title: Arabidopsis VIM proteins regulate epigenetic silencing by modulating DNA methylation and histone modification in cooperation with MET1.
abstract: Methylcytosine-binding proteins containing SRA (SET- and RING-Associated) domain are required for the establishment and/or maintenance of DNA methylation in both plants and animals. We previously proposed that Arabidopsis VIM/ORTH proteins with an SRA domain maintain DNA methylation and epigenetic gene silencing in heterochromatic regions. However, their endogenous targets of epigenetic gene silencing have not been analyzed globally and the mechanisms by which VIM proteins coordinate DNA methylation and epigenetic silencing are largely unknown. In this study, a genome-wide transcript profiling analysis revealed 544 derepressed genes in a vim1/2/3 triple mutant, including 133 known genes. VIM1 bound to promoter and transcribed regions of the up-regulated genes in vim1/2/3 and VIM deficiency caused severe DNA hypomethylation in all sequence contexts at direct VIM1 targets. We found a drastic loss of H3K9me2 at heterochromatic chromocenters in vim1/2/3 nuclei. Furthermore, aberrant changes in transcriptionally active and repressive histone modifications were observed at VIM1 targets in vim1/2/3. VIM1-binding capacity to target genes was significantly reduced in the met1 background, indicating that VIM1 primarily recognizes CG methylation deposited by MET1. Overall, our data indicate that VIM proteins regulate genome-wide epigenetic gene silencing through coordinated modulation of DNA methylation and histone modification status in collaboration with MET1.
authors.affiliation: Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 711-873, Republic of Korea.
authors.forename: Jeongsik
authors.initials: J
authors.lastname: Kim
authors.affiliation: Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 711-873, Republic of Korea.
authors.forename: Jin Hee
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Richards
authors.affiliation: Department of Microbiology and Immunology, Chonbuk National University Medical School, Jeonju, Jeollabuk-do 561-180, Republic of Korea; Institute for Medical Science, Chonbuk National University Medical School, Jeonju, Jeollabuk-do 561-180, Republic of Korea. Electronic address: kmin@jbnu.ac.kr.
authors.forename: Kyung Min
authors.initials: KM
authors.lastname: Chung
authors.affiliation: Department of New Biology, DGIST, Daegu 711-873, Republic of Korea. Electronic address: hrwoo@dgist.ac.kr.
authors.forename: Hye Ryun
authors.initials: HR
authors.lastname: Woo
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism*; D019175:DNA Methylation; D020868:Gene Silencing; D056426:Genetic Loci / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D006570:Heterochromatin / Q000235:genetics; D006657:Histones / Q000378:metabolism; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D006570:Heterochromatin; D006657:Histones; C499608:MET1 protein, Arabidopsis; D004248:DNA (Cytosine-5-)-Methyltransferases
keywords: DNA methylation; MET1; SRA; VIM/ORTH; epigenetic silencing; histone modification.