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| − | | + | The rice '''''Os03g0722400''''' was reported as '''''OsDDM1b''''' in 2012 <ref name="ref1" /> by researchers from Japan. |
| − | The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome. | |
| | ==Annotated Information== | | ==Annotated Information== |
| − | | + | [[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 newly replicated
| + | * '''''OsDDM1''''' genes function to silence endogenous loci including those related to retrotransposons in the rice genome, however, their roles on transposition of active. |
| − | DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on
| + | transposons in the genome remains unknown. |
| − | repeated sequences rather than single copy sequences.
| + | * Hypomethylation induced by the antisense '''''OsDDM1''''' disturbs normal development. |
| − | | |
| − | ===Mutant Phenotype===
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| − | 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.
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| − | | |
| − | [[File:dwarf phenotype.jpg|150px]]
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| − | | |
| | ===Expression=== | | ===Expression=== |
| − | Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease
| + | * '''''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). |
| − | in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of
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| − | cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and
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| − | designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant
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| − | lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon-
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| − | related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight
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| − | variations among various tissues, suggesting that there might be functional divergence of these two genes. | |
| − | | |
| − | [[File:expression.jpg|300px]]
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| − | | |
| − | ===Evolution===
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| − | OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the
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| − | predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships
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| − | exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA
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| − | sequence similarity shared by these two genes is 81%, even including
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| − | intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar.
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| − | The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the
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| − | OsDDM1 genes.
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| − | The protein product of OsDDM1b gene is 849 amino acids in length.
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| − | Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
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| − | amino acid motifs diagnostic for SWI2/SNF2 proteins.
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| − | | |
| − | | |
| − | [[File:Osddm1a.jpg|300px]] [[File:E_1.jpg|700px]]
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| − | | |
| − | (Higo, Hiromi, et al.,2012)
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| − | | |
| − | 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
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| − | duplication event.
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| − | | |
| − | [[File:E_2.jpg|500px|]]
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| − | | |
| − | (Higo, Hiromi, et al.,2012)
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| | | | |
| | ==Labs working on this gene== | | ==Labs working on this gene== |
| | + | * 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 |
| | | | |
| − | CREST, Japan Science and Technology Agency,Kawaguchi 332-0012, Japan
| + | ==References== |
| − | | + | <references> |
| − | Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| + | * <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> |
| | | | |
| − | Department of Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada
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| − |
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| − | Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan
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| − |
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| − | Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan
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| − |
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| − | ==References==
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| − | Higo, Hiromi, et al. "DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)." Molecular Genetics and Genomics 287.10 (2012): 785-792.
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| | | | |
| | ==Structured Information== | | ==Structured Information== |
| − | {{JaponicaGene|
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| − | GeneName = Os03g0722400|
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| − | Description = Conserved hypothetical protein|
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| − | Version = NM_001057645.2 GI:297601601 GeneID:4333943|
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| − | Length = 3180 bp|
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| − | Definition = Oryza sativa Japonica Group Os03g0722400, complete gene.|
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| − | Source = Oryza sativa Japonica Group
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| | | | |
| − | ORGANISM Oryza sativa Japonica Group
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| − | Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
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| − | Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
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| − | clade; Ehrhartoideae; Oryzeae; Oryza.
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| − | |
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| − | Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
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| − | AP = Chromosome 3:30070286..30073465|
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| − | CDS = 30072187..30072291|
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| − | GCID = <gbrowseImage1>
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| − | name=NC_008396:30070286..30073465
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| − | source=RiceChromosome03
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| − | preset=GeneLocation
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| − | </gbrowseImage1>|
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| − | GSID = <gbrowseImage2>
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| − | name=NC_008396:30070286..30073465
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| − | source=RiceChromosome03
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| − | preset=GeneLocation
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| − | </gbrowseImage2>|
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| − | CDNA = <cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>|
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| − | AA = <aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>|
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| − | DNA = <dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>|
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| − | Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001057645.2 RefSeq:Os03g0722400]|
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| − | }}
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| | [[Category:Genes]] | | [[Category:Genes]] |
| | [[Category:Japonica mRNA]] | | [[Category:Japonica mRNA]] |
