|
|
| (25 intermediate revisions by 3 users not shown) |
| Line 1: |
Line 1: |
| − | Please input one-sentence summary here.
| + | The rice '''''Os03g0722400''''' was reported as '''''OsDDM1b''''' in 2012 <ref name="ref1" /> by researchers from Japan. |
| − | | |
| − | OsDDM1b
| |
| | ==Annotated Information== | | ==Annotated Information== |
| − | Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic DNA. Although cytosine methylation could affect various aspects of plant growth and development including those related to agricultural importance, orthologs of DDM1 in plants other than Arabidopsis has not been studied in detail. In this study, we identified two rice genes with similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development and their amino acid sequences are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orientation exhibited genomic DNA hypomethylation. In those lines, repeated sequences were more severely affected than a single copy sequence as is the case in Arabidopsis ddm1 mutants. Transcripts derived from endogenous transposon-related loci were up-regulated in the antisense OsDDM1 lines, opening a possibility to identify and utilize potentially active transposons for rice functional genomics.
| + | [[File:155-Os03g0722400.png|right|thumb|327px|'''Figure 1.''' ''Expression of OsDDM1 genes during development..<ref name="ref1" />.'']] |
| − | | + | ===Gene Symbol=== |
| | + | *'''''Os03g0722400''''' '''''<=>''''' '''''OsDDM1b''''' |
| | ===Function=== | | ===Function=== |
| − | OsDDM1b is required for the maintenance of DNA methylation on
| + | * '''''OsDDM1''''' genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active. |
| − | newly replicated DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on repeated
| + | transposons in the genome remains unknown. |
| − | sequences.
| + | * Hypomethylation induced by the antisense '''''OsDDM1''''' disturbs normal development. |
| − | | |
| − | ===Mutant Phenotype===
| |
| − | We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.
| |
| − | | |
| − | [[File:dwarf phenotype.jpg|150px]]
| |
| − | | |
| | ===Expression=== | | ===Expression=== |
| − | Please input expression information here.
| + | * '''''OsDDM1a''''' and '''''OsDDM1b''''' are expressed during development with slight variations among various tissues, suggesting that there might be functional divergence of these two genes (Fig. 1c). |
| − | ===Evolution===
| |
| − | OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
| |
| − | predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
| |
| − | sequence similarity shared by these two genes is 81%, even including
| |
| − | intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
| |
| − | The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
| |
| − | OsDDM1 genes.
| |
| − | The protein product of OsDDM1b gene is 849 amino acids in length.
| |
| − | Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
| |
| − | amino acid motifs diagnostic for SWI2/SNF2 proteins.
| |
| − | | |
| − | | |
| − | [[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]
| |
| − | | |
| − | (Higo, Hiromi, et al.,2012) | |
| − | | |
| − | By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
| |
| − | duplication event.
| |
| − | | |
| − | [[File:E_2.jpg|500px|]]
| |
| − | | |
| − | (Higo, Hiromi, et al.,2012)
| |
| | | | |
| | ==Labs working on this gene== | | ==Labs working on this gene== |
| − | Please input related labs here.
| + | * CREST, Japan Science and Technology Agency,Kawaguchi 332-0012, Japan |
| | + | * Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan |
| | + | * Department of Plant Science, University of Manitoba,Winnipeg R3T 2N2, Canada |
| | + | * Department of Integrated Genetics, National Institute of Genetics, Mishima 411-0801, Japan |
| | | | |
| | ==References== | | ==References== |
| − | Higo, Hiromi, et al. "DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)." Molecular Genetics and Genomics 287.10 (2012): 785-792. | + | <references> |
| | + | * <ref name="ref1"> |
| | + | Higo H, Tahir M, Takashima K, Miura A, Watanabe K, Tagiri A, Ugaki M, Ishikawa |
| | + | R, Eiguchi M, Kurata N, Sasaki T, Richards E, Takano M, Kishimoto N, Kakutani T, |
| | + | Habu Y. DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa). Mol |
| | + | Genet Genomics. 2012 Oct;287(10):785-92. Epub 2012 Aug 24. PubMed PMID: 22915302. |
| | + | </ref> |
| | + | </references> |
| | + | |
| | | | |
| | ==Structured Information== | | ==Structured Information== |
| − | {{JaponicaGene|
| |
| − | GeneName = Os03g0722400|
| |
| − | Description = Conserved hypothetical protein|
| |
| − | Version = NM_001057645.2 GI:297601601 GeneID:4333943|
| |
| − | Length = 3180 bp|
| |
| − | Definition = Oryza sativa Japonica Group Os03g0722400, complete gene.|
| |
| − | Source = Oryza sativa Japonica Group
| |
| | | | |
| − | ORGANISM Oryza sativa Japonica Group
| |
| − | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
| |
| − | Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
| |
| − | clade; Ehrhartoideae; Oryzeae; Oryza.
| |
| − | |
| |
| − | Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
| |
| − | AP = Chromosome 3:30070286..30073465|
| |
| − | CDS = 30072187..30072291|
| |
| − | GCID = <gbrowseImage1>
| |
| − | name=NC_008396:30070286..30073465
| |
| − | source=RiceChromosome03
| |
| − | preset=GeneLocation
| |
| − | </gbrowseImage1>|
| |
| − | GSID = <gbrowseImage2>
| |
| − | name=NC_008396:30070286..30073465
| |
| − | source=RiceChromosome03
| |
| − | preset=GeneLocation
| |
| − | </gbrowseImage2>|
| |
| − | CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
| |
| − | AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
| |
| − | DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
| |
| − | Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
| |
| − | }}
| |
| | [[Category:Genes]] | | [[Category:Genes]] |
| | [[Category:Japonica mRNA]] | | [[Category:Japonica mRNA]] |
