title: A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis.
abstract: DNA methylation is an epigenetic modification associated with gene silencing. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which is targeted by small interfering RNAs through a pathway termed RNA-directed DNA methylation (RdDM). Recently, RdDM was shown to require intergenic noncoding (IGN) transcripts that are dependent on the Pol V polymerase. These transcripts are proposed to function as scaffolds for the recruitment of downstream RdDM proteins, including DRM2, to loci that produce both siRNAs and IGN transcripts. However, the mechanism(s) through which Pol V is targeted to specific genomic loci remains largely unknown. Through affinity purification of two known RdDM components, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) and DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), we found that they copurify with each other and with a novel protein, RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex we term DDR. We also found that DRD1 copurified with Pol V subunits and that RDM1, like DRD1 and DMS3, is required for the production of Pol V-dependent transcripts. These results suggest that the DDR complex acts in RdDM at a step upstream of the recruitment or activation of Pol V.
authors.affiliation: Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
authors.forename: Julie A
authors.initials: JA
authors.lastname: Law
authors.forename: Israel
authors.initials: I
authors.lastname: Ausin
authors.forename: Lianna M
authors.initials: LM
authors.lastname: Johnson
authors.forename: Ajay A
authors.initials: AA
authors.lastname: Vashisht
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
authors.forename: James A
authors.initials: JA
authors.lastname: Wohlschlegel
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D007527:Isoenzymes / Q000235:genetics / Q000378:metabolism; D013058:Mass Spectrometry; D030821:Plants, Genetically Modified; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D002868:Chromosomal Proteins, Non-Histone; C529025:DMS3 protein, Arabidopsis; D004268:DNA-Binding Proteins; D007527:Isoenzymes; C549271:RDM1 protein, Arabidopsis; D018749:RNA, Plant; D012321:DNA-Directed RNA Polymerases; C504888:DRD1 protein, Arabidopsis; D004259:DNA-Directed DNA Polymerase
references.citation: Nat Struct Mol Biol. 2009 Dec;16(12):1325-7
references.pmid: 19915591
references.citation: Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt 7):647-50
references.pmid: 16511118
references.citation: Nat Rev Genet. 2010 Mar;11(3):204-20
references.pmid: 20142834
references.citation: Plant J. 1998 Dec;16(6):735-43
references.pmid: 10069079
references.citation: J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89
references.pmid: 24226387
references.citation: Mol Cell. 2009 Jan 30;33(2):192-203
references.pmid: 19110459
references.citation: Genes Dev. 2005 Sep 1;19(17):2030-40
references.pmid: 16140984
references.citation: Nat Biotechnol. 2001 Mar;19(3):242-7
references.pmid: 11231557
references.citation: Curr Opin Cell Biol. 2009 Jun;21(3):367-76
references.pmid: 19243928
references.citation: PLoS Genet. 2008 Nov;4(11):e1000280
references.pmid: 19043555
references.citation: J Proteome Res. 2002 Jan-Feb;1(1):21-6
references.pmid: 12643522
references.citation: Genes Dev. 2009 Feb 1;23(3):318-30
references.pmid: 19204117
references.citation: Curr Biol. 2004 May 4;14(9):801-5
references.pmid: 15120073
references.citation: Nat Struct Mol Biol. 2009 Jan;16(1):91-3
references.pmid: 19079263
references.citation: Nat Genet. 2008 May;40(5):670-5
references.pmid: 18425128
references.citation: Plant J. 2006 Feb;45(4):616-29
references.pmid: 16441352
references.citation: J Mass Spectrom. 2001 Oct;36(10):1083-91
references.pmid: 11747101
references.citation: Nature. 2010 May 6;465(7294):106-9
references.pmid: 20410883
references.citation: Nat Genet. 2009 May;41(5):630-4
references.pmid: 19377477
references.citation: Methods. 2006 Dec;40(4):303-11
references.pmid: 17101441
references.citation: Cell. 2008 Nov 14;135(4):635-48
references.pmid: 19013275
references.citation: Methods Mol Biol. 2009;497:33-49
references.pmid: 19107409
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):941-6
references.pmid: 19141635