title: SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.
abstract: DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: DNA methyltransferase1 (MET1), chromomethylase3 (CMT3), domains rearranged methyltransferase2 (DRM2), and chromomethylase2 (CMT2). However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as the endoribonucleases dicer-like 2, 3, and 4, and involved in de novo2 (IDN2) interactors IDN2-like 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, as the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we used coexpression data to identify closely related genes that are coregulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-ring-helicase-like1 and -2 (FRG1 and -2) that are putative chromatin modifiers belonging to the SNF2 family of helicase-like proteins. Analysis of genome-wide bisulfite sequencing shows that simultaneous mutations of FRG1 and -2 cause defects in methylation at specific RdDM targeted loci. We also show that FRG1 physically associates with Su(var)3-9-related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as previously unidentified components of the RdDM machinery.
authors.affiliation: Department of Molecular, Cell, and Developmental Biology.
authors.forename: Martin
authors.initials: M
authors.lastname: Groth
authors.affiliation: Department of Molecular, Cell, and Developmental Biology.
authors.forename: Hume
authors.initials: H
authors.lastname: Stroud
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095; and.
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.affiliation: Department of Molecular, Cell, and Developmental Biology.
authors.forename: Maxim V C
authors.initials: MV
authors.lastname: Greenberg
authors.affiliation: Department of Biological Chemistry, David Geffen School of Medicine.
authors.forename: Ajay A
authors.initials: AA
authors.lastname: Vashisht
authors.affiliation: Department of Biological Chemistry, David Geffen School of Medicine.
authors.forename: James A
authors.initials: JA
authors.lastname: Wohlschlegel
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095; and jacobsen@ucla.edu israel.ausin@gmail.com.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.affiliation: Basic Forestry and Biotechnology Center, Fujian Agriculture and Forestry University, Fujian, Fuzhou 350002, China jacobsen@ucla.edu israel.ausin@gmail.com.
authors.forename: Israel
authors.initials: I
authors.lastname: Ausin
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D002868:Chromosomal Proteins, Non-Histone / Q000378:metabolism*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D016296:Mutagenesis; D009154:Mutation; D034622:RNA Interference; D018749:RNA, Plant / Q000737:chemistry*; D034741:RNA, Small Interfering / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; C000597307:FRG1 protein, Arabidopsis; C000597308:FRG2 protein, Arabidopsis; D018749:RNA, Plant; D034741:RNA, Small Interfering; C515572:SUVR2 protein, Arabidopsis
keywords: epigenetic; plant