Difference between revisions of "Os03g0110800"
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| − | + | The rice '''''Os03g0110800''''' was reported as '''''DRM2''''' in 2012 <ref name="ref1" /> by researchers from Japan. | |
==Annotated Information== | ==Annotated Information== | ||
| + | [[File:Fig.1 OsDRM2.png|right|thumb|327px|Fig.1 Phenotype analyses of rice osdrm2 disruptants.(From reference <ref name="ref1" />).'']] | ||
| + | ===Gene Symbol=== | ||
| + | *'''''Os03g0110800''''' '''''<=>''''' '''''DRM2''''','''''osdrm2''''','''''OsDRM2''''' | ||
===Function=== | ===Function=== | ||
| − | OsDRM2(Os03g0110800) is the | + | *''OsDRM2''(Os03g0110800) is the major DRM1/2-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<ref name="ref1" />. |
| − | + | * 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)<ref name="ref1" />. | |
| − | + | * ''OsDRM2'' is required not only for DNA methylation ofRIRE7/CRR1sequences and5S rDNA repeats, but also for transcriptional silencing of RIRE7/CRR1 retrotransposons(Fig 2)<ref name="ref1" />. | |
| − | + | * Impaired growth and abnormal DNA methylation of osdrm2 disruptants were restored by the complementation of wild-type ''OsDRM2'' cDNA(Fig 3)<ref name="ref1" />. | |
| + | |||
| + | [[File:Fig.3 OsDRM2.png|right|thumb|327px|Fig.3 Complementation of the osdrm2 disruptants by ectopic expression of OsDRM2 cDNA.(From reference <ref name="ref1" />).'']] | ||
===Expression=== | ===Expression=== | ||
| − | + | * 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)<ref name="ref1" />. | |
| − | + | ||
| − | + | * 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 OsDRM2 protein can not only methylate cytosine nucleotidesin vivo in an RdDM pathway-free cellular environment but can also methylate cytosine nucleotides in vitro(Fig 5)<ref name="ref2" />. | |
| + | |||
| + | * Non-coding RNAs, especially small RNAs, play important roles in the expression of ''OsDRM2''. For instance, miR820 negatively regulates the expression of OsDRM2<ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. And expression levels of various TEs are increased quite sensitively in response to decreased OsDRM2 expression and DNA methylation at TE loci(Fig 6)<ref name="ref3" />. | ||
===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 | + | * 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 <ref name="ref2" />. ''OsDRM2'' is homologous to the Arabidopsis DRM2 gene. We can see the phylogeny of rice cytosine DNA MTases from Fig 7<ref name="ref6" />. | ||
| + | [[File:Fig.8 OsDRM2.JPG|right|thumb|327px|Fig.8 In vivo and in vitro interaction between OsDRM2 and OseIF4A.(From reference <ref name="ref7" />).'']] | ||
| + | ===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. | |
| − | 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 | + | * Interaction between Arabidopsis eIF4AI 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)<ref name="ref7" />. |
==Labs working on this gene== | ==Labs working on this gene== | ||
| − | + | *National Institute for Basic Biology, Okazaki 444-8585, Japan | |
| − | + | *Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, PR China | |
| − | + | *Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India | |
| − | + | *Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan | |
| − | + | *State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China | |
| − | + | *University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India | |
==References== | ==References== | ||
| − | + | <references> | |
| − | + | <ref name="ref1"> Moritoh, S., Eun, C. H., Ono, A., et al. (2012). Targeted disruption of an orthologue of DOMAINS REARRANGED METHYLASE 2, OsDRM2, impairs the growth of rice plants by abnormal DNA methylation. The Plant Journal, 71(1), 85-98. PMID 22380881</ref> | |
| − | + | <ref name="ref2">Pang, J., Dong, M., Li, N., et al. (2013). Functional characterization of a rice ''de novo'' DNA methyltransferase, ''OsDRM2'', expressed in ''Escherichia coli'' and yeast. Biochemical and biophysical research communications, 432(1), 157-162.PMID 23357425</ref> | |
| − | + | <ref name="ref3"> Nosaka, M., Itoh, J. I., Nagato, Y., et al. (2012). Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS genetics, 8(9), e1002953.PMID 23028360</ref> | |
| − | + | <ref name="ref4">Wei, L., Gu, L., Song, X., et al.. (2014). Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proceedings of the National Academy of Sciences, 111(10), 3877-3882.PMID 24554078</ref> | |
| − | + | <ref name="ref5"> Arikit, S., Zhai, J., & Meyers, B. C. (2013). Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current opinion in plant biology, 16(2), 170-179.PMID 23466255</ref> | |
| − | + | <ref name="ref6">Sharma, R., Mohan Singh, R. K., Malik, G., et al. (2009). Rice cytosine DNA methyltransferases–gene expression profiling during reproductive development and abiotic stress.FEBS journal, 276(21), 6301-6311.PMID 19788421</ref> | |
| + | <ref name="ref7">Dangwal, M., Malik, G., Kapoor, S., et al. (2013). ''De Novo'' Methyltransferase, OsDRM2, Interacts with the ATP-Dependent RNA Helicase, OseIF4A, in Rice. Journal of molecular biology, 425(16), 2853-2866.PMID 23732981</ref> | ||
| + | </references> | ||
==Structured Information== | ==Structured Information== | ||
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[[Category:Genes]] | [[Category:Genes]] | ||
[[Category:Japonica mRNA]] | [[Category:Japonica mRNA]] | ||
Latest revision as of 15:15, 13 February 2017
The rice Os03g0110800 was reported as DRM2 in 2012 [1] by researchers from Japan.
Contents
Annotated Information
Fig.1 Phenotype analyses of rice osdrm2 disruptants.(From reference [1]).
Gene Symbol
- Os03g0110800 <=> DRM2,osdrm2,OsDRM2
Function
- OsDRM2(Os03g0110800) is the major DRM1/2-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].
- 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].
- OsDRM2 is required not only for DNA methylation ofRIRE7/CRR1sequences and5S rDNA repeats, but also for transcriptional silencing of RIRE7/CRR1 retrotransposons(Fig 2)[1].
- Impaired growth and abnormal DNA methylation of osdrm2 disruptants were restored by the complementation of wild-type OsDRM2 cDNA(Fig 3)[1].
Fig.3 Complementation of the osdrm2 disruptants by ectopic expression of OsDRM2 cDNA.(From reference [1]).
Expression
- 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].
- 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 OsDRM2 protein 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].
- Non-coding RNAs, especially small RNAs, play important roles in the expression of OsDRM2. For instance, miR820 negatively regulates the expression of OsDRM2[3][4][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[6].
Fig.8 In vivo and in vitro interaction between OsDRM2 and OseIF4A.(From reference [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 Arabidopsis eIF4AI 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
- National Institute for Basic Biology, Okazaki 444-8585, Japan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, Jilin 130024, PR China
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
- Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, Sector 16C, Dwarka, New Delhi 110078, India
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Moritoh, S., Eun, C. H., Ono, A., et al. (2012). Targeted disruption of an orthologue of DOMAINS REARRANGED METHYLASE 2, OsDRM2, impairs the growth of rice plants by abnormal DNA methylation. The Plant Journal, 71(1), 85-98. PMID 22380881
- ↑ 2.0 2.1 Pang, J., Dong, M., Li, N., et al. (2013). Functional characterization of a rice de novo DNA methyltransferase, OsDRM2, expressed in Escherichia coli and yeast. Biochemical and biophysical research communications, 432(1), 157-162.PMID 23357425
- ↑ 3.0 3.1 Nosaka, M., Itoh, J. I., Nagato, Y., et al. (2012). Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS genetics, 8(9), e1002953.PMID 23028360
- ↑ Wei, L., Gu, L., Song, X., et al.. (2014). Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proceedings of the National Academy of Sciences, 111(10), 3877-3882.PMID 24554078
- ↑ Arikit, S., Zhai, J., & Meyers, B. C. (2013). Biogenesis and function of rice small RNAs from non-coding RNA precursors. Current opinion in plant biology, 16(2), 170-179.PMID 23466255
- ↑ Sharma, R., Mohan Singh, R. K., Malik, G., et al. (2009). Rice cytosine DNA methyltransferases–gene expression profiling during reproductive development and abiotic stress.FEBS journal, 276(21), 6301-6311.PMID 19788421
- ↑ 7.0 7.1 Dangwal, M., Malik, G., Kapoor, S., et al. (2013). De Novo Methyltransferase, OsDRM2, Interacts with the ATP-Dependent RNA Helicase, OseIF4A, in Rice. Journal of molecular biology, 425(16), 2853-2866.PMID 23732981
