgtgtgatttctcttgttcctccttggatatcaatgtatttcccatcatgcaggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatggtattcttttcttttgcaattctgtacttctcggtccttttggcctgttgttttagaggacactactagtaatccctcaaatgcatgcaacagttcatgtattcttttcctcacatttgctggcatatcaagttgcaaacagatctatcaagaacgggattgactagtagagttccttaataatttctaaaacagcagtctgtgatatgagtttggcatgactttcctttgcagaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggtatggaaccttttctcattggcctttgtttgtcctacggttgtttggtgcattgatatttgattgctattaggtgcatcaagtaactgtccttttattactgagtatggtctaagcatttgagctctgtagtccatttggtatttcggctattcaattggtttgtgtttgctagaagtttagaacttgcgttcctttcttgagaatgtgcaaatgccatatcacatgttgtgttttaaccggagcaggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttagtttttgattcacttacacgaggaaacctcccaactggaatttgctatgtaaaaaaaagggatacaagcaggacactataatattcctttccttttgttgcctatctttttcttcgttcaacatatttctgaacaagaacaatattaacatttttgcaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcgtaagtgaaatactcctgggatgcattaggatgctaatatgtctgggtgtctgctgttccaagaaaacgaacggcagacagttgttttttttagtatatgttgtgtgttccacattatgctagtcctttcttcgtgttgttttcagacctttgaactttatatcgtccttatacattaactgtgtaaaatgttgcgcagagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttgaaaaaggttctttgtatgatgaaactggatagagaaagtctggtgctgttgcgcggtttaacagcgttaggtgggaaatactgtcaattgacttgttaggatctaacacctttgcctgcatatagtgcgtgtacgttcctactttttaatcagttacatatgctagttgcatgcagagattgcaaattcttagtcggtggtaatgattcatagtttttggctgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059260.1 RefSeq:Os04g0409600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0409600&diff=178249Os04g04096002014-06-05T11:12:51Z<p>Lina: /* Expression */</p>
<hr />
<div>OsSRT1 is one of the two SIR2-related genes found in rice.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions <ref name="ref1" />.''<br />
<br />
*OsSRT1 is one of the two SIR2-related genes found in rice<ref name="ref2" />.''<br />
<br />
*Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.''<br />
<br />
[[File:Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.jpg|right|thumb|360px|Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.''<ref name="ref1" />'']]<br />
<br />
<br />
*OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1<ref name="ref1" />.''<br />
<br />
<br />
*OsSRT1 is a histone acetylation enzyme, participating in acetylation of H3K9, inhibition of transposon and gene expression related to cell apoptosis. Rice SIR2 gene is important to maintain genomic stability and avoid DNA damage in the process of plant cell growth. OsSRT1 is involved in the safeguard against genome instability and/or oxidative stress, required for plant cell growth<ref name="ref2" />.''<br />
<br />
<br />
*Histone lysine acetylation is an important epigenetic modification for genome function and gene activity. Dynamic modulation of histone acetylation in plants has been shown to be involved in gene expression programs of plant development and responses to environmental conditions <ref name="ref13" />.''<ref name="ref14" />.''<br />
<br />
===Expression===<br />
*OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues<ref name="ref1" />.'' <br />
<br />
<br />
*Our data show that OsSRT1 was preferentially expressed in rapidly dividing young tissues/organs and the protein was nuclear localized. Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.'' <br />
<br />
<br />
[[File:Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_fragmentation.jpg|right|thumb|360px|Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_<br />
fragmentation.''<ref name="ref3" />'']]<br />
<br />
*OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress<ref name="ref3" />.'' <br />
<br />
<br />
*So far no physiological function has been assigned to plant Sir2-related proteins. As there are fewer SIR2-related genes found in plant genomes, important questions arise, such as whether plant Sir2-related proteins conserve similar functions as yeast and animal homologs. In this work, we studied the function of a rice (Oryza sativa) SIR2-like gene,by transgenic approaches OsSRT1 <ref name="ref5" />.'' <br />
<br />
<br />
<br />
*As H3K9 dimethylation is closely associated with H3K9 deacetylation <ref name="ref8" />.'' we also tested with antibodies against dimethylated H3K9. As shown in Figure 3C, the OsSRT1 RNAi had little effect on overall histone H3 acetylation. However, the acetylation of H3K9 was induced, whereas the dimethylation of H3K9 was reduced, in agreement with the antagonistic relationship between H3K9 acetylation<ref name="ref1" />.'' <br />
<br />
<br />
*The RNAi lines were selected for phenotype observation and further analysis. The RNAi plants at the two-leaf stage (about 14 d after germination) began to produce brown dots on leaves, which became larger at latter stages, leading to precocious leaf senescence. Only two of the three RNAi lines could produce seeds. The severest line died before getting into maturity. The transgenic lines showing no alteration of OsSRT1 expression or histonemodification did notmanifest the phenotype, suggesting that the lesion mimic phenotype was induced by OsSRT1 down-regulation. The lesions were reminiscent of cell death induced by hypersensitive responses during plant pathogen infections, suggesting that OsSRT1 RNAi might have induced programmed cell death (PCD). To test this hypothesis, young leaf sheaths (T1 generation) were incubated with 3,3#-diaminobenzidine (DAB) to detect H2O2 <ref name="ref12" />.'' <br />
<br />
<br />
[[File:Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment.jpg|right|thumb|360px|Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment. ''<ref name="ref3" />'']] <br />
<br />
*OsSRT1 was generally expressed in different tested rice tissues, but with higher transcript levels detected in tissues with high cell proliferation rates, such as buds, seedlings, and developing panicles HSR201 and APO, but not HSR203J, were found to be induced by OsSRT1 RNAi in the microarray data. Consistently, the RT-PCR results showed that HSR201 and APO, but not HSR203J, were activated early in 7-d-old RNAi plants. In contrast, HSR203J was repressed by OsSRT1 overexpression.<ref name="ref1" />.'' <br />
<br />
<br />
*We compared the expression of two hypersensitive response (HSR201 and HSR203J) marker genes <ref name="ref9" />.''and a cytochromeP450 gene (calledAPO) that is closely related to wheat (Triticum aestivum) CYP709C1 and CYP709C3v2, both of which are suggested to be involved in wheat defense to pathogens <ref name="ref10" />.''<ref name="ref11" />.''<br />
<br />
<br />
*Down-regulation of OsSRT1 by RNAi produces a lesion-mimic phenotype and induces H3K9 acetylation (H3K9ac) and expression of hypersensitive response-related genes in rice plants. In addition, the transcription of many transposable elements is activated in the RNAi plants, indicating that transposons and cell death-related genes might be among the primary targets of OsSRT1-mediated gene silencing.<ref name="ref15" />.'' <br />
<br />
<br />
<br />
[[File:Figure 4. Expression profiles of OsSRT1.jpg|right|thumb|360px|Figure 4. Expression profiles of OsSRT1.''<ref name="ref1" />'']]<br />
<br />
<br />
*Histone acetylation is catalyzed by histone acetyltransferases, whereas histone deacetylation is catalyzed by histone deacetylases (HDACs). Plant HDACs can be grouped into four subclasses. Three of them have primary homology to the three classes of HDACs (RDP3, HDA1, and SIR2) found in yeast and animal cells <ref name="ref5" />.'' The fourth class of plant HDACs (known as the HD2 class) is found only in plants <ref name="ref5" />.'' <ref name="ref6" />.''<br />
<br />
===Evolution===<br />
*Sir2 family proteins, known also as sirtuins, are NAD1-dependent protein deacetylases. They contain a 200-amino acid domain conserved from bacteria to humans<ref name="ref5" />.<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, Plant genomes seem to contain relatively fewer SIR2 homologs than the other eukaryotes<ref name="ref6" />.''<br />
<br />
*Sequence analysis of the rice genome revealed two SIR2-related genes, named OsSRT1 andOsSRT2.OsSRT1 and other plant SRT1 homologs are found in the same class (class IV), whereas OsSRT2 belongs to class II of the SIR2-related genes<ref name="ref5" />.''<br />
<br />
*Compared to other eukaryotes, plants have relatively fewer SIR2-related genes Plant predicted SRT1 proteins showed relatively high conservation. Only the N-terminal parts of the plant proteins were conserved with the animal homologs<ref name="ref5" />.''<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, in addition to the founding member. All of the yeast members belong to class I of the Sir2-related proteins.Mammalian cells have seven members of the SIR2 family (SIRT1–SIRT7), distributed into all four classes <ref name="ref4" />.''Three of the mammalian members are localized in the nucleus; the remaining members are either cytoplasmic or mitochondrial localized <ref name="ref7" />.''<br />
<br />
==Labs working on this gene==<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China<br />
<br />
*Department of Quartermaster, Military Economy Academy, Wuhan 430035, China<br />
<br />
*Institut de Biotechnologiedes Plantes, Universite´ Paris Sud 11, 91405 Orsay, France<br />
==References==<br />
<references><br />
<br />
<ref name="ref1" > Limin Huang2, Qianwen Sun2, Fujun Qin, Chen Li, Yu Zhao, and Dao-Xiu Zhou* Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol. Vol. 144, 2007</ref><br />
<br />
<ref name="ref2" > Blander G, Guarente L (2004) The Sir2 family of protein deacetylases.Annu Rev Biochem 73: 417–435</ref><br />
<br />
<ref name="ref3" > Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2in plants. H2O2accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref4" > Frye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793–798</ref><br />
<br />
<ref name="ref5" > PandeyR,Muller A, NapoliCA,Selinger DA,PikaardCS,Richards EJ,Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.</ref><br />
<br />
<ref name="ref6" > Lusser A, Brosch G, Loidl A, Haas H, Loidl P (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91</ref><br />
<br />
<ref name="ref7" > Haigis MC, Guarente LP (2006) Mammalian sirtuins—emerging roles in physiology, aging, and calorie restriction. Genes Dev 20: 2913–2921</ref><br />
<br />
<ref name="ref8" > Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45</ref><br />
<br />
<ref name="ref9" > Chu Z, Yuan M, Yao J, Ge X, Yuan B, Xu C, Li X, Fu B, Li Z, Bennetzen JL,et al (2006) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20: 1250–1255</ref><br />
<br />
<ref name="ref10"> Kandel S, Morant M, Benvenist I, Ble´e E, Werck-Reichhart D, Pinot F(2005) Cloning, functional expression, and characterization of CYP709C1, the first sub-terminal hydroxylase of long chain fatty acid in plants. J Biol Chem 280: 35881–35889</ref><br />
<br />
<ref name="ref11"> Kong L, Anderson JM, OhmHW(2005) Induction of wheat defense and stressrelated genes in response to Fusarium graminearum. Genome 48: 29–40</ref><br />
<br />
<ref name="ref12"> Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2 in plants. H2O2 accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref13">Servet C, Conde E, Silva N, Zhou D-X (2010) Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Molecular plant 3: 670–677.</ref><br />
<br />
<ref name="ref14">Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochimica et Biophysica Acta 1769: 295–307.</ref><br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0409600|<br />
Description = Similar to Histone deacetylase|<br />
Version = NM_001059260.1 GI:115458249 GeneID:4335765|<br />
Length = 5631 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0409600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:20272401..20278031|<br />
CDS = 20274537..20274646,20274795..20274884,20275077..20275140,20275863..20275955,20276034..20276142<br>,20276428..20276477,20276551..20276641,20276876..20276946,20277195..20277293<br>,20277457..20277523,20277723..20277808|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatgaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttga</cdnaseq>|<br />
AA = <aaseq>IIKHVILLSIGLVDXXXXXXXXXXXXXXXXXXXXXXXSFSIPCQ VLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINI PLKDGIDDSGFTRLFKTVIAKVVETYLPGAIVLQCGADSLARDRLGCFNLSIEGHAEC VKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLLDTELPNEIPDNEYIKYFAPDYT LKVSNVNMDNLNSKSYLSSIKVQVMESLRAIQHAPGVQMQEVPPDFYIPDIDEDELDP DERVDQHTQDKQIHRDDEYYEGDNDNDHEDGAR</aaseq>|<br />
DNA = <dnaseqindica>2137..2246#2395..2484#2677..2740#3463..3555#3634..3742#4028..4077#4151..4241#4476..4546#4795..4893#5057..5123#5323..5408#cggtgcctttctacagcggcgttccactcgggttggtctctcccccgaggcacggccgccgccgccgccgcgctcggtctaatcggaatctatttctcgacgcgactccgcttccccggctcccctctcacccttccgcgccgccgccgccgccgcttgtagtggttggggggcgagcggccgctcgagagcgaagcgatgctggagaaagacaggatagcctacttctacgatggtacgaccgcgcattcgctaagcccccctcatctcctctccattctccctaatcactggagcaaccctagctctagctctagatgatagagcgaaatcctacgccgtctcgatgttgtgtggcttaatttcgtcgaagaaggggcatgcaattagtacctaagctgatttctagtggtgttatatgattgtggaggttggagtggatgttacggttggacggcttatgagaaattccagaactatgaacttcccaggacttgttcaactaggatttgtggtatttcagttgccctagccctaggtgcatgacgcatgattcattatcagtcagtaacataaggtggggaagcaacccttgaatcaagatttgaattagaatcgttgatccctttatctgtttaagagggcgcagtcaggctagatttggttaacaagttcctatattctttagcgccagccattttctaaaaggtcaccaacgccagccatatgtggttatttcttagatcacacataaatttccatgataagttctctcacatattttgtactaggtggtttcatgacttgtgccctcattcacccatggtcctttacatctctgtttatagagagccactcattttgcagatgtgaaaggaagttttcattgttcaaaatgtgtaatttttattactcattttgttttgatcgtttacctttttactgtgtcaatgaacaattcaggcgatgtgggcaatgtctactttgggccaaatcacccgatgaaaccacatcgactttgtatgacacatcatcttgtgctttcatatgatcttcacaagaagatggagatatatgtcagtatgaactttatttattcccttcgtttgcacttgttaactgcctaaagttcctttcacctcttacttttcacacaacgatttatgcagaggccccacaaagcatatccaacagagctcgcacagttccattctgctgattatgtggaattcttgcatcggataactcctgacacccaacacctgtatgaaaatgaattacgtagatgtatgaattatgaaacttttctcctctatgaactagtactctgggatttgttaattttacaataaaatggttgtcacatatcttgctactcatgtttaaattattataaatttatttattaagttccttacctggatctaataagtagcttagatcttcatgtacagttaaactataaggaatctcatacacaacttaaggctaattagcttcacttacatgaatgctgtcaggtgtatattcacgatatgcctatttgacaattcaaggaaaatgagggcatgtttggtcccctttcaagctcaagcaacttcccatctaacgctgcctagatagcgttggtgtttagtacagcttagcaagtcattcttcataggatgtatatccttgcccattgaagcgcatcccttgtggtcaaggtttacatgatttggtgcactaaatagttttggatatctttacagtatttatatagtattagttgcactcttctaggacacatgtgcttattttacagtttcagggcaaaataactgaacacctaacctaagtagcagagtaatctggacaaaagatccaacttacccactcttagagcttttccccaattgaagttggtttccaacataatcctcatgccttttggagctttctaacttcatttatctggttccttcatatttgttcccagacaatcttggagaagactgcccagtctttgataatctgtttgagttttgccaaatatatgctggaggaactctaggtaatatgaaaattctgaatgcttctttctaaagtgaactcttaagttcttctttgctattttagatgcggctcgcagattgaatcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcttttttggattctgagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacaggttcatgctgtttccaataaagtcatggatatgtagttaatcatttattgctgccaatatttttccaatccaatttccatctctgtgcattttgtgaattttggtggtaccataatatttatactaattccagtctcgggcttttgattttgcagggtatactaatattgtatacttattttgattttgcagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaatattttttatgtactttttggtatgatgtggttggtgattggcccttctctgcattctgttttatccttacccttttcgcatgaagtgtgtgtgacatgcgtactctcatttgtgtgaaaaaagaagagacagattaaccaaagatggtccccagttgattttgtaatgcacaaaattgatagcacctgtaggtaattgtttatgagcagttaatcttgtttctttttagttctacccgccaagaggctgtaaatatgtaacatcatagagttgaactttggttttttttactggagattcttggcatgttattctatttaaatatcaaccattgtaattgggaattcaggtggttatgtatttgaaaaacgtcatactagaatgcatcataattcgtatacgcatgcttaattgtcatctgggctgacaaaaaaaaaacatgtgcacatatacgcccgtcatttgaatcttgtagtatgttaatttgttatgtatccactgtactactaggcaactttattaaataaaaatatcccaaataactggaaggtagagcaagtgtgctacaaaaagggcaaggttgaaaatgaacataaaacatgccatgttcttctcagtaacgatgatactttatatagcttcgttttaaatgattgtgctgcttcatattgatttacctgactctcatttgaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagtaagcccactttacattactttctcatctttcatgtcattgtttagtcttatcaagttatgcatgtctattatgtaggttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggttctgtacttcttaaatctgatgtgtacttgttgattcagcagaactgtgctctagatgtaaagttagtgaactgtgctgcatattcttggatgagctattagggttcaggcggtatcttcgagataatgtgaaaccttctctcaagtctcaattatttcttaccatagttttgagattgttattgcactaatagttctgacttattttgaaatttaaattttgtttctttgagctatacttagtgaatgatcttttaatacttgcatgtgtacttgcaaacaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtaaggacaaaccgttactgcgtgtgatttctcttgttcctccttggatatcaatgtatttcccatcatgcaggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatggtattcttttcttttgcaattctgtacttctcggtccttttggcctgttgttttagaggacactactagtaatccctcaaatgcatgcaacagttcatgtattcttttcctcacatttgctggcatatcaagttgcaaacagatctatcaagaacgggattgactagtagagttccttaataatttctaaaacagcagtctgtgatatgagtttggcatgactttcctttgcagaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggtatggaaccttttctcattggcctttgtttgtcctacggttgtttggtgcattgatatttgattgctattaggtgcatcaagtaactgtccttttattactgagtatggtctaagcatttgagctctgtagtccatttggtatttcggctattcaattggtttgtgtttgctagaagtttagaacttgcgttcctttcttgagaatgtgcaaatgccatatcacatgttgtgttttaaccggagcaggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttagtttttgattcacttacacgaggaaacctcccaactggaatttgctatgtaaaaaaaagggatacaagcaggacactataatattcctttccttttgttgcctatctttttcttcgttcaacatatttctgaacaagaacaatattaacatttttgcaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcgtaagtgaaatactcctgggatgcattaggatgctaatatgtctgggtgtctgctgttccaagaaaacgaacggcagacagttgttttttttagtatatgttgtgtgttccacattatgctagtcctttcttcgtgttgttttcagacctttgaactttatatcgtccttatacattaactgtgtaaaatgttgcgcagagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttgaaaaaggttctttgtatgatgaaactggatagagaaagtctggtgctgttgcgcggtttaacagcgttaggtgggaaatactgtcaattgacttgttaggatctaacacctttgcctgcatatagtgcgtgtacgttcctactttttaatcagttacatatgctagttgcatgcagagattgcaaattcttagtcggtggtaatgattcatagtttttggctgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059260.1 RefSeq:Os04g0409600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0409600&diff=178248Os04g04096002014-06-05T11:12:00Z<p>Lina: /* Expression */</p>
<hr />
<div>OsSRT1 is one of the two SIR2-related genes found in rice.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions <ref name="ref1" />.''<br />
<br />
*OsSRT1 is one of the two SIR2-related genes found in rice<ref name="ref2" />.''<br />
<br />
*Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.''<br />
<br />
[[File:Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.jpg|right|thumb|360px|Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.''<ref name="ref1" />'']]<br />
<br />
<br />
*OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1<ref name="ref1" />.''<br />
<br />
<br />
*OsSRT1 is a histone acetylation enzyme, participating in acetylation of H3K9, inhibition of transposon and gene expression related to cell apoptosis. Rice SIR2 gene is important to maintain genomic stability and avoid DNA damage in the process of plant cell growth. OsSRT1 is involved in the safeguard against genome instability and/or oxidative stress, required for plant cell growth<ref name="ref2" />.''<br />
<br />
<br />
*Histone lysine acetylation is an important epigenetic modification for genome function and gene activity. Dynamic modulation of histone acetylation in plants has been shown to be involved in gene expression programs of plant development and responses to environmental conditions <ref name="ref13" />.''<ref name="ref14" />.''<br />
<br />
===Expression===<br />
*OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues<ref name="ref1" />.'' <br />
<br />
<br />
*Our data show that OsSRT1 was preferentially expressed in rapidly dividing young tissues/organs and the protein was nuclear localized. Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.'' <br />
<br />
<br />
[[File:Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_fragmentation.jpg|right|thumb|360px|Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_<br />
fragmentation.''<ref name="ref3" />'']]<br />
<br />
*OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress<ref name="ref3" />.'' <br />
<br />
<br />
*So far no physiological function has been assigned to plant Sir2-related proteins. As there are fewer SIR2-related genes found in plant genomes, important questions arise, such as whether plant Sir2-related proteins conserve similar functions as yeast and animal homologs. In this work, we studied the function of a rice (Oryza sativa) SIR2-like gene,by transgenic approaches OsSRT1 <ref name="ref5" />.'' <br />
<br />
<br />
<br />
*As H3K9 dimethylation is closely associated with H3K9 deacetylation <ref name="ref8" />.'' we also tested with antibodies against dimethylated H3K9. As shown in Figure 3C, the OsSRT1 RNAi had little effect on overall histone H3 acetylation. However, the acetylation of H3K9 was induced, whereas the dimethylation of H3K9 was reduced, in agreement with the antagonistic relationship between H3K9 acetylation<ref name="ref1" />.'' <br />
<br />
<br />
*The RNAi lines were selected for phenotype observation and further analysis. The RNAi plants at the two-leaf stage (about 14 d after germination) began to produce brown dots on leaves, which became larger at latter stages, leading to precocious leaf senescence. Only two of the three RNAi lines could produce seeds. The severest line died before getting into maturity. The transgenic lines showing no alteration of OsSRT1 expression or histonemodification did notmanifest the phenotype, suggesting that the lesion mimic phenotype was induced by OsSRT1 down-regulation. The lesions were reminiscent of cell death induced by hypersensitive responses during plant pathogen infections, suggesting that OsSRT1 RNAi might have induced programmed cell death (PCD). To test this hypothesis, young leaf sheaths (T1 generation) were incubated with 3,3#-diaminobenzidine (DAB) to detect H2O2 <ref name="ref12" />.'' <br />
<br />
<br />
[[File:Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment.jpg|right|thumb|360px|Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment. ''<ref name="ref3" />'']] <br />
<br />
*OsSRT1 was generally expressed in different tested rice tissues, but with higher transcript levels detected in tissues with high cell proliferation rates, such as buds, seedlings, and developing panicles HSR201 and APO, but not HSR203J, were found to be induced by OsSRT1 RNAi in the microarray data. Consistently, the RT-PCR results showed that HSR201 and APO, but not HSR203J, were activated early in 7-d-old RNAi plants. In contrast, HSR203J was repressed by OsSRT1 overexpression.<ref name="ref1" />.'' <br />
<br />
<br />
*We compared the expression of two hypersensitive response (HSR201 and HSR203J) marker genes <ref name="ref9" />.''and a cytochromeP450 gene (calledAPO) that is closely related to wheat (Triticum aestivum) CYP709C1 and CYP709C3v2, both of which are suggested to be involved in wheat defense to pathogens <ref name="ref10" />.''<ref name="ref11" />.''<br />
<br />
*Down-regulation of OsSRT1 by RNAi produces a lesion-mimic phenotype and induces H3K9 acetylation (H3K9ac) and expression of hypersensitive response-related genes in rice plants. In addition, the transcription of many transposable elements is activated in the RNAi plants, indicating<br />
that transposons and cell death-related genes might be among the primary targets of OsSRT1-mediated gene silencing.<ref name="ref15" />.'' <br />
<br />
<br />
<br />
[[File:Figure 4. Expression profiles of OsSRT1.jpg|right|thumb|360px|Figure 4. Expression profiles of OsSRT1.''<ref name="ref1" />'']]<br />
<br />
<br />
*Histone acetylation is catalyzed by histone acetyltransferases, whereas histone deacetylation is catalyzed by histone deacetylases (HDACs). Plant HDACs can be grouped into four subclasses. Three of them have primary homology to the three classes of HDACs (RDP3, HDA1, and SIR2) found in yeast and animal cells <ref name="ref5" />.'' The fourth class of plant HDACs (known as the HD2 class) is found only in plants <ref name="ref5" />.'' <ref name="ref6" />.''<br />
<br />
===Evolution===<br />
*Sir2 family proteins, known also as sirtuins, are NAD1-dependent protein deacetylases. They contain a 200-amino acid domain conserved from bacteria to humans<ref name="ref5" />.<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, Plant genomes seem to contain relatively fewer SIR2 homologs than the other eukaryotes<ref name="ref6" />.''<br />
<br />
*Sequence analysis of the rice genome revealed two SIR2-related genes, named OsSRT1 andOsSRT2.OsSRT1 and other plant SRT1 homologs are found in the same class (class IV), whereas OsSRT2 belongs to class II of the SIR2-related genes<ref name="ref5" />.''<br />
<br />
*Compared to other eukaryotes, plants have relatively fewer SIR2-related genes Plant predicted SRT1 proteins showed relatively high conservation. Only the N-terminal parts of the plant proteins were conserved with the animal homologs<ref name="ref5" />.''<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, in addition to the founding member. All of the yeast members belong to class I of the Sir2-related proteins.Mammalian cells have seven members of the SIR2 family (SIRT1–SIRT7), distributed into all four classes <ref name="ref4" />.''Three of the mammalian members are localized in the nucleus; the remaining members are either cytoplasmic or mitochondrial localized <ref name="ref7" />.''<br />
<br />
==Labs working on this gene==<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China<br />
<br />
*Department of Quartermaster, Military Economy Academy, Wuhan 430035, China<br />
<br />
*Institut de Biotechnologiedes Plantes, Universite´ Paris Sud 11, 91405 Orsay, France<br />
==References==<br />
<references><br />
<br />
<ref name="ref1" > Limin Huang2, Qianwen Sun2, Fujun Qin, Chen Li, Yu Zhao, and Dao-Xiu Zhou* Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol. Vol. 144, 2007</ref><br />
<br />
<ref name="ref2" > Blander G, Guarente L (2004) The Sir2 family of protein deacetylases.Annu Rev Biochem 73: 417–435</ref><br />
<br />
<ref name="ref3" > Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2in plants. H2O2accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref4" > Frye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793–798</ref><br />
<br />
<ref name="ref5" > PandeyR,Muller A, NapoliCA,Selinger DA,PikaardCS,Richards EJ,Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.</ref><br />
<br />
<ref name="ref6" > Lusser A, Brosch G, Loidl A, Haas H, Loidl P (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91</ref><br />
<br />
<ref name="ref7" > Haigis MC, Guarente LP (2006) Mammalian sirtuins—emerging roles in physiology, aging, and calorie restriction. Genes Dev 20: 2913–2921</ref><br />
<br />
<ref name="ref8" > Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45</ref><br />
<br />
<ref name="ref9" > Chu Z, Yuan M, Yao J, Ge X, Yuan B, Xu C, Li X, Fu B, Li Z, Bennetzen JL,et al (2006) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20: 1250–1255</ref><br />
<br />
<ref name="ref10"> Kandel S, Morant M, Benvenist I, Ble´e E, Werck-Reichhart D, Pinot F(2005) Cloning, functional expression, and characterization of CYP709C1, the first sub-terminal hydroxylase of long chain fatty acid in plants. J Biol Chem 280: 35881–35889</ref><br />
<br />
<ref name="ref11"> Kong L, Anderson JM, OhmHW(2005) Induction of wheat defense and stressrelated genes in response to Fusarium graminearum. Genome 48: 29–40</ref><br />
<br />
<ref name="ref12"> Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2 in plants. H2O2 accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref13">Servet C, Conde E, Silva N, Zhou D-X (2010) Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Molecular plant 3: 670–677.</ref><br />
<br />
<ref name="ref14">Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochimica et Biophysica Acta 1769: 295–307.</ref><br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0409600|<br />
Description = Similar to Histone deacetylase|<br />
Version = NM_001059260.1 GI:115458249 GeneID:4335765|<br />
Length = 5631 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0409600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:20272401..20278031|<br />
CDS = 20274537..20274646,20274795..20274884,20275077..20275140,20275863..20275955,20276034..20276142<br>,20276428..20276477,20276551..20276641,20276876..20276946,20277195..20277293<br>,20277457..20277523,20277723..20277808|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatgaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttga</cdnaseq>|<br />
AA = <aaseq>IIKHVILLSIGLVDXXXXXXXXXXXXXXXXXXXXXXXSFSIPCQ VLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINI PLKDGIDDSGFTRLFKTVIAKVVETYLPGAIVLQCGADSLARDRLGCFNLSIEGHAEC VKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLLDTELPNEIPDNEYIKYFAPDYT LKVSNVNMDNLNSKSYLSSIKVQVMESLRAIQHAPGVQMQEVPPDFYIPDIDEDELDP DERVDQHTQDKQIHRDDEYYEGDNDNDHEDGAR</aaseq>|<br />
DNA = <dnaseqindica>2137..2246#2395..2484#2677..2740#3463..3555#3634..3742#4028..4077#4151..4241#4476..4546#4795..4893#5057..5123#5323..5408#cggtgcctttctacagcggcgttccactcgggttggtctctcccccgaggcacggccgccgccgccgccgcgctcggtctaatcggaatctatttctcgacgcgactccgcttccccggctcccctctcacccttccgcgccgccgccgccgccgcttgtagtggttggggggcgagcggccgctcgagagcgaagcgatgctggagaaagacaggatagcctacttctacgatggtacgaccgcgcattcgctaagcccccctcatctcctctccattctccctaatcactggagcaaccctagctctagctctagatgatagagcgaaatcctacgccgtctcgatgttgtgtggcttaatttcgtcgaagaaggggcatgcaattagtacctaagctgatttctagtggtgttatatgattgtggaggttggagtggatgttacggttggacggcttatgagaaattccagaactatgaacttcccaggacttgttcaactaggatttgtggtatttcagttgccctagccctaggtgcatgacgcatgattcattatcagtcagtaacataaggtggggaagcaacccttgaatcaagatttgaattagaatcgttgatccctttatctgtttaagagggcgcagtcaggctagatttggttaacaagttcctatattctttagcgccagccattttctaaaaggtcaccaacgccagccatatgtggttatttcttagatcacacataaatttccatgataagttctctcacatattttgtactaggtggtttcatgacttgtgccctcattcacccatggtcctttacatctctgtttatagagagccactcattttgcagatgtgaaaggaagttttcattgttcaaaatgtgtaatttttattactcattttgttttgatcgtttacctttttactgtgtcaatgaacaattcaggcgatgtgggcaatgtctactttgggccaaatcacccgatgaaaccacatcgactttgtatgacacatcatcttgtgctttcatatgatcttcacaagaagatggagatatatgtcagtatgaactttatttattcccttcgtttgcacttgttaactgcctaaagttcctttcacctcttacttttcacacaacgatttatgcagaggccccacaaagcatatccaacagagctcgcacagttccattctgctgattatgtggaattcttgcatcggataactcctgacacccaacacctgtatgaaaatgaattacgtagatgtatgaattatgaaacttttctcctctatgaactagtactctgggatttgttaattttacaataaaatggttgtcacatatcttgctactcatgtttaaattattataaatttatttattaagttccttacctggatctaataagtagcttagatcttcatgtacagttaaactataaggaatctcatacacaacttaaggctaattagcttcacttacatgaatgctgtcaggtgtatattcacgatatgcctatttgacaattcaaggaaaatgagggcatgtttggtcccctttcaagctcaagcaacttcccatctaacgctgcctagatagcgttggtgtttagtacagcttagcaagtcattcttcataggatgtatatccttgcccattgaagcgcatcccttgtggtcaaggtttacatgatttggtgcactaaatagttttggatatctttacagtatttatatagtattagttgcactcttctaggacacatgtgcttattttacagtttcagggcaaaataactgaacacctaacctaagtagcagagtaatctggacaaaagatccaacttacccactcttagagcttttccccaattgaagttggtttccaacataatcctcatgccttttggagctttctaacttcatttatctggttccttcatatttgttcccagacaatcttggagaagactgcccagtctttgataatctgtttgagttttgccaaatatatgctggaggaactctaggtaatatgaaaattctgaatgcttctttctaaagtgaactcttaagttcttctttgctattttagatgcggctcgcagattgaatcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcttttttggattctgagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacaggttcatgctgtttccaataaagtcatggatatgtagttaatcatttattgctgccaatatttttccaatccaatttccatctctgtgcattttgtgaattttggtggtaccataatatttatactaattccagtctcgggcttttgattttgcagggtatactaatattgtatacttattttgattttgcagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaatattttttatgtactttttggtatgatgtggttggtgattggcccttctctgcattctgttttatccttacccttttcgcatgaagtgtgtgtgacatgcgtactctcatttgtgtgaaaaaagaagagacagattaaccaaagatggtccccagttgattttgtaatgcacaaaattgatagcacctgtaggtaattgtttatgagcagttaatcttgtttctttttagttctacccgccaagaggctgtaaatatgtaacatcatagagttgaactttggttttttttactggagattcttggcatgttattctatttaaatatcaaccattgtaattgggaattcaggtggttatgtatttgaaaaacgtcatactagaatgcatcataattcgtatacgcatgcttaattgtcatctgggctgacaaaaaaaaaacatgtgcacatatacgcccgtcatttgaatcttgtagtatgttaatttgttatgtatccactgtactactaggcaactttattaaataaaaatatcccaaataactggaaggtagagcaagtgtgctacaaaaagggcaaggttgaaaatgaacataaaacatgccatgttcttctcagtaacgatgatactttatatagcttcgttttaaatgattgtgctgcttcatattgatttacctgactctcatttgaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagtaagcccactttacattactttctcatctttcatgtcattgtttagtcttatcaagttatgcatgtctattatgtaggttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggttctgtacttcttaaatctgatgtgtacttgttgattcagcagaactgtgctctagatgtaaagttagtgaactgtgctgcatattcttggatgagctattagggttcaggcggtatcttcgagataatgtgaaaccttctctcaagtctcaattatttcttaccatagttttgagattgttattgcactaatagttctgacttattttgaaatttaaattttgtttctttgagctatacttagtgaatgatcttttaatacttgcatgtgtacttgcaaacaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtaaggacaaaccgttactgcgtgtgatttctcttgttcctccttggatatcaatgtatttcccatcatgcaggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatggtattcttttcttttgcaattctgtacttctcggtccttttggcctgttgttttagaggacactactagtaatccctcaaatgcatgcaacagttcatgtattcttttcctcacatttgctggcatatcaagttgcaaacagatctatcaagaacgggattgactagtagagttccttaataatttctaaaacagcagtctgtgatatgagtttggcatgactttcctttgcagaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggtatggaaccttttctcattggcctttgtttgtcctacggttgtttggtgcattgatatttgattgctattaggtgcatcaagtaactgtccttttattactgagtatggtctaagcatttgagctctgtagtccatttggtatttcggctattcaattggtttgtgtttgctagaagtttagaacttgcgttcctttcttgagaatgtgcaaatgccatatcacatgttgtgttttaaccggagcaggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttagtttttgattcacttacacgaggaaacctcccaactggaatttgctatgtaaaaaaaagggatacaagcaggacactataatattcctttccttttgttgcctatctttttcttcgttcaacatatttctgaacaagaacaatattaacatttttgcaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcgtaagtgaaatactcctgggatgcattaggatgctaatatgtctgggtgtctgctgttccaagaaaacgaacggcagacagttgttttttttagtatatgttgtgtgttccacattatgctagtcctttcttcgtgttgttttcagacctttgaactttatatcgtccttatacattaactgtgtaaaatgttgcgcagagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttgaaaaaggttctttgtatgatgaaactggatagagaaagtctggtgctgttgcgcggtttaacagcgttaggtgggaaatactgtcaattgacttgttaggatctaacacctttgcctgcatatagtgcgtgtacgttcctactttttaatcagttacatatgctagttgcatgcagagattgcaaattcttagtcggtggtaatgattcatagtttttggctgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059260.1 RefSeq:Os04g0409600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178244Os09g03078002014-06-05T11:10:56Z<p>Lina: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase|300px|thumb|left|Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase.jpg]]<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0409600&diff=178243Os04g04096002014-06-05T11:09:04Z<p>Lina: /* References */</p>
<hr />
<div>OsSRT1 is one of the two SIR2-related genes found in rice.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions <ref name="ref1" />.''<br />
<br />
*OsSRT1 is one of the two SIR2-related genes found in rice<ref name="ref2" />.''<br />
<br />
*Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.''<br />
<br />
[[File:Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.jpg|right|thumb|360px|Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.''<ref name="ref1" />'']]<br />
<br />
<br />
*OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1<ref name="ref1" />.''<br />
<br />
<br />
*OsSRT1 is a histone acetylation enzyme, participating in acetylation of H3K9, inhibition of transposon and gene expression related to cell apoptosis. Rice SIR2 gene is important to maintain genomic stability and avoid DNA damage in the process of plant cell growth. OsSRT1 is involved in the safeguard against genome instability and/or oxidative stress, required for plant cell growth<ref name="ref2" />.''<br />
<br />
<br />
*Histone lysine acetylation is an important epigenetic modification for genome function and gene activity. Dynamic modulation of histone acetylation in plants has been shown to be involved in gene expression programs of plant development and responses to environmental conditions <ref name="ref13" />.''<ref name="ref14" />.''<br />
<br />
===Expression===<br />
*OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues<ref name="ref1" />.'' <br />
<br />
<br />
*Our data show that OsSRT1 was preferentially expressed in rapidly dividing young tissues/organs and the protein was nuclear localized. Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.'' <br />
<br />
<br />
[[File:Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_fragmentation.jpg|right|thumb|360px|Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_<br />
fragmentation.''<ref name="ref3" />'']]<br />
<br />
*OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress<ref name="ref3" />.'' <br />
<br />
<br />
*So far no physiological function has been assigned to plant Sir2-related proteins. As there are fewer SIR2-related genes found in plant genomes, important questions arise, such as whether plant Sir2-related proteins conserve similar functions as yeast and animal homologs. In this work, we studied the function of a rice (Oryza sativa) SIR2-like gene,by transgenic approaches OsSRT1 <ref name="ref5" />.'' <br />
<br />
<br />
<br />
*As H3K9 dimethylation is closely associated with H3K9 deacetylation <ref name="ref8" />.'' we also tested with antibodies against dimethylated H3K9. As shown in Figure 3C, the OsSRT1 RNAi had little effect on overall histone H3 acetylation. However, the acetylation of H3K9 was induced, whereas the dimethylation of H3K9 was reduced, in agreement with the antagonistic relationship between H3K9 acetylation<ref name="ref1" />.'' <br />
<br />
<br />
*The RNAi lines were selected for phenotype observation and further analysis. The RNAi plants at the two-leaf stage (about 14 d after germination) began to produce brown dots on leaves, which became larger at latter stages, leading to precocious leaf senescence. Only two of the three RNAi lines could produce seeds. The severest line died before getting into maturity. The transgenic lines showing no alteration of OsSRT1 expression or histonemodification did notmanifest the phenotype, suggesting that the lesion mimic phenotype was induced by OsSRT1 down-regulation. The lesions were reminiscent of cell death induced by hypersensitive responses during plant pathogen infections, suggesting that OsSRT1 RNAi might have induced programmed cell death (PCD). To test this hypothesis, young leaf sheaths (T1 generation) were incubated with 3,3#-diaminobenzidine (DAB) to detect H2O2 <ref name="ref12" />.'' <br />
<br />
<br />
[[File:Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment.jpg|right|thumb|360px|Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment. ''<ref name="ref3" />'']] <br />
<br />
*OsSRT1 was generally expressed in different tested rice tissues, but with higher transcript levels detected in tissues with high cell proliferation rates, such as buds, seedlings, and developing panicles HSR201 and APO, but not HSR203J, were found to be induced by OsSRT1 RNAi in the microarray data. Consistently, the RT-PCR results showed that HSR201 and APO, but not HSR203J, were activated early in 7-d-old RNAi plants. In contrast, HSR203J was repressed by OsSRT1 overexpression.<ref name="ref1" />.'' <br />
<br />
<br />
*We compared the expression of two hypersensitive response (HSR201 and HSR203J) marker genes <ref name="ref9" />.''and a cytochromeP450 gene (calledAPO) that is closely related to wheat (Triticum aestivum) CYP709C1 and CYP709C3v2, both of which are suggested to be involved in wheat defense to pathogens <ref name="ref10" />.''<ref name="ref11" />.''<br />
<br />
<br />
<br />
[[File:Figure 4. Expression profiles of OsSRT1.jpg|right|thumb|360px|Figure 4. Expression profiles of OsSRT1.''<ref name="ref1" />'']]<br />
<br />
<br />
*Histone acetylation is catalyzed by histone acetyltransferases, whereas histone deacetylation is catalyzed by histone deacetylases (HDACs). Plant HDACs can be grouped into four subclasses. Three of them have primary homology to the three classes of HDACs (RDP3, HDA1, and SIR2) found in yeast and animal cells <ref name="ref5" />.'' The fourth class of plant HDACs (known as the HD2 class) is found only in plants <ref name="ref5" />.'' <ref name="ref6" />.''<br />
<br />
===Evolution===<br />
*Sir2 family proteins, known also as sirtuins, are NAD1-dependent protein deacetylases. They contain a 200-amino acid domain conserved from bacteria to humans<ref name="ref5" />.<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, Plant genomes seem to contain relatively fewer SIR2 homologs than the other eukaryotes<ref name="ref6" />.''<br />
<br />
*Sequence analysis of the rice genome revealed two SIR2-related genes, named OsSRT1 andOsSRT2.OsSRT1 and other plant SRT1 homologs are found in the same class (class IV), whereas OsSRT2 belongs to class II of the SIR2-related genes<ref name="ref5" />.''<br />
<br />
*Compared to other eukaryotes, plants have relatively fewer SIR2-related genes Plant predicted SRT1 proteins showed relatively high conservation. Only the N-terminal parts of the plant proteins were conserved with the animal homologs<ref name="ref5" />.''<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, in addition to the founding member. All of the yeast members belong to class I of the Sir2-related proteins.Mammalian cells have seven members of the SIR2 family (SIRT1–SIRT7), distributed into all four classes <ref name="ref4" />.''Three of the mammalian members are localized in the nucleus; the remaining members are either cytoplasmic or mitochondrial localized <ref name="ref7" />.''<br />
<br />
==Labs working on this gene==<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China<br />
<br />
*Department of Quartermaster, Military Economy Academy, Wuhan 430035, China<br />
<br />
*Institut de Biotechnologiedes Plantes, Universite´ Paris Sud 11, 91405 Orsay, France<br />
==References==<br />
<references><br />
<br />
<ref name="ref1" > Limin Huang2, Qianwen Sun2, Fujun Qin, Chen Li, Yu Zhao, and Dao-Xiu Zhou* Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol. Vol. 144, 2007</ref><br />
<br />
<ref name="ref2" > Blander G, Guarente L (2004) The Sir2 family of protein deacetylases.Annu Rev Biochem 73: 417–435</ref><br />
<br />
<ref name="ref3" > Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2in plants. H2O2accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref4" > Frye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793–798</ref><br />
<br />
<ref name="ref5" > PandeyR,Muller A, NapoliCA,Selinger DA,PikaardCS,Richards EJ,Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.</ref><br />
<br />
<ref name="ref6" > Lusser A, Brosch G, Loidl A, Haas H, Loidl P (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91</ref><br />
<br />
<ref name="ref7" > Haigis MC, Guarente LP (2006) Mammalian sirtuins—emerging roles in physiology, aging, and calorie restriction. Genes Dev 20: 2913–2921</ref><br />
<br />
<ref name="ref8" > Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45</ref><br />
<br />
<ref name="ref9" > Chu Z, Yuan M, Yao J, Ge X, Yuan B, Xu C, Li X, Fu B, Li Z, Bennetzen JL,et al (2006) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20: 1250–1255</ref><br />
<br />
<ref name="ref10"> Kandel S, Morant M, Benvenist I, Ble´e E, Werck-Reichhart D, Pinot F(2005) Cloning, functional expression, and characterization of CYP709C1, the first sub-terminal hydroxylase of long chain fatty acid in plants. J Biol Chem 280: 35881–35889</ref><br />
<br />
<ref name="ref11"> Kong L, Anderson JM, OhmHW(2005) Induction of wheat defense and stressrelated genes in response to Fusarium graminearum. Genome 48: 29–40</ref><br />
<br />
<ref name="ref12"> Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2 in plants. H2O2 accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref13">Servet C, Conde E, Silva N, Zhou D-X (2010) Histone acetyltransferase AtGCN5/HAG1 is a versatile regulator of developmental and inducible gene expression in Arabidopsis. Molecular plant 3: 670–677.</ref><br />
<br />
<ref name="ref14">Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochimica et Biophysica Acta 1769: 295–307.</ref><br />
<br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0409600|<br />
Description = Similar to Histone deacetylase|<br />
Version = NM_001059260.1 GI:115458249 GeneID:4335765|<br />
Length = 5631 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0409600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:20272401..20278031|<br />
CDS = 20274537..20274646,20274795..20274884,20275077..20275140,20275863..20275955,20276034..20276142<br>,20276428..20276477,20276551..20276641,20276876..20276946,20277195..20277293<br>,20277457..20277523,20277723..20277808|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatgaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttga</cdnaseq>|<br />
AA = <aaseq>IIKHVILLSIGLVDXXXXXXXXXXXXXXXXXXXXXXXSFSIPCQ VLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINI PLKDGIDDSGFTRLFKTVIAKVVETYLPGAIVLQCGADSLARDRLGCFNLSIEGHAEC VKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLLDTELPNEIPDNEYIKYFAPDYT LKVSNVNMDNLNSKSYLSSIKVQVMESLRAIQHAPGVQMQEVPPDFYIPDIDEDELDP DERVDQHTQDKQIHRDDEYYEGDNDNDHEDGAR</aaseq>|<br />
DNA = <dnaseqindica>2137..2246#2395..2484#2677..2740#3463..3555#3634..3742#4028..4077#4151..4241#4476..4546#4795..4893#5057..5123#5323..5408#cggtgcctttctacagcggcgttccactcgggttggtctctcccccgaggcacggccgccgccgccgccgcgctcggtctaatcggaatctatttctcgacgcgactccgcttccccggctcccctctcacccttccgcgccgccgccgccgccgcttgtagtggttggggggcgagcggccgctcgagagcgaagcgatgctggagaaagacaggatagcctacttctacgatggtacgaccgcgcattcgctaagcccccctcatctcctctccattctccctaatcactggagcaaccctagctctagctctagatgatagagcgaaatcctacgccgtctcgatgttgtgtggcttaatttcgtcgaagaaggggcatgcaattagtacctaagctgatttctagtggtgttatatgattgtggaggttggagtggatgttacggttggacggcttatgagaaattccagaactatgaacttcccaggacttgttcaactaggatttgtggtatttcagttgccctagccctaggtgcatgacgcatgattcattatcagtcagtaacataaggtggggaagcaacccttgaatcaagatttgaattagaatcgttgatccctttatctgtttaagagggcgcagtcaggctagatttggttaacaagttcctatattctttagcgccagccattttctaaaaggtcaccaacgccagccatatgtggttatttcttagatcacacataaatttccatgataagttctctcacatattttgtactaggtggtttcatgacttgtgccctcattcacccatggtcctttacatctctgtttatagagagccactcattttgcagatgtgaaaggaagttttcattgttcaaaatgtgtaatttttattactcattttgttttgatcgtttacctttttactgtgtcaatgaacaattcaggcgatgtgggcaatgtctactttgggccaaatcacccgatgaaaccacatcgactttgtatgacacatcatcttgtgctttcatatgatcttcacaagaagatggagatatatgtcagtatgaactttatttattcccttcgtttgcacttgttaactgcctaaagttcctttcacctcttacttttcacacaacgatttatgcagaggccccacaaagcatatccaacagagctcgcacagttccattctgctgattatgtggaattcttgcatcggataactcctgacacccaacacctgtatgaaaatgaattacgtagatgtatgaattatgaaacttttctcctctatgaactagtactctgggatttgttaattttacaataaaatggttgtcacatatcttgctactcatgtttaaattattataaatttatttattaagttccttacctggatctaataagtagcttagatcttcatgtacagttaaactataaggaatctcatacacaacttaaggctaattagcttcacttacatgaatgctgtcaggtgtatattcacgatatgcctatttgacaattcaaggaaaatgagggcatgtttggtcccctttcaagctcaagcaacttcccatctaacgctgcctagatagcgttggtgtttagtacagcttagcaagtcattcttcataggatgtatatccttgcccattgaagcgcatcccttgtggtcaaggtttacatgatttggtgcactaaatagttttggatatctttacagtatttatatagtattagttgcactcttctaggacacatgtgcttattttacagtttcagggcaaaataactgaacacctaacctaagtagcagagtaatctggacaaaagatccaacttacccactcttagagcttttccccaattgaagttggtttccaacataatcctcatgccttttggagctttctaacttcatttatctggttccttcatatttgttcccagacaatcttggagaagactgcccagtctttgataatctgtttgagttttgccaaatatatgctggaggaactctaggtaatatgaaaattctgaatgcttctttctaaagtgaactcttaagttcttctttgctattttagatgcggctcgcagattgaatcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcttttttggattctgagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacaggttcatgctgtttccaataaagtcatggatatgtagttaatcatttattgctgccaatatttttccaatccaatttccatctctgtgcattttgtgaattttggtggtaccataatatttatactaattccagtctcgggcttttgattttgcagggtatactaatattgtatacttattttgattttgcagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaatattttttatgtactttttggtatgatgtggttggtgattggcccttctctgcattctgttttatccttacccttttcgcatgaagtgtgtgtgacatgcgtactctcatttgtgtgaaaaaagaagagacagattaaccaaagatggtccccagttgattttgtaatgcacaaaattgatagcacctgtaggtaattgtttatgagcagttaatcttgtttctttttagttctacccgccaagaggctgtaaatatgtaacatcatagagttgaactttggttttttttactggagattcttggcatgttattctatttaaatatcaaccattgtaattgggaattcaggtggttatgtatttgaaaaacgtcatactagaatgcatcataattcgtatacgcatgcttaattgtcatctgggctgacaaaaaaaaaacatgtgcacatatacgcccgtcatttgaatcttgtagtatgttaatttgttatgtatccactgtactactaggcaactttattaaataaaaatatcccaaataactggaaggtagagcaagtgtgctacaaaaagggcaaggttgaaaatgaacataaaacatgccatgttcttctcagtaacgatgatactttatatagcttcgttttaaatgattgtgctgcttcatattgatttacctgactctcatttgaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagtaagcccactttacattactttctcatctttcatgtcattgtttagtcttatcaagttatgcatgtctattatgtaggttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggttctgtacttcttaaatctgatgtgtacttgttgattcagcagaactgtgctctagatgtaaagttagtgaactgtgctgcatattcttggatgagctattagggttcaggcggtatcttcgagataatgtgaaaccttctctcaagtctcaattatttcttaccatagttttgagattgttattgcactaatagttctgacttattttgaaatttaaattttgtttctttgagctatacttagtgaatgatcttttaatacttgcatgtgtacttgcaaacaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtaaggacaaaccgttactgcgtgtgatttctcttgttcctccttggatatcaatgtatttcccatcatgcaggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatggtattcttttcttttgcaattctgtacttctcggtccttttggcctgttgttttagaggacactactagtaatccctcaaatgcatgcaacagttcatgtattcttttcctcacatttgctggcatatcaagttgcaaacagatctatcaagaacgggattgactagtagagttccttaataatttctaaaacagcagtctgtgatatgagtttggcatgactttcctttgcagaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggtatggaaccttttctcattggcctttgtttgtcctacggttgtttggtgcattgatatttgattgctattaggtgcatcaagtaactgtccttttattactgagtatggtctaagcatttgagctctgtagtccatttggtatttcggctattcaattggtttgtgtttgctagaagtttagaacttgcgttcctttcttgagaatgtgcaaatgccatatcacatgttgtgttttaaccggagcaggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttagtttttgattcacttacacgaggaaacctcccaactggaatttgctatgtaaaaaaaagggatacaagcaggacactataatattcctttccttttgttgcctatctttttcttcgttcaacatatttctgaacaagaacaatattaacatttttgcaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcgtaagtgaaatactcctgggatgcattaggatgctaatatgtctgggtgtctgctgttccaagaaaacgaacggcagacagttgttttttttagtatatgttgtgtgttccacattatgctagtcctttcttcgtgttgttttcagacctttgaactttatatcgtccttatacattaactgtgtaaaatgttgcgcagagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttgaaaaaggttctttgtatgatgaaactggatagagaaagtctggtgctgttgcgcggtttaacagcgttaggtgggaaatactgtcaattgacttgttaggatctaacacctttgcctgcatatagtgcgtgtacgttcctactttttaatcagttacatatgctagttgcatgcagagattgcaaattcttagtcggtggtaatgattcatagtttttggctgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059260.1 RefSeq:Os04g0409600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os09g0307800&diff=178241Os09g03078002014-06-05T11:08:18Z<p>Lina: /* Evolution */</p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
SDG724 is a class II SET domain protein and is constitutively expressed in various kinds of tissues. <br />
==Annotated Information==<br />
===Function===<br />
*SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of globalhistone H3 lysine 36 (H3K36) methylation in vivo<ref name="ref1" />.<br />
<br />
*Histone Lys methylation in plants functions in biological processes such as flowering transition, floral organ development,carotenoid biosynthesis, shoot and root branching, pollen and macro-trichome development, and the brassinosteroid signaling pathway<ref name="ref2" />.<br />
<br />
*lesions in SDG724 were responsible for the late-flowering phenotype of lvp1 plants Heading date analyses showed that the flowering time defect was rescued in thetransgenic plant lines<ref name="ref1" />.<br />
<br />
*Long vegetative phase 1 (LVP1)/SDG724, is required for H3K36 methylation and promotes heading date in rice. The loss of function mutant lvp1 has a late flowering phenotype under both LD and SD conditions, associated with the suppressed expression of MADS50, MADS51, Ehd1, RFT1, and Hd3a. Furthermore, our results suggest a novel mechanism for the epigenetic regulation of flowering in rice, in which SDG724 mediates H3K36me2/3 deposition at the MADS50 and RFT1loci and promotes flowering through MADS50/MADS51-Ehd1-Hd3a/RFT1 pathways<ref name="ref3" />.<br />
<br />
===Expression===<br />
*Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod<ref name="ref1" />.<br />
<br />
*To investigate the role of SDG724 in aphotoperiod-insensitive background, lvp1 se5 double mutants were created using a se5 nonsense mutation in Nipponbare,the same genetic background as for the lvp1 mutant<ref name="ref1" />.<br />
<br />
*Genetic analysis demonstrated that the late flowering phenotype of lvp1 segregated as a complete monogenic recessive trait.Therefore, we carefully selected 1147 extremely late-heading plants from an F2 population derived from a cross between lvp1 and Minghui 63 and used a map-based cloning strategy to identify the candidate gene<ref name="ref1" />.<br />
<br />
[[File:Figure 1. Map-Based Cloning of LVP1.jpg|right|thumb|400px|Figure 1. Map-Based Cloning of LVP1.''<ref name="ref1" />'']] <br />
<br />
<br />
*Under Beijing field conditions,lvp1 plants did not show heading even in November, 160 d after germination, when the weather became too cold for rice growth<ref name="ref1" />.<br />
<br />
[[File:Figure 2. Phenotype of the lvp1 Mutant.jpg|right|thumb|300px|Figure 2. Phenotype of the lvp1 Mutant.''<ref name="ref5" />'']]<br />
<br />
<br />
<br />
*Chromatin structure is important for eukaryotic gene expression, and histone Lys methylation has drawn special attention due to its complex role in this process<ref name="ref5" />.<br />
<br />
*Ehd1, which encodes a B-type response regulator, is a unique transcriptionalregulator and promotes flowering by controlling FT-like gene expression independent of Hd1 under both SD and LD condi-tions in rice<ref name="ref6" />.<br />
<br />
===Evolution===<br />
*SET domain–containing proteins are well annotated and characterized in Arabidopsis<ref name="ref4" />.<br />
[[File:Figure 3.SDG724 Acts as a SET Domain–Containing Histone Methyltransferase|||.jpg]]<br />
*There are at least two independent flowering pathways in rice.The Heading date1 (Hd1) pathway is conserved between rice and Arabidopsis, but the Early heading date1 (Ehd1) pathway is unique to rice<ref name="ref6" />.<br />
<br />
*RFT1 and Hd3a encode two rice florigens and are closely linked in the genome, separated by only 11.5 kb. However, RFT1 and Hd3a have functionally diverged to control the LD and SD flowering time pathways, respectively<ref name="ref7" />.<br />
<br />
==Labs working on this gene==<br />
<br />
*State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics andDevelopmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China<br />
<br />
*Key Laboratory for Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, 100875 Beijing, China<br />
<br />
*Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China<br />
<br />
*State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences,Hangzhou 310006, China<br />
<br />
==References==<br />
<references><br />
<ref name="ref1"> ChanghuiSun,1JunFang,TaolanZhao,BoXu,FantaoZhang,LinchuanLiu,JiuyouTang,GenfaZhang,Xiaojian Deng,Fan Chen,dQian Qian,eXiaofeng Cao,and Chengcai Chu The Histone Methyltransferase SDG724 Mediates H3K36me2/3 Deposition at MADS50 and RFT1 and Promotes Flowering in Rice The Plant Cell, Vol. 24: 3235–3247</ref><br />
<br />
<ref name="ref2"> Kim, S.Y., He, Y., Jacob, Y., Noh, Y.S., Michaels, S., and Amasino,R. (2005). Establishment of the vernalization-responsive, winter-annual habit in Arabidopsis requires a putative histone H3 methyltransferase. Plant Cell 17: 3301–3310.</ref><br />
<br />
<ref name="ref3"> Ma, Y.M., et al. (2009). Molecular analysis of rice plants harboring a multi-functional T-DNA tagging system. J. Genet. Genomics 36:267–276.</ref><br />
<br />
<ref name="ref4"> Springer, N.M., Napoli, C.A., Selinger, D.A., Pandey, R., Cone, K.C.,Chandler, V.L., Kaeppler, H.F., and Kaeppler, S.M. (2003). Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots. Plant Physiol. 132: 907–925.</ref><br />
<br />
<ref name="ref5"> Wu, J.I., Lessard, J., and Crabtree, G.R. (2009). Understanding the words of chromatin regulation. Cell 136: 200–206.</ref><br />
<br />
<ref name="ref6"> Doi, K., Izawa, T., Fuse, T., Yamanouchi, U., Kubo, T., Shimatani, Z., Yano, M., and Yoshimura, A. (2004). Ehd1, a B-type response regulator in rice,confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev.18: 926–936.</ref><br />
<br />
<ref name="ref7"> Komiya, R., Ikegami, A., Tamaki, S., Yokoi, S., and Shimamoto, K.(2008). Hd3a and RFT1 are essential for flowering in rice. Development 135: 767–774.</ref><br />
〈/references〉<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os09g0307800|<br />
Description = Nuclear protein SET domain containing protein|<br />
Version = NM_001069362.1 GI:115478463 GeneID:4346677|<br />
Length = 7580 bp|<br />
Definition = Oryza sativa Japonica Group Os09g0307800, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|<br />
AP = Chromosome 9:8605019..8612598|<br />
CDS = 8605843..8605869,8606906..8606971,8607055..8607106,8607517..8607720,8607837..8607917<br>,8608003..8608174,8609280..8609358,8610514..8610613,8610960..8611059<br>,8611590..8611707,8612450..8612473|<br />
GCID = <gbrowseImage1><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008402:8605019..8612598<br />
source=RiceChromosome09<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atgcctcggccggcgaaaatcaggaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggaatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacattattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggatccagatggtcctgaggaagtgtga</cdnaseq>|<br />
AA = <aaseq>MPRPAKIRKKHENVFDQLIKAIKAPVDFDLPPVLKEWKSNYYVP IKRNAYITRKRVEDDGIFCSCTPSGSSATCDKDCQCGMLFSCCSSTCKCENKCANKPF QHRTLRKTKLIKTEKCGNGVVAEEDIKKGEFVIEYVGEVIDDRTCEQRLWKMKRQGDT NFYLCEVSSNMVIDATNKGNMSRFINHSCEPNTEMQKWTVEGETRVGIFALRDIKTGE ELTYDYKFVQFGADQDCHCGSSNCRKMLGITKPVNSIVLHNGNLSQDQHVRKKRKTYL ENCIGEIVRLWHRRHSMYLAASIYDFNERNGIHTLLFTDATIEEFDLREEDWDFLPDP DGPEEV</aaseq>|<br />
DNA = <dnaseqindica>6730..6756#5628..5693#5493..5544#4879..5082#4682..4762#4425..4596#3241..3319#1986..2085#1540..1639#892..1009#126..149#ttctgctccgacctcacctcgcctccttcctccgccgactccctcccctccgccattgcagcctcgcctacggccttgagctcgtcgccgatccccgccaccgccgcgacctctgcctgccccccatgcctcggccggcgaaaatcagggtacacttcctcccatgcttgcacctcttcccctttccgcgtaaaccctaaacccgaaatttcctgcaatttttttttaaaaaaattttggtcgaatcttcgctagggaaccgcatctctaccgtttttgttgtgccttgcaaaggtttgtctccccttcgagagaagcagcaaggggagttatggagtatatggattaggggttcagggtctcagatgcgttcttgtgctaccttggaaggagtattttgttcattagattttttttcttttttttttttgcggggaaaagttgttgatcagacttgggatggctacagtggaaattacaggagcgatgtggtgttaggtctctaacctgcaggaaacagggcgagtattttgaattggaatacgatggcctaagtgagtgaagctttgttgggactgctagtgttgaccaggactgttggattaatccgttgaaatgagtgaacacatgactggactcttattgaccaaacgtatcttatattcgatgggattataacatggcacggccaatactctacacccattacttcattgcttttatttctccgttgttgcatacacgtgcatgacagaaaagaggctacaccatatctgagtagactgattctgttactatctctatttttgttttatatgcttgttacctcattttttgttggttaactcataattctatatgcttatttatcttcatgtctctatgctgcagaaaaaacatgagaatgtgtttgatcaattgatcaaggcgataaaagctcctgtggactttgatctgccgcctgtattgaaagaatggaagtcaaattactatgtgccaattaagcggagtatccttacccaccattgcatttaatctgtttcctttctcggagcagcaatgatttgcgtcctcctcatttatacttgcaatgtctctggttaaaatttcattccttggagcaatcattctacaaacttgagtgtatatttatcagtctctgctgtagcattctagattgattgtatatccgaaaatttactaaatcctaatgtactacaaagtataatatagcataggaaagtcagtggtttgttttttcaataatgtgtcttgtcacagggatgcatttaacaacggcttcaacaacgtgttttcacatggggttgtatttcaaaattgcttaagatggtatcttcaatattccaatctgttgaatctcatttttataacatagccatccaattactcgtttacaattgcatggctggaacatcttaatttcacaatgtaaacagaggacttgccttttactgctgtaaaatttctgtttgtctaaaattttatttagcattacggttgtccttaattctacgtaagatgcttatattactcggaaacgcgttgaggatgatggcattttttgttcctgtaccccttctggatcatccgcaacttgtgacaaagattgccaatgcgggtaatctctctctcccccctctctgctccaacttgcatccatcatatagccatgatactattatgaatatagctcgtattgaataatagcctcaaggaggcaatatatagagtgcatatagcgttaggactctaacctatagcatgtaaagggataacccatatatgcaaaagactttatattcctaactgatacaacctagagtgtttgagtctgctcttttttttttttttgtcttgaacctaacctcattaataaaatggtaagtttcttattagaataacctgtaaactttattggtattgagtgttgaggcattctaaaatactgtatttttgtgatgcaggatgttgttctcttgttgttcgtcgacctgtaaatgtgagaataaatgtgctaacaaaccgttccagcataggactttgaggaaaaccaaattaattaaggtatgattgaatcaagtttctaccattgttgagttggcagattaccatttaagctgactgtggataaatatgccattgctgtagctgatgctaataaagttttgatgcaataaatgttataaaaatagtctttcaactatgtgttccttgttaaaaatgtcagcttttcttgtgtaaagtgtaaactgtaaagtaatataggagtataggacacttgttaaaaatgtcagcttttctcgtggaaactataaagtagtatacgagtataggacgctgtgaatgataaaggaaatgttagccatatgaaataaatgagaagaaaaacttaaactatgaatccagttatggtaggatagatctcaatcagattatggtagattattaatttctttcaaaactttccgtataatatcgatacgattgggaataaacctccttgtttgggcattccttcttaagtaatgtctattatatacccctcaagtacggtaaccaggtaaaacgcccccccccccccctaggcagaatccaacctgattttaatggtgattttcatgattttaacatccattaatctggttgtctgctctcctagtttcataatgcattcctacttcctagtatagcatgattccttggtgtcctgtgaatattccactgttatgcttcttcggatttgaccaggacagggatgggttatttcttacccaatagtgctaggtcagtgtggtcaggaattctcttcatcctgctgcccatgctccttatttgtctggcctgtttgtttcacaattttcaaatcctcgttctatcatttacaactcataatacagtgcctttttacttgcttaataatcagacattttagaaacattatatccatatccctttatattttctgtatgtttggccttatgtctatgtacaatacgcgattaactaatttgtagtataccttccaacatcgccttcatatagaggcatattctatcgtcagcatatcctgtaccatagccatccaaattcctttatatctttgtgatctcatgattgacattcataatctactttcccatgtttctatactgtatttagtatttagtacagatttatccctttttatctataccctaaatgactaacagtttcttctagacagagaaatgtggcaatggggtggtagctgaggaagatattaaaaaaggagaatttgtaatcgaatatgttggagaaggtatggttttctacatcctgtgcacatacgtaaactttatttgtaagtacgtaaggatcaaaacaattcaactttattattacttctatacaaaagtatactcactccttaccatagtataagggttattgggtggatgtgacacatcatagtacaatgaatctggacagacggtctgtccagattcattgtactaggatgtgttacagccatccaaaatcacttatattatgggatggagggagtataccgaatccacagtaatacttatttttttactttttatttttttcatttttaattattaaacaattagaattaatatatacaatggtttacttgtcacggagtcttaatttttgtttgtccttgatttttttttttgcaagatatgaattgtagtactgagattcgaaagtaatgaataaaagctttacatacaaagctgtaactggtttaagtctcaaaattcaattttggtaagtcgtattctgtcccaaaatatagctacctttgtagttcaaggctatgttttgggacagggagtataaatttgttgtttgtacgtagttctaatcttatttgttcttgatgaaacaaattctaagtttggaattaatatagaagttgtacttgtcttggagttgcaatttgagtttttttatatttagtaattccaaaactcagaattcataaatattgtatctgtcttggaatctcaaccttctatcctgttaatttagttatggatttagaaattactaaaaagcaagttgtaacttacttcacttggactcttcttttaattcaagtcgtcatggtttagtcccacctagattaatgaccagatttttatccactactgtgcttaaacgtgagattttcctcagagtgtccgattagtataggtatagatagatcgataattcgatctattgatatgagttctcacattgaacatattggtaatcaaactaaagtccagaatccagattgtgggttggagggctatcatatcctccagtaaatctttttcaaactgttacaatatacaataacttggagctaaaaactaatatccacatatcttgcaaacatattgtagttattgatgacagaacatgtgagcagagactatggaaaatgaagaggcagggtgacactaatttctatctttgtgaggtcagtagtaatatggtgatcgacgcgaccaacaaaggaaacatgtcgcgcttcataaatcatagctgtgagccaaacacagagatgcagaaatggtaagttatactcttgtcagctcattcatatatgctgttcttctaacatcaccctgatatatgactagtatttatattgtttcaggactgttgagggagagaccagagttggaatttttgctcttcgtgacataaaaacgggggaggagctgacctatgattacaagtatttttgttctagttctatccttgacttcttttcatttcactcgggcataatgattcatcattttctgtatatggaactactcctggtatttaatttctcggctttacctacaggtttgtccaatttggagctgatcaagattgtcactgtggatcttcaaactgtcgaaaaatgcttggcatcacaaagcctgttaactcaattgtacttcataatggaaatctgtcacaagatcagcatgtccggaagaaaagaaagacatatttggagaattgtattggggagattgtccgtttgtggcatcgacgtcacagcatgtaagctttggtaactgtagattcttctaaccatcggatgatgtatttttcctataatctgagaatctacctatctagttatcatatactatttgggaaaatgtgataagttgtccaattcaacacctgctctctactggattgataaactcggtgttaaggttggaaatggggttagtttttcatggctgcctatgagtaacattttggctccaagtggttatgtatatcactagttttgacttcatctaacaaaaccattgagagtagatgcacagtttattttaacttccaagatgttttagtacatctgattgaggaagttgatttccctttctttctttctttcttttttaactttttgagattagatccattataaccacttgattatttatctcattgttcaggtatctcgcagcaagtatatatgacttcaatgagcgcaatggaatacatacagtgagtttgtcaacatatggcttgcatagtgtagggtgtgtaatttctggaaaaacaattttatatgttttgtattgttgtagttattgtttaccgatgcaactattgaagaatttgatttgagagaggaagattgggacttcttaccggtatgatgttcttagcattaaccaagttacaaatatgtcctatttttcttatttaacatttggatctaccgtggcaacatgcggggtatcatctagttctctatatttctagcaaccatagcctgaagtttccatgatgttgtccactttatcctctacgtcatgcagaccttttgtataatccaattttatcataaatatatttattatttcagtaggtctttcctctactttatataaaaaatagtgtttagcattgccgtctttgatttttttatgtaaaaaaaggataatagtacttctgtatcctggtggtagcattaagtgtaatggagaacaacattctatagaaacttttggccgaatgtagctttccacatcgttatagcacatgttcggatggacctgtcttttcttcttgtcagcaacattgcttgtgctccccattgagtgtgtcaaccgcaaacttttttttgtttttactgattgggctgcgtataacctcctgatctgggctcttagcaggattatgtctaagatgttcttttattgaaggtttaacttgcataatgtttaggatttaatgtgcttgtttacgattctagttgaggaccaagagcttaggaaatgtttttgtgaacctatgagcacctgcactcattctcactgtaaaaggagttgtaactgaactagtatatacctctgttagcagcaatatgttatgcaggaatccttagcaattagacaatttaccctcctctaaaattcactggaatcttgaaatatgataacaattgattgaacctcatcctccattgctcttggaataactttgatgcatctatcgcaccatcattccttggtttgtagcttacagtgtagaagtaaataatgctcactatctgagcttgggcctagtttacttgatgtttcctgactgtttacctgaacttgctgtttatgaagcctgacttaaataaccgaaccttatcatttgcttctggcaaagtaacttaaccttatatgttattttcaggatccagatggtcctgaggaagtgtgagtgatctgaaggtattggcaaaaatagtgtgcatacccaggcattttatttttctgtttatattatttgttgaggttggttatgctaggagtaggaacatattactgtactacttaagcagaacattggcctttaccatcatcagatagagcatccggtaggggtttattttctgcatcagtggttcgtgtaccccttttccattttctaaaggttaatttgaaatttccttttccatttcctaaaggagttatttgaaatttcctttctgttttttctatagtattcatggcagttgcatattatttacattcatgttagattgtctcctgtatcatttgcgtgcctagacaaacaatataacttaattctgcaatagcatgtgaattgacactcctaaatatttcaagctaatcattcccatgtccttgtggttctctgtatgaacagcttcatatgaggatgtcatcgcaactgtgtcaatcggatgattgtactgttgggatttaacatgtggaagtgtttagctgcaatcatccacccacaaatcaattcttcagagcgtgtacccaacatgatactgtcctcctaaactgtaaaaagcttttttcaattgttgaatgttcattaatttttttcaggtttgtatcaatcgaagtgcatcttgtgatgcttgtaaaaattgttggctgggtgagtttacaatcgttgttgtaacgtgcgatggtgatagtttattagtttagtttatgctgttataccatgtagttatgcttgtactgagagctacttgaaccataagatatttcggtatgtctgctctt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069362.1 RefSeq:Os09g0307800]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 9]]<br />
[[Category:Chromosome 9]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os04g0409600&diff=178238Os04g04096002014-06-05T11:06:50Z<p>Lina: /* Function */</p>
<hr />
<div>OsSRT1 is one of the two SIR2-related genes found in rice.<br />
<br />
==Annotated Information==<br />
===Function===<br />
*Sir2 is involved in chromatin silencing at the mating-type loci, rDNA, and telomeres in yeast and is associated with lifespan extension in yeast, worms, and flies, but also in a broader range of additional functions <ref name="ref1" />.''<br />
<br />
*OsSRT1 is one of the two SIR2-related genes found in rice<ref name="ref2" />.''<br />
<br />
*Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.''<br />
<br />
[[File:Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.jpg|right|thumb|360px|Figure_1.OsSRT1_RNAi_induced_a_lesion_mimic_phenotype.''<ref name="ref1" />'']]<br />
<br />
<br />
*OsSRT1 down-regulation induced histone H3K9 acetylation on the transposable elements and some of the hypersensitive response-related genes, suggesting that these genes may be among the primary targets of deacetylation regulated by OsSRT1<ref name="ref1" />.''<br />
<br />
<br />
*OsSRT1 is a histone acetylation enzyme, participating in acetylation of H3K9, inhibition of transposon and gene expression related to cell apoptosis. Rice SIR2 gene is important to maintain genomic stability and avoid DNA damage in the process of plant cell growth. OsSRT1 is involved in the safeguard against genome instability and/or oxidative stress, required for plant cell growth<ref name="ref2" />.''<br />
<br />
<br />
*Histone lysine acetylation is an important epigenetic modification for genome function and gene activity. Dynamic modulation of histone acetylation in plants has been shown to be involved in gene expression programs of plant development and responses to environmental conditions <ref name="ref13" />.''<ref name="ref14" />.''<br />
<br />
===Expression===<br />
*OsSRT1 is a widely expressed nuclear protein with higher levels in rapidly dividing tissues<ref name="ref1" />.'' <br />
<br />
<br />
*Our data show that OsSRT1 was preferentially expressed in rapidly dividing young tissues/organs and the protein was nuclear localized. Phenotypic and molecular analysis of RNA interference (RNAi) transgenic plants suggests that OsSRT1 is involved in H3K9 (Lys-9 of H3) deacetylation required for transcriptional repression of transposable elements and apoptosis-related genes. Our data suggest that OsSRT1 may have a function in the safeguard against genome instability andDNAdamage to ensure plant cell growth<ref name="ref1" />.'' <br />
<br />
<br />
[[File:Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_fragmentation.jpg|right|thumb|360px|Figure_2.OsSRT1_RNAi_induced_H2O2_production_and_genomic_DNA_<br />
fragmentation.''<ref name="ref3" />'']]<br />
<br />
*OsSRT1 RNA interference induced an increase of histone H3K9 (lysine-9 of H3) acetylation and a decrease of H3K9 dimethylation, leading to H2O2 production, DNA fragmentation, cell death, and lesions mimicking plant hypersensitive responses during incompatible interactions with pathogens, whereas overexpression of OsSRT1 enhanced tolerance to oxidative stress<ref name="ref3" />.'' <br />
<br />
<br />
*So far no physiological function has been assigned to plant Sir2-related proteins. As there are fewer SIR2-related genes found in plant genomes, important questions arise, such as whether plant Sir2-related proteins conserve similar functions as yeast and animal homologs. In this work, we studied the function of a rice (Oryza sativa) SIR2-like gene,by transgenic approaches OsSRT1 <ref name="ref5" />.'' <br />
<br />
<br />
<br />
*As H3K9 dimethylation is closely associated with H3K9 deacetylation <ref name="ref8" />.'' we also tested with antibodies against dimethylated H3K9. As shown in Figure 3C, the OsSRT1 RNAi had little effect on overall histone H3 acetylation. However, the acetylation of H3K9 was induced, whereas the dimethylation of H3K9 was reduced, in agreement with the antagonistic relationship between H3K9 acetylation<ref name="ref1" />.'' <br />
<br />
<br />
*The RNAi lines were selected for phenotype observation and further analysis. The RNAi plants at the two-leaf stage (about 14 d after germination) began to produce brown dots on leaves, which became larger at latter stages, leading to precocious leaf senescence. Only two of the three RNAi lines could produce seeds. The severest line died before getting into maturity. The transgenic lines showing no alteration of OsSRT1 expression or histonemodification did notmanifest the phenotype, suggesting that the lesion mimic phenotype was induced by OsSRT1 down-regulation. The lesions were reminiscent of cell death induced by hypersensitive responses during plant pathogen infections, suggesting that OsSRT1 RNAi might have induced programmed cell death (PCD). To test this hypothesis, young leaf sheaths (T1 generation) were incubated with 3,3#-diaminobenzidine (DAB) to detect H2O2 <ref name="ref12" />.'' <br />
<br />
<br />
[[File:Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment.jpg|right|thumb|360px|Figure 3. Overexpression of OsSRT1 conferred tolerance to paraquat treatment. ''<ref name="ref3" />'']] <br />
<br />
*OsSRT1 was generally expressed in different tested rice tissues, but with higher transcript levels detected in tissues with high cell proliferation rates, such as buds, seedlings, and developing panicles HSR201 and APO, but not HSR203J, were found to be induced by OsSRT1 RNAi in the microarray data. Consistently, the RT-PCR results showed that HSR201 and APO, but not HSR203J, were activated early in 7-d-old RNAi plants. In contrast, HSR203J was repressed by OsSRT1 overexpression.<ref name="ref1" />.'' <br />
<br />
<br />
*We compared the expression of two hypersensitive response (HSR201 and HSR203J) marker genes <ref name="ref9" />.''and a cytochromeP450 gene (calledAPO) that is closely related to wheat (Triticum aestivum) CYP709C1 and CYP709C3v2, both of which are suggested to be involved in wheat defense to pathogens <ref name="ref10" />.''<ref name="ref11" />.''<br />
<br />
<br />
<br />
[[File:Figure 4. Expression profiles of OsSRT1.jpg|right|thumb|360px|Figure 4. Expression profiles of OsSRT1.''<ref name="ref1" />'']]<br />
<br />
<br />
*Histone acetylation is catalyzed by histone acetyltransferases, whereas histone deacetylation is catalyzed by histone deacetylases (HDACs). Plant HDACs can be grouped into four subclasses. Three of them have primary homology to the three classes of HDACs (RDP3, HDA1, and SIR2) found in yeast and animal cells <ref name="ref5" />.'' The fourth class of plant HDACs (known as the HD2 class) is found only in plants <ref name="ref5" />.'' <ref name="ref6" />.''<br />
<br />
===Evolution===<br />
*Sir2 family proteins, known also as sirtuins, are NAD1-dependent protein deacetylases. They contain a 200-amino acid domain conserved from bacteria to humans<ref name="ref5" />.<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, Plant genomes seem to contain relatively fewer SIR2 homologs than the other eukaryotes<ref name="ref6" />.''<br />
<br />
*Sequence analysis of the rice genome revealed two SIR2-related genes, named OsSRT1 andOsSRT2.OsSRT1 and other plant SRT1 homologs are found in the same class (class IV), whereas OsSRT2 belongs to class II of the SIR2-related genes<ref name="ref5" />.''<br />
<br />
*Compared to other eukaryotes, plants have relatively fewer SIR2-related genes Plant predicted SRT1 proteins showed relatively high conservation. Only the N-terminal parts of the plant proteins were conserved with the animal homologs<ref name="ref5" />.''<br />
<br />
*Yeast has four additional Sir2 homologs, termedHst1 to Hst4, in addition to the founding member. All of the yeast members belong to class I of the Sir2-related proteins.Mammalian cells have seven members of the SIR2 family (SIRT1–SIRT7), distributed into all four classes <ref name="ref4" />.''Three of the mammalian members are localized in the nucleus; the remaining members are either cytoplasmic or mitochondrial localized <ref name="ref7" />.''<br />
<br />
==Labs working on this gene==<br />
*National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University,Wuhan 430070, China<br />
<br />
*Department of Quartermaster, Military Economy Academy, Wuhan 430035, China<br />
<br />
*Institut de Biotechnologiedes Plantes, Universite´ Paris Sud 11, 91405 Orsay, France<br />
==References==<br />
<references><br />
<br />
<ref name="ref1" > Limin Huang2, Qianwen Sun2, Fujun Qin, Chen Li, Yu Zhao, and Dao-Xiu Zhou* Down-Regulation of a SILENT INFORMATION REGULATOR2-Related Histone Deacetylase Gene, OsSRT1, Induces DNA Fragmentation and Cell Death in Rice. Plant Physiol. Vol. 144, 2007</ref><br />
<br />
<ref name="ref2" > Blander G, Guarente L (2004) The Sir2 family of protein deacetylases.Annu Rev Biochem 73: 417–435</ref><br />
<br />
<ref name="ref3" > Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2in plants. H2O2accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
<br />
<ref name="ref4" > Frye RA (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793–798</ref><br />
<br />
<ref name="ref5" > PandeyR,Muller A, NapoliCA,Selinger DA,PikaardCS,Richards EJ,Bender J, Mount DW, Jorgensen RA (2002) Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes.</ref><br />
<br />
<ref name="ref6" > Lusser A, Brosch G, Loidl A, Haas H, Loidl P (1997) Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277: 88–91</ref><br />
<br />
<ref name="ref7" > Haigis MC, Guarente LP (2006) Mammalian sirtuins—emerging roles in physiology, aging, and calorie restriction. Genes Dev 20: 2913–2921</ref><br />
<br />
<ref name="ref8" > Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45</ref><br />
<br />
<ref name="ref9" > Chu Z, Yuan M, Yao J, Ge X, Yuan B, Xu C, Li X, Fu B, Li Z, Bennetzen JL,et al (2006) Promoter mutations of an essential gene for pollen development result in disease resistance in rice. Genes Dev 20: 1250–1255</ref><br />
<br />
<ref name="ref10"> Kandel S, Morant M, Benvenist I, Ble´e E, Werck-Reichhart D, Pinot F(2005) Cloning, functional expression, and characterization of CYP709C1, the first sub-terminal hydroxylase of long chain fatty acid in plants. J Biol Chem 280: 35881–35889</ref><br />
<br />
<ref name="ref11"> Kong L, Anderson JM, OhmHW(2005) Induction of wheat defense and stressrelated genes in response to Fusarium graminearum. Genome 48: 29–40</ref><br />
<br />
<ref name="ref12"> Thordal-Christensen H, Zhang Z, Wei Y, Collinge DB (1997) Subcellular localization of H2O2 in plants. H2O2 accumulation in papillae and hypersensitive response during the barley powdery mildew interaction. Plant J 11: 1187–1194</ref><br />
</references><br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os04g0409600|<br />
Description = Similar to Histone deacetylase|<br />
Version = NM_001059260.1 GI:115458249 GeneID:4335765|<br />
Length = 5631 bp|<br />
Definition = Oryza sativa Japonica Group Os04g0409600, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|<br />
AP = Chromosome 4:20272401..20278031|<br />
CDS = 20274537..20274646,20274795..20274884,20275077..20275140,20275863..20275955,20276034..20276142<br>,20276428..20276477,20276551..20276641,20276876..20276946,20277195..20277293<br>,20277457..20277523,20277723..20277808|<br />
GCID = <gbrowseImage1><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008397:20272401..20278031<br />
source=RiceChromosome04<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>atcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatgaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttga</cdnaseq>|<br />
AA = <aaseq>IIKHVILLSIGLVDXXXXXXXXXXXXXXXXXXXXXXXSFSIPCQ VLYIDIDVHHGDGVEEAFYFTDRVMTVSFHKYGDFFFPGTGDIKDIGEREGKYYAINI PLKDGIDDSGFTRLFKTVIAKVVETYLPGAIVLQCGADSLARDRLGCFNLSIEGHAEC VKFVKKFNIPLLVTGGGGYTKENVARCWAVETGVLLDTELPNEIPDNEYIKYFAPDYT LKVSNVNMDNLNSKSYLSSIKVQVMESLRAIQHAPGVQMQEVPPDFYIPDIDEDELDP DERVDQHTQDKQIHRDDEYYEGDNDNDHEDGAR</aaseq>|<br />
DNA = <dnaseqindica>2137..2246#2395..2484#2677..2740#3463..3555#3634..3742#4028..4077#4151..4241#4476..4546#4795..4893#5057..5123#5323..5408#cggtgcctttctacagcggcgttccactcgggttggtctctcccccgaggcacggccgccgccgccgccgcgctcggtctaatcggaatctatttctcgacgcgactccgcttccccggctcccctctcacccttccgcgccgccgccgccgccgcttgtagtggttggggggcgagcggccgctcgagagcgaagcgatgctggagaaagacaggatagcctacttctacgatggtacgaccgcgcattcgctaagcccccctcatctcctctccattctccctaatcactggagcaaccctagctctagctctagatgatagagcgaaatcctacgccgtctcgatgttgtgtggcttaatttcgtcgaagaaggggcatgcaattagtacctaagctgatttctagtggtgttatatgattgtggaggttggagtggatgttacggttggacggcttatgagaaattccagaactatgaacttcccaggacttgttcaactaggatttgtggtatttcagttgccctagccctaggtgcatgacgcatgattcattatcagtcagtaacataaggtggggaagcaacccttgaatcaagatttgaattagaatcgttgatccctttatctgtttaagagggcgcagtcaggctagatttggttaacaagttcctatattctttagcgccagccattttctaaaaggtcaccaacgccagccatatgtggttatttcttagatcacacataaatttccatgataagttctctcacatattttgtactaggtggtttcatgacttgtgccctcattcacccatggtcctttacatctctgtttatagagagccactcattttgcagatgtgaaaggaagttttcattgttcaaaatgtgtaatttttattactcattttgttttgatcgtttacctttttactgtgtcaatgaacaattcaggcgatgtgggcaatgtctactttgggccaaatcacccgatgaaaccacatcgactttgtatgacacatcatcttgtgctttcatatgatcttcacaagaagatggagatatatgtcagtatgaactttatttattcccttcgtttgcacttgttaactgcctaaagttcctttcacctcttacttttcacacaacgatttatgcagaggccccacaaagcatatccaacagagctcgcacagttccattctgctgattatgtggaattcttgcatcggataactcctgacacccaacacctgtatgaaaatgaattacgtagatgtatgaattatgaaacttttctcctctatgaactagtactctgggatttgttaattttacaataaaatggttgtcacatatcttgctactcatgtttaaattattataaatttatttattaagttccttacctggatctaataagtagcttagatcttcatgtacagttaaactataaggaatctcatacacaacttaaggctaattagcttcacttacatgaatgctgtcaggtgtatattcacgatatgcctatttgacaattcaaggaaaatgagggcatgtttggtcccctttcaagctcaagcaacttcccatctaacgctgcctagatagcgttggtgtttagtacagcttagcaagtcattcttcataggatgtatatccttgcccattgaagcgcatcccttgtggtcaaggtttacatgatttggtgcactaaatagttttggatatctttacagtatttatatagtattagttgcactcttctaggacacatgtgcttattttacagtttcagggcaaaataactgaacacctaacctaagtagcagagtaatctggacaaaagatccaacttacccactcttagagcttttccccaattgaagttggtttccaacataatcctcatgccttttggagctttctaacttcatttatctggttccttcatatttgttcccagacaatcttggagaagactgcccagtctttgataatctgtttgagttttgccaaatatatgctggaggaactctaggtaatatgaaaattctgaatgcttctttctaaagtgaactcttaagttcttctttgctattttagatgcggctcgcagattgaatcataaaacatgtgatattgctatcaattgggctggtggatnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnatcttttttggattctgagcttctcaataccatgccaggttctctatattgatatcgatgttcatcacggggatggagttgaagaagccttttatttcactgacaggttcatgctgtttccaataaagtcatggatatgtagttaatcatttattgctgccaatatttttccaatccaatttccatctctgtgcattttgtgaattttggtggtaccataatatttatactaattccagtctcgggcttttgattttgcagggtatactaatattgtatacttattttgattttgcagggtaatgactgtaagtttccacaagtatggtgattttttcttccctggcacaggtgatattaaggtaatgttccactaacaagctcctgaatattttttatgtactttttggtatgatgtggttggtgattggcccttctctgcattctgttttatccttacccttttcgcatgaagtgtgtgtgacatgcgtactctcatttgtgtgaaaaaagaagagacagattaaccaaagatggtccccagttgattttgtaatgcacaaaattgatagcacctgtaggtaattgtttatgagcagttaatcttgtttctttttagttctacccgccaagaggctgtaaatatgtaacatcatagagttgaactttggttttttttactggagattcttggcatgttattctatttaaatatcaaccattgtaattgggaattcaggtggttatgtatttgaaaaacgtcatactagaatgcatcataattcgtatacgcatgcttaattgtcatctgggctgacaaaaaaaaaacatgtgcacatatacgcccgtcatttgaatcttgtagtatgttaatttgttatgtatccactgtactactaggcaactttattaaataaaaatatcccaaataactggaaggtagagcaagtgtgctacaaaaagggcaaggttgaaaatgaacataaaacatgccatgttcttctcagtaacgatgatactttatatagcttcgttttaaatgattgtgctgcttcatattgatttacctgactctcatttgaaggatataggagaaagagaaggaaaatattatgccattaacattccacttaaagatgggatagatgactccggctttactcgcctttttaaaacagtaagcccactttacattactttctcatctttcatgtcattgtttagtcttatcaagttatgcatgtctattatgtaggttattgccaaagttgttgagacatatctgccaggtgctattgttcttcaatgcggggctgattccttggcacgggaccgtctggggtgcttcaatctgtccattgaaggttctgtacttcttaaatctgatgtgtacttgttgattcagcagaactgtgctctagatgtaaagttagtgaactgtgctgcatattcttggatgagctattagggttcaggcggtatcttcgagataatgtgaaaccttctctcaagtctcaattatttcttaccatagttttgagattgttattgcactaatagttctgacttattttgaaatttaaattttgtttctttgagctatacttagtgaatgatcttttaatacttgcatgtgtacttgcaaacaggccatgctgaatgtgtgaagtttgtcaagaaattcaatatccctctactggtaaggacaaaccgttactgcgtgtgatttctcttgttcctccttggatatcaatgtatttcccatcatgcaggtgactgggggtggtggatacacaaaagagaatgtagcacgctgttgggctgttgaaactggtgttcttctagatacggagctcccaaatggtattcttttcttttgcaattctgtacttctcggtccttttggcctgttgttttagaggacactactagtaatccctcaaatgcatgcaacagttcatgtattcttttcctcacatttgctggcatatcaagttgcaaacagatctatcaagaacgggattgactagtagagttccttaataatttctaaaacagcagtctgtgatatgagtttggcatgactttcctttgcagaaattccagacaatgaatacatcaaatactttgctccagattatacattgaaagtatcgaatgtgaacatggtatggaaccttttctcattggcctttgtttgtcctacggttgtttggtgcattgatatttgattgctattaggtgcatcaagtaactgtccttttattactgagtatggtctaagcatttgagctctgtagtccatttggtatttcggctattcaattggtttgtgtttgctagaagtttagaacttgcgttcctttcttgagaatgtgcaaatgccatatcacatgttgtgttttaaccggagcaggacaacttgaatagcaagtcatatctaagttcaatcaaagtgcaagtcatggagagtttgcgggccatacaacatgcgcctggtgttcagatgcaagaggttagtttttgattcacttacacgaggaaacctcccaactggaatttgctatgtaaaaaaaagggatacaagcaggacactataatattcctttccttttgttgcctatctttttcttcgttcaacatatttctgaacaagaacaatattaacatttttgcaggttccaccagatttttatatcccagatattgatgaagatgagctggatcctgatgaacgtgtagatcgtaagtgaaatactcctgggatgcattaggatgctaatatgtctgggtgtctgctgttccaagaaaacgaacggcagacagttgttttttttagtatatgttgtgtgttccacattatgctagtcctttcttcgtgttgttttcagacctttgaactttatatcgtccttatacattaactgtgtaaaatgttgcgcagagcatacccaagacaagcagattcatcgcgatgacgagtactatgaaggtgacaacgacaatgatcatgaggacggggcccgttgaaaaaggttctttgtatgatgaaactggatagagaaagtctggtgctgttgcgcggtttaacagcgttaggtgggaaatactgtcaattgacttgttaggatctaacacctttgcctgcatatagtgcgtgtacgttcctactttttaatcagttacatatgctagttgcatgcagagattgcaaattcttagtcggtggtaatgattcatagtttttggctgc</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001059260.1 RefSeq:Os04g0409600]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 4]]<br />
[[Category:Chromosome 4]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0445900&diff=177806Os05g04459002014-06-05T03:22:22Z<p>Lina: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. As well, there are some proteins coded for DNA demethylation. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation are DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3). Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1orthologs and twoDML3orthologs, but no DME orthologs.It has been demonstrated that rice ROS1a protein is a bi-functional DNA glycosylase/lyase for 5-meC DNA demethylation, although biochemical characterization of the ROS1a enzyme remains to be performed to confirm this.<br />
<br />
ROS1a is the most abundantly expressed gene in tissues. It was recently reported that null mutants of ROS1c, which encodes a 5-meC DNA glycosylase/lyase, show no effects on transmission of the null alleles and produce a small portion of wrinkled seeds.And the null mutation, ros1a-GUS1, was hardly ever transmitted to progeny.Even in the presence of the wild-type paternal ROS1a allele, the maternal nullros1a-GUS1allele caused failure of early stage endosperm development, indicating non-equivalent contribution of maternal and paternal ROS1a to endosperm development.<br />
<br />
===Expression===<br />
Rice contains four ROS1 orthologs and two DML3 orthologs tentatively named ROS1a–d and DML3a and DML3b, that contain characteristic DNA glycosylase domains flanked by conserved domains of unknown functions. Of these, ROS1ais the longest gene, comprising 17 exons that encode a protein with 1952 amino acids, and 5¢ and 3¢ UTRs of 73 and 607 bp, respectively. RT-PCR analysis revealed thatROS1awas expressed in all vegetative and reproductive tissues tested . Quantitative RT-PCR analysis revealed that ROS1ais the most extensively expressed gene among the four genes(ROS1a, ROS1c, ROS1d and DML3a) expressed in five selected tissues examined, including anthers and pistils,whereas ROS1b and DML3bare scarcely expressed in these tissues. Interestingly, moderate levels of transcripts for ROS1c, ROS1dandDML3awere detected in pistils and immature seeds 2 days after pollination.<br />
<br />
<br />
===Evolution===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation [DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3) are bi-functional DNA glycosylases that not only recognize and remove5-meC from double-stranded DNA, but also show lyase activity, which nicks double-stranded DNA at an abasic site.Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1 orthologs and two DML3 orthologs, but no DME orthologs.Rice endosperm DNA is hypomethylated in all sequence contexts, implying that hypomethylation in rice endosperm relies on some of these DNA glycosylases or alternative biochemical mechanisms.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
1.A. Zemach et al., Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107, 18729 (Oct 26, 2010).<br />
<br />
2.A. Ono et al., A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny. Plant J 71, 564 (Aug, 2012).<br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0445900|<br />
Description = Similar to ROS1 (Fragment)|<br />
Version = NM_001062220.1 GI:115464170 GeneID:4338940|<br />
Length = 5779 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0445900, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:21889157..21894935|<br />
CDS = 21889581..21889708,21890545..21890583,21890664..21890778,21890883..21890948,21892020..21892159<br>,21892239..21892302,21892380..21892416,21892564..21893001,21893713..21893795<br>,21893897..21893933,21894150..21894218,21894322..21894413,21894487..21894571<br>,21894906..21894934|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>ttaagagatgttcctccagactcagcaaaggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtatgagttacattatcagatgattacttttggaaaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtttacgaacttccagattcacatcccctcatgcaacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggtctaacaactgaagaaatacagcactgcttctggagaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactga</cdnaseq>|<br />
AA = <aaseq>LRDVPPDSAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVG RICVRLGWVPIQPLPESLQLHLLELYPVLETIQKYLWPRLCKLDQQTLYELHYQMITF GKVFCTKSKPNCNACPMRSECRHFASAFASARLALPSPQDKRLVNLSNQFAFHNGTMP TPNSTPLPQLEGSIHARDVHANNTNPIIEEPASPREEECRELLENDIEDFDEDTDEIP IIKLNMEAFSQNLENCIKESNKDFQSDDITKALVAISNEAASIPVPKLKNVHRLRTEH YVYELPDSHPLMQQLALDQREPDDPSPYLLAIWTPDELKDTREAPKPCCNPQTEGGLC SNEMCHNCVSERENQYRYVRGTVLVPCRTAMRGSFPLNGTYFQVNEVFADHSSSHNPI NIPREQLWNLHRRMVYFGTSVPTIFKGLTTEEIQHCFWRGFVCVRGFNMETRAPRPLC PHFHLAASKLRRSSKKAATEQTH</aaseq>|<br />
DNA = <dnaseqindica>5228..5355#4353..4391#4158..4272#3988..4053#2777..2916#2634..2697#2520..2556#1935..2372#1141..1223#1003..1039#718..786#523..614#365..449#2..30#gttaagagatgttcctccagactcagcaaagtaagatactacacctgtattcaatatttacaaatcccattgccctgctgatgagatttttctagttctggaaatgataaatcaagtatcaaagaagtttgtgaaccaattaaatggagcaagctgatccaagaacttgccagttaatatctagaattaaatactatgagcaaagttctatgaaatgggcacgcagaacagaaaaggctgtataatgtatgacacatgatcgaagcagtgaaggaatttttttttaggaaagaaaattccatgaaccctatttatttcacaggcgagaagtatgtcaattacaatgtgttcgaattattttcagggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagtaagtttctgttggattaattctccttcacctgcagccaatttgaaatttacactacattgttgcaactcaggttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctgtaagaatgttgcattgtctactacagttgtataaatactctctgcaattttatacgatgatgtttcaatttgaatatattgattttgtttgtgccttcaaagataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtgagttataaccaattaaccatacccactcatagttgcccttcttattagtttttttttacgcaagcccttcttattagtttgtgtaacttctaggttatttctttttcatgcaaattacagtatttggaatcatgaataattaaggcaataaggagtaaataacataatttataactataaggaattattaacagagtttcatggttttcacaggtatgagttacattatcagatgattacttttggaaaggtacttcattagcattaaggagtttggtctcttcattagcatctaccgacgcatttgttctcttttgtttgagtaaagataaattatcataacaaatgcaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaaggtattatggcaagcagaaaatgggagccttctggctgcaaggagacttacaaaataaacactatttgcttcagtagtcacttttttccgataaaggaagctttattaaaactcagtcaaatacaccaagatgatacattctaactgagccactcccggcctctgcatgaaatgcacaccgccacaaaacaggatctaactagaccctcaacacaaaacaaataaattagtgactatcaagccgtagactatatcgccacccatgctccagggtaaaaaactcctgtgccacctgatagtgcacagcaaaaaccacgagaaggatgtgctttcgttggtggagagaccgaattagctccattaacataatatgaccactaagagcgcaaaatagtgcttttgaagaataaaagggaaaatatgctaggagaaaaatcaatatatggttctagtacaccgccatggcactttgtgtagtctctgtctgcaacaaaatatatttgccgctttcacttatcttacctgggaattttgttatcacgtatttcctcgttccactatctttcttgttttgtttgtgcgcgcgcgcatgcctgatatatcttgctctttcagttgaccttacctgggagccttcattttgcatatttcttcatttgttattttttccttattaactctgttatattttgtttgacttttttaaatgaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtgtaagtgttggactgatattttatttagcttgaacatgtacctgtttaaacttacatttattatagagcccaccatctaagtaattctatacatcctgaacaaaatattttttaatttctattactgacttaaggttctgctcgcagttacgaacttccagattcacatcccctcatgcaacaggtgagaccatgagaaattgtgccatctttctttaaaacacttcaagatattatttctgattgcaaatgatcttacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccaggcaagtgcatttttctttaaatttataactgtccgtgtgtgtgtgctggttttcgtcgagtcatgtggctactgtgcagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggtaaatcaaccaacattatgtagcaatcatcaacattgaagagctgaacctctgcattagtcagctagtaaacaaaatattcattataatccaaacattggaatgaattcaggaattcaagaaaatgttgaagataacttttaatgaaaactagtgcttacaaagtgccaagcaaagctattctgttgtctgtgtaatctcttttcttgcatgaaatagcccactgtcttcactttaaacaataagaatagcatagattttgggtttccggctatacaacacatcttaatatgaacttttgtggaagtctaaaagagaacctctctgaacctttaaactgtacactatttaaccaacaatcaaagccgatcacttctcaacgtcattctgaattagctttgggcgatgtttcttaaccaggagatgtggtctgagattttagattttttttttcatctcctttatattagtagacgacttaaaattttctggaataatcttacttcgctgtgaagtatttataacccagataaatcggtaagattgaagtaaagtattattgtcccacgaaatttagtgtgtgaaagtagacaacatttttttctactgtccgattaaactttatttaactctgccccattttatctaggctataaatggtgatttcttctaggctatacggtttttcaatccaattttaccttattttgctttaccaaatttgtcaacattataatactttgtagtgcaagtgagattttttttttcaattttgttatgtcatttactaattttaaaattgaaaacctggttcagccttgggccattttgccacattagggacacatagtccaaagccactttaaatttgagacaaggttgaaaagcgcatggttttgatacttcaggttctgggttgaattgtgtccagttttctgctttggggttgtctctggactaacagaaaagttcagtattgcaaaacagactgtttcctatacaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacggttactggaacatgaacaggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttgactttacgatttctggatttgtttttgcaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggttaccaccattcacccatacaatgactcaaagaaatcttatctgcaactttaccgacaactgttattttcattctttaggtctaacaactgaagaaatacagcactgcttctggagaggtattaacagtatttttttcactcgctgtttcagcgcattctcctctgggacatatcttgtttcctcatatgatcaaacaatttgcagaatgcagatgccatcatataatcacaatatgtttctacagttatatagcattcgtgtgattgtgtcaaggtgtccacacacttttcacaaaaacttactccccctgtcccataatataagggattttgagcttttgtttgcactgtttgaccattcgtcttattcaaaaaaatttagaattatattttttttctttgtgacttactttattatccaaaatactttaagcacaacttttcgttttttatatttgcacaaattttttgaataagacgagtggtcaaacattataatcaaaaaactcaaaatcccttgtattatgggacggagggagtagtattaagggtctaaaaggagcctgaatatttggttcagttagagtctatatctgagtccattttaattcctagtgctatggataaaggtgtcctccttcaataaataaataaaggtctctccagttattagtcaccagcatccaatataactgcctgataatatatgtggtaagttatatggtgccaaagaggcaaagatactgctaccatgactaaccccctttttttttctgagttaataagggtgttagcatacatatagcttccaaattggtttagttaggtggaaaaagtcgtcatttcaggatgcagatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactgatttcaacagggacatatcaattctataaaataatgttgatggtgattacatcagttctcgatctgtgcatgggtcatattagttcctgcaggacgatagccattcttctaggaaataaacagtggagttggaaacagttaactttaagatgtgggagccaattgggcacgagaaagcaccaatatttcatatgcacctctggggcaggtcggatgcggatcatcatcatcagttaacatgggcgtagaatatcattccgttttttttttctgtggctttggtgtatcttattcacttttcatttgttttatccattcaactagcttgccaagagaccttaccatctgttctcatgacatgttagtttttcagaacttatagcaggtagtaccttcatattgatgatatgactttgattttcatt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062220.1 RefSeq:Os05g0445900]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0445900&diff=177805Os05g04459002014-06-05T03:21:58Z<p>Lina: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. As well, there are some proteins coded for DNA demethylation. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation are DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3). Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1orthologs and twoDML3orthologs, but no DME orthologs.It has been demonstrated that rice ROS1a protein is a bi-functional DNA glycosylase/lyase for 5-meC DNA demethylation, although biochemical characterization of the ROS1a enzyme remains to be performed to confirm this.<br />
ROS1a is the most abundantly expressed gene in tissues. It was recently reported that null mutants of ROS1c, which encodes a 5-meC DNA glycosylase/lyase, show no effects on transmission of the null alleles and produce a small portion of wrinkled seeds.And the null mutation, ros1a-GUS1, was hardly ever transmitted to progeny.Even in the presence of the wild-type paternal ROS1a allele, the maternal nullros1a-GUS1allele caused failure of early stage endosperm development, indicating non-equivalent contribution of maternal and paternal ROS1a to endosperm development.<br />
<br />
===Expression===<br />
Rice contains four ROS1 orthologs and two DML3 orthologs tentatively named ROS1a–d and DML3a and DML3b, that contain characteristic DNA glycosylase domains flanked by conserved domains of unknown functions. Of these, ROS1ais the longest gene, comprising 17 exons that encode a protein with 1952 amino acids, and 5¢ and 3¢ UTRs of 73 and 607 bp, respectively. RT-PCR analysis revealed thatROS1awas expressed in all vegetative and reproductive tissues tested . Quantitative RT-PCR analysis revealed that ROS1ais the most extensively expressed gene among the four genes(ROS1a, ROS1c, ROS1d and DML3a) expressed in five selected tissues examined, including anthers and pistils,whereas ROS1b and DML3bare scarcely expressed in these tissues. Interestingly, moderate levels of transcripts for ROS1c, ROS1dandDML3awere detected in pistils and immature seeds 2 days after pollination.<br />
<br />
<br />
===Evolution===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation [DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3) are bi-functional DNA glycosylases that not only recognize and remove5-meC from double-stranded DNA, but also show lyase activity, which nicks double-stranded DNA at an abasic site.Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1 orthologs and two DML3 orthologs, but no DME orthologs.Rice endosperm DNA is hypomethylated in all sequence contexts, implying that hypomethylation in rice endosperm relies on some of these DNA glycosylases or alternative biochemical mechanisms.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
1.A. Zemach et al., Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107, 18729 (Oct 26, 2010).<br />
<br />
2.A. Ono et al., A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny. Plant J 71, 564 (Aug, 2012).<br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0445900|<br />
Description = Similar to ROS1 (Fragment)|<br />
Version = NM_001062220.1 GI:115464170 GeneID:4338940|<br />
Length = 5779 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0445900, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:21889157..21894935|<br />
CDS = 21889581..21889708,21890545..21890583,21890664..21890778,21890883..21890948,21892020..21892159<br>,21892239..21892302,21892380..21892416,21892564..21893001,21893713..21893795<br>,21893897..21893933,21894150..21894218,21894322..21894413,21894487..21894571<br>,21894906..21894934|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>ttaagagatgttcctccagactcagcaaaggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtatgagttacattatcagatgattacttttggaaaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtttacgaacttccagattcacatcccctcatgcaacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggtctaacaactgaagaaatacagcactgcttctggagaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactga</cdnaseq>|<br />
AA = <aaseq>LRDVPPDSAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVG RICVRLGWVPIQPLPESLQLHLLELYPVLETIQKYLWPRLCKLDQQTLYELHYQMITF GKVFCTKSKPNCNACPMRSECRHFASAFASARLALPSPQDKRLVNLSNQFAFHNGTMP TPNSTPLPQLEGSIHARDVHANNTNPIIEEPASPREEECRELLENDIEDFDEDTDEIP IIKLNMEAFSQNLENCIKESNKDFQSDDITKALVAISNEAASIPVPKLKNVHRLRTEH YVYELPDSHPLMQQLALDQREPDDPSPYLLAIWTPDELKDTREAPKPCCNPQTEGGLC SNEMCHNCVSERENQYRYVRGTVLVPCRTAMRGSFPLNGTYFQVNEVFADHSSSHNPI NIPREQLWNLHRRMVYFGTSVPTIFKGLTTEEIQHCFWRGFVCVRGFNMETRAPRPLC PHFHLAASKLRRSSKKAATEQTH</aaseq>|<br />
DNA = <dnaseqindica>5228..5355#4353..4391#4158..4272#3988..4053#2777..2916#2634..2697#2520..2556#1935..2372#1141..1223#1003..1039#718..786#523..614#365..449#2..30#gttaagagatgttcctccagactcagcaaagtaagatactacacctgtattcaatatttacaaatcccattgccctgctgatgagatttttctagttctggaaatgataaatcaagtatcaaagaagtttgtgaaccaattaaatggagcaagctgatccaagaacttgccagttaatatctagaattaaatactatgagcaaagttctatgaaatgggcacgcagaacagaaaaggctgtataatgtatgacacatgatcgaagcagtgaaggaatttttttttaggaaagaaaattccatgaaccctatttatttcacaggcgagaagtatgtcaattacaatgtgttcgaattattttcagggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagtaagtttctgttggattaattctccttcacctgcagccaatttgaaatttacactacattgttgcaactcaggttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctgtaagaatgttgcattgtctactacagttgtataaatactctctgcaattttatacgatgatgtttcaatttgaatatattgattttgtttgtgccttcaaagataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtgagttataaccaattaaccatacccactcatagttgcccttcttattagtttttttttacgcaagcccttcttattagtttgtgtaacttctaggttatttctttttcatgcaaattacagtatttggaatcatgaataattaaggcaataaggagtaaataacataatttataactataaggaattattaacagagtttcatggttttcacaggtatgagttacattatcagatgattacttttggaaaggtacttcattagcattaaggagtttggtctcttcattagcatctaccgacgcatttgttctcttttgtttgagtaaagataaattatcataacaaatgcaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaaggtattatggcaagcagaaaatgggagccttctggctgcaaggagacttacaaaataaacactatttgcttcagtagtcacttttttccgataaaggaagctttattaaaactcagtcaaatacaccaagatgatacattctaactgagccactcccggcctctgcatgaaatgcacaccgccacaaaacaggatctaactagaccctcaacacaaaacaaataaattagtgactatcaagccgtagactatatcgccacccatgctccagggtaaaaaactcctgtgccacctgatagtgcacagcaaaaaccacgagaaggatgtgctttcgttggtggagagaccgaattagctccattaacataatatgaccactaagagcgcaaaatagtgcttttgaagaataaaagggaaaatatgctaggagaaaaatcaatatatggttctagtacaccgccatggcactttgtgtagtctctgtctgcaacaaaatatatttgccgctttcacttatcttacctgggaattttgttatcacgtatttcctcgttccactatctttcttgttttgtttgtgcgcgcgcgcatgcctgatatatcttgctctttcagttgaccttacctgggagccttcattttgcatatttcttcatttgttattttttccttattaactctgttatattttgtttgacttttttaaatgaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtgtaagtgttggactgatattttatttagcttgaacatgtacctgtttaaacttacatttattatagagcccaccatctaagtaattctatacatcctgaacaaaatattttttaatttctattactgacttaaggttctgctcgcagttacgaacttccagattcacatcccctcatgcaacaggtgagaccatgagaaattgtgccatctttctttaaaacacttcaagatattatttctgattgcaaatgatcttacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccaggcaagtgcatttttctttaaatttataactgtccgtgtgtgtgtgctggttttcgtcgagtcatgtggctactgtgcagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggtaaatcaaccaacattatgtagcaatcatcaacattgaagagctgaacctctgcattagtcagctagtaaacaaaatattcattataatccaaacattggaatgaattcaggaattcaagaaaatgttgaagataacttttaatgaaaactagtgcttacaaagtgccaagcaaagctattctgttgtctgtgtaatctcttttcttgcatgaaatagcccactgtcttcactttaaacaataagaatagcatagattttgggtttccggctatacaacacatcttaatatgaacttttgtggaagtctaaaagagaacctctctgaacctttaaactgtacactatttaaccaacaatcaaagccgatcacttctcaacgtcattctgaattagctttgggcgatgtttcttaaccaggagatgtggtctgagattttagattttttttttcatctcctttatattagtagacgacttaaaattttctggaataatcttacttcgctgtgaagtatttataacccagataaatcggtaagattgaagtaaagtattattgtcccacgaaatttagtgtgtgaaagtagacaacatttttttctactgtccgattaaactttatttaactctgccccattttatctaggctataaatggtgatttcttctaggctatacggtttttcaatccaattttaccttattttgctttaccaaatttgtcaacattataatactttgtagtgcaagtgagattttttttttcaattttgttatgtcatttactaattttaaaattgaaaacctggttcagccttgggccattttgccacattagggacacatagtccaaagccactttaaatttgagacaaggttgaaaagcgcatggttttgatacttcaggttctgggttgaattgtgtccagttttctgctttggggttgtctctggactaacagaaaagttcagtattgcaaaacagactgtttcctatacaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacggttactggaacatgaacaggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttgactttacgatttctggatttgtttttgcaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggttaccaccattcacccatacaatgactcaaagaaatcttatctgcaactttaccgacaactgttattttcattctttaggtctaacaactgaagaaatacagcactgcttctggagaggtattaacagtatttttttcactcgctgtttcagcgcattctcctctgggacatatcttgtttcctcatatgatcaaacaatttgcagaatgcagatgccatcatataatcacaatatgtttctacagttatatagcattcgtgtgattgtgtcaaggtgtccacacacttttcacaaaaacttactccccctgtcccataatataagggattttgagcttttgtttgcactgtttgaccattcgtcttattcaaaaaaatttagaattatattttttttctttgtgacttactttattatccaaaatactttaagcacaacttttcgttttttatatttgcacaaattttttgaataagacgagtggtcaaacattataatcaaaaaactcaaaatcccttgtattatgggacggagggagtagtattaagggtctaaaaggagcctgaatatttggttcagttagagtctatatctgagtccattttaattcctagtgctatggataaaggtgtcctccttcaataaataaataaaggtctctccagttattagtcaccagcatccaatataactgcctgataatatatgtggtaagttatatggtgccaaagaggcaaagatactgctaccatgactaaccccctttttttttctgagttaataagggtgttagcatacatatagcttccaaattggtttagttaggtggaaaaagtcgtcatttcaggatgcagatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactgatttcaacagggacatatcaattctataaaataatgttgatggtgattacatcagttctcgatctgtgcatgggtcatattagttcctgcaggacgatagccattcttctaggaaataaacagtggagttggaaacagttaactttaagatgtgggagccaattgggcacgagaaagcaccaatatttcatatgcacctctggggcaggtcggatgcggatcatcatcatcagttaacatgggcgtagaatatcattccgttttttttttctgtggctttggtgtatcttattcacttttcatttgttttatccattcaactagcttgccaagagaccttaccatctgttctcatgacatgttagtttttcagaacttatagcaggtagtaccttcatattgatgatatgactttgattttcatt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062220.1 RefSeq:Os05g0445900]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Linahttps://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0445900&diff=177804Os05g04459002014-06-05T03:21:10Z<p>Lina: </p>
<hr />
<div>Please input one-sentence summary here.<br />
<br />
==Annotated Information==<br />
===Function===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. As well, there are some proteins coded for DNA demethylation. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation are DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3). Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1orthologs and twoDML3orthologs, but no DME orthologs.It has been demonstrated that rice ROS1a protein is a bi-functional DNA glycosylase/lyase for 5-meC DNA demethylation, although biochemical characterization of the ROS1a enzyme remains to be performed to confirm this.<br />
ROS1a is the most abundantly expressed gene in tissues. It was recently reported that null mutants of ROS1c, which encodes a 5-meC DNA glycosylase/lyase, show no effects on transmission of the null alleles and produce a small portion of wrinkled seeds.And the null mutation, ros1a-GUS1, was hardly ever transmitted to progeny.Even in the presence of the wild-type paternal ROS1a allele, the maternal nullros1a-GUS1allele caused failure of early stage endosperm development, indicating non-equivalent contribution of maternal and paternal ROS1a to endosperm development.<br />
<br />
===Expression===<br />
Rice contains four ROS1 orthologs and two DML3 orthologs tentatively named ROS1a–d and DML3a and DML3b, that contain characteristic DNA glycosylase domains flanked by conserved domains of unknown functions. Of these, ROS1ais the longest gene, comprising 17 exons that encode a protein with 1952 amino acids, and 5¢ and 3¢ UTRs of 73 and 607 bp, respectively. RT-PCR analysis revealed thatROS1awas expressed in all vegetative and reproductive tissues tested . Quantitative RT-PCR analysis revealed that ROS1ais the most extensively expressed gene among the four genes(ROS1a, ROS1c, ROS1d and DML3a) expressed in five selected tissues examined, including anthers and pistils,whereas ROS1b and DML3bare scarcely expressed in these tissues. Interestingly, moderate levels of transcripts for ROS1c, ROS1dandDML3awere detected in pistils and immature seeds 2 days after pollination.<br />
<br />
<br />
===Evolution===<br />
Cytosine DNA methylation, which occurs in the CG, CHG(H = A, C or T) and CHH sequence contexts, is an epigenetic modification in plants. The genes and the corresponding encoded enzymes that mediate DNA methylation and demethylation have been characterized mainly in Arabidopsis. The Arabidopsis enzymes that mediate 5-methylcytosine (5-meC) DNA demethylation [DEMETER (DME), REPRESSOR OFSILENCING 1 (ROS1),DEMETER-LIKE 2 (DML2) and DEMETER-LIKE 3 (DML3) are bi-functional DNA glycosylases that not only recognize and remove5-meC from double-stranded DNA, but also show lyase activity, which nicks double-stranded DNA at an abasic site.Phylogenetic analysis revealed that the rice (Oryza sativa)genome encodes six putative bi-functional DNA glycosylases that mediate cytosine DNA demethylation: four ROS1 orthologs and two DML3 orthologs, but no DME orthologs.Rice endosperm DNA is hypomethylated in all sequence contexts, implying that hypomethylation in rice endosperm relies on some of these DNA glycosylases or alternative biochemical mechanisms.<br />
<br />
You can also add sub-section(s) at will.<br />
<br />
==Labs working on this gene==<br />
Please input related labs here.<br />
<br />
==References==<br />
1.A. Zemach et al., Local DNA hypomethylation activates genes in rice endosperm. Proc Natl Acad Sci U S A 107, 18729 (Oct 26, 2010).<br />
2.A. Ono et al., A null mutation of ROS1a for DNA demethylation in rice is not transmittable to progeny. Plant J 71, 564 (Aug, 2012).<br />
<br />
<br />
==Structured Information==<br />
{{JaponicaGene|<br />
GeneName = Os05g0445900|<br />
Description = Similar to ROS1 (Fragment)|<br />
Version = NM_001062220.1 GI:115464170 GeneID:4338940|<br />
Length = 5779 bp|<br />
Definition = Oryza sativa Japonica Group Os05g0445900, complete gene.|<br />
Source = Oryza sativa Japonica Group<br />
<br />
ORGANISM Oryza sativa Japonica Group<br />
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;<br />
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP<br />
clade; Ehrhartoideae; Oryzeae; Oryza.<br />
|<br />
Chromosome = [[:category:Japonica Chromosome 5|Chromosome 5]]|<br />
AP = Chromosome 5:21889157..21894935|<br />
CDS = 21889581..21889708,21890545..21890583,21890664..21890778,21890883..21890948,21892020..21892159<br>,21892239..21892302,21892380..21892416,21892564..21893001,21893713..21893795<br>,21893897..21893933,21894150..21894218,21894322..21894413,21894487..21894571<br>,21894906..21894934|<br />
GCID = <gbrowseImage1><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage1>|<br />
GSID = <gbrowseImage2><br />
name=NC_008398:21889157..21894935<br />
source=RiceChromosome05<br />
preset=GeneLocation<br />
</gbrowseImage2>|<br />
CDNA = <cdnaseq>ttaagagatgttcctccagactcagcaaaggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtatgagttacattatcagatgattacttttggaaaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtttacgaacttccagattcacatcccctcatgcaacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggtctaacaactgaagaaatacagcactgcttctggagaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactga</cdnaseq>|<br />
AA = <aaseq>LRDVPPDSAKDYLLSIRGLGLKSVECVRLLTLHHLAFPVDTNVG RICVRLGWVPIQPLPESLQLHLLELYPVLETIQKYLWPRLCKLDQQTLYELHYQMITF GKVFCTKSKPNCNACPMRSECRHFASAFASARLALPSPQDKRLVNLSNQFAFHNGTMP TPNSTPLPQLEGSIHARDVHANNTNPIIEEPASPREEECRELLENDIEDFDEDTDEIP IIKLNMEAFSQNLENCIKESNKDFQSDDITKALVAISNEAASIPVPKLKNVHRLRTEH YVYELPDSHPLMQQLALDQREPDDPSPYLLAIWTPDELKDTREAPKPCCNPQTEGGLC SNEMCHNCVSERENQYRYVRGTVLVPCRTAMRGSFPLNGTYFQVNEVFADHSSSHNPI NIPREQLWNLHRRMVYFGTSVPTIFKGLTTEEIQHCFWRGFVCVRGFNMETRAPRPLC PHFHLAASKLRRSSKKAATEQTH</aaseq>|<br />
DNA = <dnaseqindica>5228..5355#4353..4391#4158..4272#3988..4053#2777..2916#2634..2697#2520..2556#1935..2372#1141..1223#1003..1039#718..786#523..614#365..449#2..30#gttaagagatgttcctccagactcagcaaagtaagatactacacctgtattcaatatttacaaatcccattgccctgctgatgagatttttctagttctggaaatgataaatcaagtatcaaagaagtttgtgaaccaattaaatggagcaagctgatccaagaacttgccagttaatatctagaattaaatactatgagcaaagttctatgaaatgggcacgcagaacagaaaaggctgtataatgtatgacacatgatcgaagcagtgaaggaatttttttttaggaaagaaaattccatgaaccctatttatttcacaggcgagaagtatgtcaattacaatgtgttcgaattattttcagggactatctgcttagtatacgtggattggggctcaaaagtgttgagtgtgtccgccttttgacattacatcatcttgcattcccagtaagtttctgttggattaattctccttcacctgcagccaatttgaaatttacactacattgttgcaactcaggttgatactaatgttggtcgtatatgtgtacgattgggatgggtgccaattcaacccctccctgaatctcttcagttacaccttctggagctgtaagaatgttgcattgtctactacagttgtataaatactctctgcaattttatacgatgatgtttcaatttgaatatattgattttgtttgtgccttcaaagataccctgtcttggagactatacaaaagtacctctggcctcgtctgtgtaaacttgatcaacaaacactgtgagttataaccaattaaccatacccactcatagttgcccttcttattagtttttttttacgcaagcccttcttattagtttgtgtaacttctaggttatttctttttcatgcaaattacagtatttggaatcatgaataattaaggcaataaggagtaaataacataatttataactataaggaattattaacagagtttcatggttttcacaggtatgagttacattatcagatgattacttttggaaaggtacttcattagcattaaggagtttggtctcttcattagcatctaccgacgcatttgttctcttttgtttgagtaaagataaattatcataacaaatgcaggtgttctgtaccaaaagcaagccgaattgcaatgcatgtccaatgaggagtgaatgcaggcattttgcaagtgcctttgcaaggtattatggcaagcagaaaatgggagccttctggctgcaaggagacttacaaaataaacactatttgcttcagtagtcacttttttccgataaaggaagctttattaaaactcagtcaaatacaccaagatgatacattctaactgagccactcccggcctctgcatgaaatgcacaccgccacaaaacaggatctaactagaccctcaacacaaaacaaataaattagtgactatcaagccgtagactatatcgccacccatgctccagggtaaaaaactcctgtgccacctgatagtgcacagcaaaaaccacgagaaggatgtgctttcgttggtggagagaccgaattagctccattaacataatatgaccactaagagcgcaaaatagtgcttttgaagaataaaagggaaaatatgctaggagaaaaatcaatatatggttctagtacaccgccatggcactttgtgtagtctctgtctgcaacaaaatatatttgccgctttcacttatcttacctgggaattttgttatcacgtatttcctcgttccactatctttcttgttttgtttgtgcgcgcgcgcatgcctgatatatcttgctctttcagttgaccttacctgggagccttcattttgcatatttcttcatttgttattttttccttattaactctgttatattttgtttgacttttttaaatgaagtgcaagacttgcacttccttctcctcaggacaaaaggttggtgaatctgagcaatcaatttgctttccataatggcacaatgcccacaccaaattcaactcctctgcctcagctcgaggggagtatccatgcaagggatgttcatgctaacaacacaaatccaataattgaggagccagcaagtccaagagaggaagaatgccgagaacttttagagaatgatattgaagattttgatgaagatactgatgaaatcccaataataaaacttaacatggaagctttttctcaaaacttggaaaattgcataaaagaaagcaataaggatttccaatctgatgatattacaaaagcattggttgctatcagcaatgaagcagcttcaattcctgtacctaaactaaagaatgtgcatagacttcggacagaacactatgtgtaagtgttggactgatattttatttagcttgaacatgtacctgtttaaacttacatttattatagagcccaccatctaagtaattctatacatcctgaacaaaatattttttaatttctattactgacttaaggttctgctcgcagttacgaacttccagattcacatcccctcatgcaacaggtgagaccatgagaaattgtgccatctttctttaaaacacttcaagatattatttctgattgcaaatgatcttacagctagcactcgaccaacgggagcctgatgatccaagtccttacctgttggccatatggacaccaggcaagtgcatttttctttaaatttataactgtccgtgtgtgtgtgctggttttcgtcgagtcatgtggctactgtgcagatgaactaaaggacacaagggaggcaccaaaaccgtgctgcaatcctcaaactgaaggtggcttatgcagcaatgagatgtgccacaactgtgtatctgaacgagaaaaccaatatagatacgtcagaggcacggttctggtaaatcaaccaacattatgtagcaatcatcaacattgaagagctgaacctctgcattagtcagctagtaaacaaaatattcattataatccaaacattggaatgaattcaggaattcaagaaaatgttgaagataacttttaatgaaaactagtgcttacaaagtgccaagcaaagctattctgttgtctgtgtaatctcttttcttgcatgaaatagcccactgtcttcactttaaacaataagaatagcatagattttgggtttccggctatacaacacatcttaatatgaacttttgtggaagtctaaaagagaacctctctgaacctttaaactgtacactatttaaccaacaatcaaagccgatcacttctcaacgtcattctgaattagctttgggcgatgtttcttaaccaggagatgtggtctgagattttagattttttttttcatctcctttatattagtagacgacttaaaattttctggaataatcttacttcgctgtgaagtatttataacccagataaatcggtaagattgaagtaaagtattattgtcccacgaaatttagtgtgtgaaagtagacaacatttttttctactgtccgattaaactttatttaactctgccccattttatctaggctataaatggtgatttcttctaggctatacggtttttcaatccaattttaccttattttgctttaccaaatttgtcaacattataatactttgtagtgcaagtgagattttttttttcaattttgttatgtcatttactaattttaaaattgaaaacctggttcagccttgggccattttgccacattagggacacatagtccaaagccactttaaatttgagacaaggttgaaaagcgcatggttttgatacttcaggttctgggttgaattgtgtccagttttctgctttggggttgtctctggactaacagaaaagttcagtattgcaaaacagactgtttcctatacaatcatgcattgttggtttgtgaagttgcaagtattgcttgactaatgacggttactggaacatgaacaggttccttgccgaacagccatgagaggtagttttccacttaatggcacttactttcaagttaatgaggtatgctgagttatatctgtcaaagtatgagtaggatagtggagagttgctatccatgggcctttatagagttgactttacgatttctggatttgtttttgcaggtttttgctgatcacagttctagccacaatcccataaatatcccaagggagcagttatggaacttgcataggcgtatggtttactttgggacttcagtgccaaccatattcaaaggttaccaccattcacccatacaatgactcaaagaaatcttatctgcaactttaccgacaactgttattttcattctttaggtctaacaactgaagaaatacagcactgcttctggagaggtattaacagtatttttttcactcgctgtttcagcgcattctcctctgggacatatcttgtttcctcatatgatcaaacaatttgcagaatgcagatgccatcatataatcacaatatgtttctacagttatatagcattcgtgtgattgtgtcaaggtgtccacacacttttcacaaaaacttactccccctgtcccataatataagggattttgagcttttgtttgcactgtttgaccattcgtcttattcaaaaaaatttagaattatattttttttctttgtgacttactttattatccaaaatactttaagcacaacttttcgttttttatatttgcacaaattttttgaataagacgagtggtcaaacattataatcaaaaaactcaaaatcccttgtattatgggacggagggagtagtattaagggtctaaaaggagcctgaatatttggttcagttagagtctatatctgagtccattttaattcctagtgctatggataaaggtgtcctccttcaataaataaataaaggtctctccagttattagtcaccagcatccaatataactgcctgataatatatgtggtaagttatatggtgccaaagaggcaaagatactgctaccatgactaaccccctttttttttctgagttaataagggtgttagcatacatatagcttccaaattggtttagttaggtggaaaaagtcgtcatttcaggatgcagatataagttagggcatatcctcttgttggggttttcatttcagctgtgtcttatactttatatggtgtctcattaacatgcactaaaatgcaatgcaggatttgtctgtgtgagaggattcaacatggaaactagggcaccaaggcctctatgcccccatttccaccttgcagcaagcaaactgcgaagatcctctaaaaaagcagcaactgagcaaacacactgatttcaacagggacatatcaattctataaaataatgttgatggtgattacatcagttctcgatctgtgcatgggtcatattagttcctgcaggacgatagccattcttctaggaaataaacagtggagttggaaacagttaactttaagatgtgggagccaattgggcacgagaaagcaccaatatttcatatgcacctctggggcaggtcggatgcggatcatcatcatcagttaacatgggcgtagaatatcattccgttttttttttctgtggctttggtgtatcttattcacttttcatttgttttatccattcaactagcttgccaagagaccttaccatctgttctcatgacatgttagtttttcagaacttatagcaggtagtaccttcatattgatgatatgactttgattttcatt</dnaseqindica>|<br />
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001062220.1 RefSeq:Os05g0445900]|<br />
}}<br />
[[Category:Genes]]<br />
[[Category:Japonica mRNA]]<br />
[[Category:Oryza Sativa Japonica Group]]<br />
[[Category:Japonica Genes]]<br />
[[Category:Japonica Chromosome 5]]<br />
[[Category:Chromosome 5]]</div>Lina