title: Autocatalytic differentiation of epigenetic modifications within the Arabidopsis genome.
abstract: In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Although selective H3K9me is critical for maintaining genome integrity, mechanisms to exclude H3K9me from active genes remain largely unexplored. Here, we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation). Loss-of-function ibm1 mutation results in ectopic H3K9me and non-CG methylation in thousands of genes. The ibm1-induced genic H3K9me depends on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks--H3K9me and non-CG methylation. Notably, IBM1 enhances loss of H3K9me in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induces ectopic non-CG methylation, which mimics the loss of IBM1 function. We propose that active chromatin is stabilized by an autocatalytic loop of transcription and H3K9 demethylation. This process counteracts a similarly autocatalytic accumulation of silent epigenetic marks, H3K9me and non-CG methylation.
authors.affiliation: Department of Integrated Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Soichi
authors.initials: S
authors.lastname: Inagaki
authors.forename: Asuka
authors.initials: A
authors.lastname: Miura-Kamio
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Falong
authors.initials: F
authors.lastname: Lu
authors.forename: Xia
authors.initials: X
authors.lastname: Cui
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Cao
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kimura
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Saze
authors.forename: Tetsuji
authors.initials: T
authors.lastname: Kakutani
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D056466:Histone Demethylases / Q000235:genetics* / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism; D056484:Jumonji Domain-Containing Histone Demethylases; D009154:Mutation; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; D006657:Histones; D056466:Histone Demethylases; C526313:IBM1 protein, Arabidopsis; D056484:Jumonji Domain-Containing Histone Demethylases