Difference between revisions of "Os03g0110800"
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===Evolution=== | ===Evolution=== | ||
| − | + | There are three known classes of methyltransferases in plants: MET1, a homologue of mammalian DNMT1; CMT3, a plant-specific DNA methyltransferase; and DRM2, a de novo methyltransferase. MET1 is primarily responsible for the maintenance of established CG methylation. CMT3 possesses a chromodomain catalytic motif and specifically maintains the methylation of hemimethylated CHG sites. Both MET1 and CMT3 belong to the family of maintenance DNA methyltransferases. DRM is a homologue of human DNMT3, it can methylate both unmethylated and hemimethylated cytosine nucleotides in any sequence context [2]. OsDRM2 is homologous to the Arabidopsis DRM2 gene. We can see the phylogeny of rice cytosine DNA MTases from fig 7. | |
| − | + | ===Knowledge Extension=== | |
| + | Deletion analysis reveals that interaction between OsDRM2 and OseIF4A is specifically mediated through ubiquitin-associated domain of OsDRM2 while, both domains 1 and 2 of OseIF4A are critical for mediating strong interaction with OsDRM2 in vivo. Interaction between ArabidopsiseIF4AI and eIF4AII with OsDRM2 and nuclear localization of these complexes suggests possible conservation of functional interaction betweende novomethyltransferases and the translation initiation factor, eIF4A, in RdDM across plant species(fig8)[7]. | ||
==Labs working on this gene== | ==Labs working on this gene== | ||
Revision as of 17:26, 17 May 2014
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Contents
Annotated Information
Function
OsDRM2(Os03g0110800) is the majorDRM1/2-type methyltransferase gene in rice. OsDRM2 is responsible for de novo, CG and non-CG methylation in rice genomic sequences, and that DNA methylation regulated by OsDRM2 is essential for proper rice development in both vegetative and reproductive stages[1]. 1. Targeted disruptants of rice OsDRM2 displayed pleiotropic developmental phenotypes in both vegetative and reproductive stages, including growth defects, semi-dwarfed stature, reductions in tiller number, delayed heading or no heading, abnormal panicle and spikelet morphology, and complete sterility(Fig 1)[1]. 2. OsDRM2is required not only for DNA methylation ofRIRE7/CRR1sequences and5S rDNA repeats, but also for transcriptional silencing of RIRE7/CRR1 retrotransposons(Fig 2)[1]. 3. Impaired growth and abnormal DNA methylation of osdrm2 disruptants were restored by the complementation of wild-typeOsDRM2cDNA(Fig 3)[1].
Expression
1. RT-PCR analysis revealed that OsDRM2 is expressed constitutively. OsDRM2 encodes a protein of 584 amino acids, containing two ubiquitin-associated (UBA) domains and conserved catalytic domains(Fig 4)[1]. 2. Peng. et al. cloned and expressed one of these homologues,OsDRM2(DMT706), in both E. coli and S.cerevisiae. De novo methylation activity was present in the transformants of both organisms. The recombinant OsDRM protein can methylate any type of cytosine nucleotide, including those in the patterns CG, CHG, and CHH. Evidence of cytosine methylation was observed in the genomic DNA of S. cerevisiae that expressed the OsDRM2 gene based on MSAP assays, bisulfite sequencing and a test of cytosine methylation by endonuclease digestion. This evidence demonstrated that the OsDRM2protein can not only methylate cytosine nucleotidesin vivo in an RdDM pathway-free cellular environment but can also methylate cytosine nucleotides in vitro(Fig 5)[2]. 3. Non-coding RNAs, especially small RNAs, play important roles in the expression of OsDRM2. For instance, miR820 negatively regulates the expression of OsDRM2[3-5]. And expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci(Fig 6)[3].
Evolution
There are three known classes of methyltransferases in plants: MET1, a homologue of mammalian DNMT1; CMT3, a plant-specific DNA methyltransferase; and DRM2, a de novo methyltransferase. MET1 is primarily responsible for the maintenance of established CG methylation. CMT3 possesses a chromodomain catalytic motif and specifically maintains the methylation of hemimethylated CHG sites. Both MET1 and CMT3 belong to the family of maintenance DNA methyltransferases. DRM is a homologue of human DNMT3, it can methylate both unmethylated and hemimethylated cytosine nucleotides in any sequence context [2]. OsDRM2 is homologous to the Arabidopsis DRM2 gene. We can see the phylogeny of rice cytosine DNA MTases from fig 7.
Knowledge Extension
Deletion analysis reveals that interaction between OsDRM2 and OseIF4A is specifically mediated through ubiquitin-associated domain of OsDRM2 while, both domains 1 and 2 of OseIF4A are critical for mediating strong interaction with OsDRM2 in vivo. Interaction between ArabidopsiseIF4AI and eIF4AII with OsDRM2 and nuclear localization of these complexes suggests possible conservation of functional interaction betweende novomethyltransferases and the translation initiation factor, eIF4A, in RdDM across plant species(fig8)[7].
Labs working on this gene
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References
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Structured Information
| Gene Name |
Os03g0110800 |
|---|---|
| Description |
Similar to DNA methyltransferase |
| Version |
NM_001055253.1 GI:115450234 GeneID:4331357 |
| Length |
3670 bp |
| Definition |
Oryza sativa Japonica Group Os03g0110800, 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 | |
| Location |
Chromosome 3:611011..614680 |
| Sequence Coding Region |
611181..611186,611747..611869,611985..612084,612169..612215,612294..612452 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008396:611011..614680 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008396:611011..614680 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggtggactgggcttcagatagcgacaatgataagttcgagtgggacacagacggtgaggctgagacctcatctgccccggccctaaggaacatagatgctcctggtccgtccacgaggctgccgcaggatgcaaatgggaaggccaacgggtcaggtgctttggttgctgaatttatgggaatgggattcccaaaagaaatgatcttgaaagcgattaaggagattggggatacagatacagagcaattgcttgagttacttctgacttatcaggcaataggcggtgacgcttcagtgggtaactgctctgcttcggcctgtgccccccagactcttgaagtcgacgaggaggaggatgatactaattgggatgaatatgatactgctggcaattgtgacaggactcctcactctgatggttctggtgacgaggatttctttcaagaaatgtcagagaaggatgaaaaaatgaagtccttagtcaacatgggttttcctgaagatgaagcaaagatggctatcgatagatgtctcgatgcgcctgtagcagtgttggttgattcaatctatgcatcacaggaagcaggaaatggttactctgcaaacttatctgactatgaggatacagagttcagttcctttggaggaagaaagaaaacaagatttgtggatggaagcaagaagagaaagcggtatggaagtgggccatctgggaatcaagtgccgtttgatggcagccacgaagagcccatgcctcttccaaatccaatggtgggattcagcttgcccaatgagaggttaaggtcagtccacagaaatcttcctgaccaagctcttgggccaccattcttttactatgaaaacgtggccctagctccaaaaggtgtatggacaaccatctcaaggtttttatatgacattcagcctgagtttgtggactccaagtacttttgtgctgctgccaggaagaggggttatattcataacctgccgattgagaacaggtcacctgttctcccaatgcctcccaaaacaatatctgaagcctttcctaataccaagaggtggtggccttcctgggatccaaggaggcagttcaactgcttgcaaacttgtatggcaagcgcaaagcttacagagcgaattcgttgtgctttgggtagattcagtgatgtaccaactccacaagttcagaagtatgtcttggacgaatgtaggaaatggaacctagtttgggtcggaaagaataaggtcgctcctctagagcctgatgagatggagttcctgttagggtaccctagaaaccacactaggggagttagcaggacggagaggtacagggctctcgggaattcattccaagttgatacagtagcataccatctctctgtgctgagggacctgtttcccaatggaatgaatgtcttatccctgttttctggtattggaggagcagaggtagctctccacagactggggatacatatgaaaacagtgatctctgttgagaaatcagaagtgaacagaacgattctgaagagctggtgggatcagacacaaactggaacgctgattgaaatcgccgacgtgcggcatcttactactgaaagaattgaaacattcatcagaaggtttggcggttttgacctggtgattggtggcagcccgtgcaacaaccttgctggcagcaaccgccatcaccgagatggtctggagggcgagcactccgcgctcttctacgattacattagaatattagaacatgtaaaggctaccatgtcagcagtctag</cdnaseq> |
| Protein Sequence |
<aaseq>MVDWASDSDNDKFEWDTDGEAETSSAPALRNIDAPGPSTRLPQD ANGKANGSGALVAEFMGMGFPKEMILKAIKEIGDTDTEQLLELLLTYQAIGGDASVGN CSASACAPQTLEVDEEEDDTNWDEYDTAGNCDRTPHSDGSGDEDFFQEMSEKDEKMKS LVNMGFPEDEAKMAIDRCLDAPVAVLVDSIYASQEAGNGYSANLSDYEDTEFSSFGGR KKTRFVDGSKKRKRYGSGPSGNQVPFDGSHEEPMPLPNPMVGFSLPNERLRSVHRNLP DQALGPPFFYYENVALAPKGVWTTISRFLYDIQPEFVDSKYFCAAARKRGYIHNLPIE NRSPVLPMPPKTISEAFPNTKRWWPSWDPRRQFNCLQTCMASAKLTERIRCALGRFSD VPTPQVQKYVLDECRKWNLVWVGKNKVAPLEPDEMEFLLGYPRNHTRGVSRTERYRAL GNSFQVDTVAYHLSVLRDLFPNGMNVLSLFSGIGGAEVALHRLGIHMKTVISVEKSEV NRTILKSWWDQTQTGTLIEIADVRHLTTERIETFIRRFGGFDLVIGGSPCNNLAGSNR HHRDGLEGEHSALFYDYIRILEHVKATMSAV</aaseq> |
| Gene Sequence |
<dnaseqindica>171..176#737..859#975..1074#1159..1205#1284..1442#2025..2121#2201..2292#2382..3551#aacgccgtgtggtcgccatcgccatcgccttcctcctcctcctcctccgccgccgcgcgcttcctcgccaccgcgcgcccagggccatcggcggcggacgccctcgcccacgcgcgcgagagaggggggcgagagattatcggacgagtcgctttgcggagctttctagaatggtggtaagggctcccgctccccccctccgaagcctcctcttcctctctcctccaatctccatcctgctgctgctgcatgatgttagtttggccgtgccgcggcggacgaccctcctcgtcgttgttcgtggattgctccgtgcacgattaggttgtgggtttccgtttgggattgggatggaggggctcctctggtctgtttagtcgcgaaagaatgatactttcttgtatgttttgctgcattttggatcctaaaattatctgatactgtattgatgtcgcgcttgagaattcgattttgcgatgtcgcgtgaacagttcgggcttgcggagcgtggaggagcagaatatttccccccttttgatttggatttagggtttaactgtttggctatccccttgaaatttgatgagggctacgtgatataggggtggcagtatgcctcatacaagatgctacattcaacccgattcagtacttgcgttaatttttctcctctgaatcgccttgttttcactgttagtcgggatatttcagacgtgttgcttaatttatgtcacaggactgggcttcagatagcgacaatgataagttcgagtgggacacagacggtgaggctgagacctcatctgccccggccctaaggaacatagatgctcctggtccgtccacgaggctgccgcaggtaggagatagaggtctatctttgaacacacgtgctagtcatttgttcaaaccatgttgttactttactgtaattataatcaaaatgtggtgtttgtttgtggaactgtctgaaggatgcaaatgggaaggccaacgggtcaggtgctttggttgctgaatttatgggaatgggattcccaaaagaaatgatcttgaaagcgattaaggagattggtaacgataacaataatctagttctcttatttgcttctggttgcattttgaatcttctgtttcaactgctgtcttttctttcaggggatacagatacagagcaattgcttgagttacttctgacttatcaggtatttgcccacatggttgcatcactctgtttattattatctaatgctctactgtacaagtgatgccgtgtaatgcaggcaataggcggtgacgcttcagtgggtaactgctctgcttcggcctgtgccccccagactcttgaagtcgacgaggaggaggatgatactaattgggatgaatatgatactgctggcaattgtgacaggactcctcactctgatggttctggtgacgaggtatttacatgaccccctccttggtcattatatatttatatgcacttgctgtgtctatttcttgaccagtttccctgatcatggctgcaccattttttgcacttgcttcatgctaagaacacattcccttattaatacctatgtaagtgaactactggtcgtataataaattagaaaatttcatacctgtgttctatttcactcttagtaaacaagtatagatatggttagctatactgcagtgctgtagtcttttgtatctataaaaccatacatgtccctgtagggttgttaaaggagctttgttgatccagcccttccttccatcattctatgcatctccagttagcattttctttatggtgcctttgtagtgagagttagcagaactactgtagaaccatcagagagaggatcatatatttggtagcagtaaattgtaggctttgcaaatggtatatgtgtataactgtatatgtgatgcctgcattagttgctttattaataggttattctggactgcaagtcattagagagatgtaacaagtgttttcaatttgcctttaatgtgcttttatgcaggatttctttcaagaaatgtcagagaaggatgaaaaaatgaagtccttagtcaacatgggttttcctgaagatgaagcaaagatggctatcgatagatgtggtatgcctctattgaatttgatgctttgacaggaaggaaccttattctgctgcctttgttggcttaaatttcccaggtctcgatgcgcctgtagcagtgttggttgattcaatctatgcatcacaggaagcaggaaatggttactctgcaaacttatctgactatgaggtaccttgtgattataatgcatctgaatcaataggttgtttcatttcattaaatataacggcattggcatcatctttataattgtgcaggatacagagttcagttcctttggaggaagaaagaaaacaagatttgtggatggaagcaagaagagaaagcggtatggaagtgggccatctgggaatcaagtgccgtttgatggcagccacgaagagcccatgcctcttccaaatccaatggtgggattcagcttgcccaatgagaggttaaggtcagtccacagaaatcttcctgaccaagctcttgggccaccattcttttactatgaaaacgtggccctagctccaaaaggtgtatggacaaccatctcaaggtttttatatgacattcagcctgagtttgtggactccaagtacttttgtgctgctgccaggaagaggggttatattcataacctgccgattgagaacaggtcacctgttctcccaatgcctcccaaaacaatatctgaagcctttcctaataccaagaggtggtggccttcctgggatccaaggaggcagttcaactgcttgcaaacttgtatggcaagcgcaaagcttacagagcgaattcgttgtgctttgggtagattcagtgatgtaccaactccacaagttcagaagtatgtcttggacgaatgtaggaaatggaacctagtttgggtcggaaagaataaggtcgctcctctagagcctgatgagatggagttcctgttagggtaccctagaaaccacactaggggagttagcaggacggagaggtacagggctctcgggaattcattccaagttgatacagtagcataccatctctctgtgctgagggacctgtttcccaatggaatgaatgtcttatccctgttttctggtattggaggagcagaggtagctctccacagactggggatacatatgaaaacagtgatctctgttgagaaatcagaagtgaacagaacgattctgaagagctggtgggatcagacacaaactggaacgctgattgaaatcgccgacgtgcggcatcttactactgaaagaattgaaacattcatcagaaggtttggcggttttgacctggtgattggtggcagcccgtgcaacaaccttgctggcagcaaccgccatcaccgagatggtctggagggcgagcactccgcgctcttctacgattacattagaatattagaacatgtaaaggctaccatgtcagcagtctagtttaagctatcacattaactaactctgtgatttattgttgttaacgaagttagaacctgttgattgatattgctgaacctgatgtgatgttattgcactcaaacaggagtgttttttcc</dnaseqindica> |
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