Os03g0110800 - Revision history

Xysj2017 at 15:15, 13 February 2017

2017-02-13T15:15:29Z

Xysj2017: /* Knowledge Extension */

2017-02-13T15:13:42Z

‎Knowledge Extension

Xysj2017 at 15:13, 13 February 2017

2017-02-13T15:13:18Z

Xysj2017: /* Annotated Information */

2017-02-13T15:11:38Z

‎Annotated Information

Xysj2017: /* Annotated Information */

2017-02-13T15:10:54Z

‎Annotated Information

Xysj2017 at 15:09, 13 February 2017

2017-02-13T15:09:59Z

Xysj2017 at 15:08, 13 February 2017

2017-02-13T15:08:48Z

Rice2012: /* Structured Information */

2015-06-12T04:57:12Z

‎Structured Information

Gaowei1160: /* Annotated Information */

2014-05-21T14:17:01Z

‎Annotated Information

Gaowei1160: /* Knowledge Extension */

2014-05-18T14:55:01Z

‎Knowledge Extension

← Older revision		Revision as of 15:15, 13 February 2017
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−	~~OsDRM2(~~Os03g0110800~~) is the major DRM1~~/~~2-type methyltransferase gene in rice~~.	+	The rice '''''Os03g0110800''''' was reported as '''''DRM2''''' in 2012 <ref name="ref1" /> by researchers from Japan.

	==Annotated Information==		==Annotated Information==

@@ Line 26: / Line 26: @@
 ===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)<ref name="ref7" />.
+* 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.
 ==Labs working on this gene==

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 [[File:Fig.1 OsDRM2.png|right|thumb|327px|Fig.1 Phenotype analyses of rice osdrm2 disruptants.(From reference <ref name="ref1" />).'']]
 ===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<ref name="ref1" />.
@@ Line 9: / Line 11: @@
 * 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|left|thumb|327px|Fig.3  Complementation of the  osdrm2 disruptants by ectopic expression of OsDRM2 cDNA.(From reference <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===
@@ Line 21: / Line 23: @@
 * 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" />.
 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)<ref name="ref7" />.

@@ Line 2: / Line 2: @@
 ==Annotated Information==
 ===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<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" />.
@@ Line 9: / Line 9: @@
 * 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|left|thumb|327px|Fig.3  Complementation of the  osdrm2 disruptants by ectopic expression of OsDRM2 cDNA.(From reference <ref name="ref1" />).'']]
 ===Expression===
@@ Line 24: / Line 23: @@
 ===Knowledge Extension===
-[[File:Fig.8 OsDRM2.JPG|right|thumb|250px|Fig.8 In vivo and in vitro interaction between OsDRM2 and OseIF4A.(From reference <ref name="ref7" />).'']]
+[[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" />).'']]
 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)<ref name="ref7" />.

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===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<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" />.
+[[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===

@@ Line 3: / Line 3: @@
 ==Annotated Information==
 ===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<ref name="ref1" />.
+*''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" />.
@@ Line 11: / Line 11: @@
 . 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.1 OsDRM2.png|right|thumb|250px|Fig.1 Phenotype analyses of rice osdrm2 disruptants.(From reference <ref name="ref1" />).'']]
-[[File:Fig.2 OsDRM2.png|right|thumb|250px|Fig.2 Expression of  RIRE7/CRR1 retrotransposons and DNA methylation status of repetitive sequences in osdrm2 disruptants.(From reference <ref name="ref1" />).'']]
 [[File:Fig.3 OsDRM2.png|right|thumb|250px|Fig.3  Complementation of the  osdrm2 disruptants by ectopic expression of OsDRM2 cDNA.(From reference <ref name="ref1" />).'']]
 ===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" />.
+* 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" />.
+* 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" />.
+* 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===
-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" />.
+* 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.
-[[File:Fig.7 OsDRM2.png|right|thumb|250px|Fig.7 Phylogeny of rice cytosine DNA MTases. (From reference <ref name="ref6" />).'']]
+* 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" />.
 ===Knowledge Extension===

← Older revision		Revision as of 15:08, 13 February 2017
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	3. 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" />.		3. 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" />.
−	~~[[File:Fig.4 OsDRM2.png\|right\|thumb\|250px\|Fig.4 RT-PCR expression analysis of OsDRM genes in rice. (From reference <ref name="ref1" />).'']]~~
−	~~[[File:Fig.5 OsDRM2.JPG\|right\|thumb\|250px\|Fig.5 MSAP analysis of genomic DNA from pBOsDRM2-transformed S. cerevisiae.(From reference <ref name="ref2" />).'']]~~
−	~~[[File:Fig.6 OsDRM2.png\|right\|thumb\|250px\|Fig.6 OsDRM2 is negatively regulated by miR820.(From reference <ref name="ref3" />).'']]~~

	===Evolution===		===Evolution===

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 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]