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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. |
| | ===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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| − | | |
| − | | |
| − | ===Mutant Phenotype===
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| − | We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology. [[File:dwarf phenotype.jpg|right|thumb|150px|''Dwarf phenotype in OsDDM1-mutant lines (from reference <ref name="ref1" />).'']]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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| − | ===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|right|thumb|200px|''Structure of OsDDM1 and Arabidopsis DDM1 (from reference <ref name="ref1" />).'']]
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| − | [[File:E_1.jpg|right|thumb|300px|''Alignment of proteins encoded by DDM1-like genes among speciecs (from reference <ref name="ref1" />).'']]
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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|right|thumb|200px|''envolution relationship in rice,maize,Arabidopsis and mouse (from reference <ref name="ref1" />).'']]
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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> |
| | + | * <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 Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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| − |
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| − | 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]] |
