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| | ==Crystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region== | | ==Crystal structure of Arabidopsis IDN2 XS domain along with a small segment of adjacent coiled-coil region== |
| - | <StructureSection load='4e8u' size='340' side='right' caption='[[4e8u]], [[Resolution|resolution]] 2.70Å' scene=''> | + | <StructureSection load='4e8u' size='340' side='right'caption='[[4e8u]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4e8u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8U FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4e8u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8U FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.701Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IDN2, T8P19.180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4e8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8u OCA], [http://pdbe.org/4e8u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e8u RCSB], [http://www.ebi.ac.uk/pdbsum/4e8u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8u ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4e8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8u OCA], [https://pdbe.org/4e8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8u RCSB], [https://www.ebi.ac.uk/pdbsum/4e8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8u ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/IDN2_ARATH IDN2_ARATH] Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway (PubMed:22570638, PubMed:22592791) and downstream of small interfering RNA (siRNA) formation (PubMed:22810086). Required for de novo DNA methylation, siRNA accumulation and siRNA-mediated maintenance methylation (PubMed:19915591). Required for several post-transcriptional gene silencing pathways (PubMed:20059743). Binds double-stranded RNAs (dsRNAs) with 5'-overhangs through its XS domain (PubMed:19915591, PubMed:20059743). Binds long non-coding RNA (lncRNA) in an AGO4-dependent manner and associates with DRM2, resulting in DNA methylation of RdDM target loci (PubMed:23246435, PubMed:24862207). Mediates the silencing of a subset of MORC6 target loci (PubMed:27171427).<ref>PMID:19915591</ref> <ref>PMID:20059743</ref> <ref>PMID:22570638</ref> <ref>PMID:22592791</ref> <ref>PMID:22810086</ref> <ref>PMID:23246435</ref> <ref>PMID:24862207</ref> <ref>PMID:27171427</ref> |
| - | At least three pathways control maintenance of DNA cytosine methylation in Arabidopsis thaliana. However, the RNA-directed DNA methylation (RdDM) pathway is solely responsible for establishment of this silencing mark. We previously described INVOLVED IN DE NOVO 2 (IDN2) as being an RNA-binding RdDM component that is required for DNA methylation establishment. In this study, we describe the discovery of two partially redundant proteins that are paralogous to IDN2 and that form a stable complex with IDN2 in vivo. Null mutations in both genes, termed IDN2-LIKE 1 and IDN2-LIKE 2 (IDNL1 and IDNL2), result in a phenotype that mirrors, but does not further enhance, the idn2 mutant phenotype. Genetic analysis suggests that this complex acts in a step in the downstream portion of the RdDM pathway. We also have performed structural analysis showing that the IDN2 XS domain adopts an RNA recognition motif (RRM) fold. Finally, genome-wide DNA methylation and expression analysis confirms the placement of the IDN proteins in an RdDM pathway that affects DNA methylation and transcriptional control at many sites in the genome. Results from this study identify and describe two unique components of the RdDM machinery, adding to our understanding of DNA methylation control in the Arabidopsis genome.
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| - | | + | |
| - | INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis.,Ausin I, Greenberg MV, Simanshu DK, Hale CJ, Vashisht AA, Simon SA, Lee TF, Feng S, Espanola SD, Meyers BC, Wohlschlegel JA, Patel DJ, Jacobsen SE Proc Natl Acad Sci U S A. 2012 May 29;109(22):8374-81. Epub 2012 May 16. PMID:22592791<ref>PMID:22592791</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div> | + | |
| - | <div class="pdbe-citations 4e8u" style="background-color:#fffaf0;"></div> | + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Patel, D J]] | + | [[Category: Large Structures]] |
| - | [[Category: Simanshu, D K]] | + | [[Category: Patel DJ]] |
| - | [[Category: Rna]] | + | [[Category: Simanshu DK]] |
| - | [[Category: Rna binding protein]]
| + | |
| - | [[Category: Rna directed dna methylation]]
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| - | [[Category: Xs domain]]
| + | |
| Structural highlights
Function
IDN2_ARATH Forms a complex with FDM1/IDNL1 and FDM2/IDNL2 that is required for RNA-directed DNA methylation (RdDM) and that functions at a downstream step of the RdDM pathway (PubMed:22570638, PubMed:22592791) and downstream of small interfering RNA (siRNA) formation (PubMed:22810086). Required for de novo DNA methylation, siRNA accumulation and siRNA-mediated maintenance methylation (PubMed:19915591). Required for several post-transcriptional gene silencing pathways (PubMed:20059743). Binds double-stranded RNAs (dsRNAs) with 5'-overhangs through its XS domain (PubMed:19915591, PubMed:20059743). Binds long non-coding RNA (lncRNA) in an AGO4-dependent manner and associates with DRM2, resulting in DNA methylation of RdDM target loci (PubMed:23246435, PubMed:24862207). Mediates the silencing of a subset of MORC6 target loci (PubMed:27171427).[1] [2] [3] [4] [5] [6] [7] [8]
References
- ↑ Ausin I, Mockler TC, Chory J, Jacobsen SE. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat Struct Mol Biol. 2009 Dec;16(12):1325-7. doi: 10.1038/nsmb.1690. Epub 2009, Nov 15. PMID:19915591 doi:http://dx.doi.org/10.1038/nsmb.1690
- ↑ Zheng Z, Xing Y, He XJ, Li W, Hu Y, Yadav SK, Oh J, Zhu JK. An SGS3-like protein functions in RNA-directed DNA methylation and transcriptional gene silencing in Arabidopsis. Plant J. 2010 Apr 1;62(1):92-9. doi: 10.1111/j.1365-313X.2010.04130.x. Epub 2010 , Jan 6. PMID:20059743 doi:http://dx.doi.org/10.1111/j.1365-313X.2010.04130.x
- ↑ Zhang CJ, Ning YQ, Zhang SW, Chen Q, Shao CR, Guo YW, Zhou JX, Li L, Chen S, He XJ. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet. 2012;8(5):e1002693. doi: 10.1371/journal.pgen.1002693. Epub 2012 May , 3. PMID:22570638 doi:http://dx.doi.org/10.1371/journal.pgen.1002693
- ↑ Ausin I, Greenberg MV, Simanshu DK, Hale CJ, Vashisht AA, Simon SA, Lee TF, Feng S, Espanola SD, Meyers BC, Wohlschlegel JA, Patel DJ, Jacobsen SE. INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A. 2012 May 29;109(22):8374-81. Epub 2012 May 16. PMID:22592791 doi:10.1073/pnas.1206638109
- ↑ Finke A, Kuhlmann M, Mette MF. IDN2 has a role downstream of siRNA formation in RNA-directed DNA methylation. Epigenetics. 2012 Aug;7(8):950-60. doi: 10.4161/epi.21237. Epub 2012 Jul 19. PMID:22810086 doi:http://dx.doi.org/10.4161/epi.21237
- ↑ Zhu Y, Rowley MJ, Bohmdorfer G, Wierzbicki AT. A SWI/SNF chromatin-remodeling complex acts in noncoding RNA-mediated transcriptional silencing. Mol Cell. 2013 Jan 24;49(2):298-309. doi: 10.1016/j.molcel.2012.11.011. Epub 2012, Dec 13. PMID:23246435 doi:http://dx.doi.org/10.1016/j.molcel.2012.11.011
- ↑ Bohmdorfer G, Rowley MJ, Kucinski J, Zhu Y, Amies I, Wierzbicki AT. RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA. Plant J. 2014 Jul;79(2):181-91. doi: 10.1111/tpj.12563. Epub 2014 Jun 23. PMID:24862207 doi:http://dx.doi.org/10.1111/tpj.12563
- ↑ Liu ZW, Zhou JX, Huang HW, Li YQ, Shao CR, Li L, Cai T, Chen S, He XJ. Two Components of the RNA-Directed DNA Methylation Pathway Associate with MORC6 and Silence Loci Targeted by MORC6 in Arabidopsis. PLoS Genet. 2016 May 12;12(5):e1006026. doi: 10.1371/journal.pgen.1006026., eCollection 2016 May. PMID:27171427 doi:http://dx.doi.org/10.1371/journal.pgen.1006026
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