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Arabidopsis VIM Proteins Regulate Epigenetic Silencing by Modulating DNA Methylation and Histone Modification in Cooperation with MET1

Arabidopsis VIM Proteins Regulate Epigenetic Silencing by Modulating DNA Methylation and Histone Modification in Cooperation with MET1
Kim, JeongsikKim, Jin HeeRichards, Eric J.Chung, Kyung MinWoo, Hye Ryun
DGIST Authors
Kim, Jeongsik; Kim, Jin Hee; Woo, Hye Ryun
Issue Date
Molecular Plant, 7(9), 1470-1485
Article Type
AnimaliaArabidopsisArabidopsis ProteinArabidopsis ProteinsDNA (Cytosine-5-)-MethyltransferaseDNA MethylationEpigenetic SilencingGene LocusGene SilencingGenetic LociGenetic TranscriptionGeneticsGenome, PlantHeterochromatinHistoneHistone ModificationHistonesMET1MET1 Protein, ArabidopsisMetabolismMutationPlant GenomePromoter RegionPromoter Regions, GeneticSRATranscription, GeneticVIM/ORTH
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. © 2014 The Authors. All rights reserved.
Cell Press
Related Researcher
  • Author Woo, Hye Ryun CBRG(Complex Biology Research Group)
  • Research Interests Genome biology ;Epigenomics ; Plant senescence
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Department of New BiologyCBRG(Complex Biology Research Group)1. Journal Articles

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