title: Gene-body chromatin modification dynamics mediate epigenome differentiation inArabidopsis.
abstract: Heterochromatin is marked by methylation of lysine 9 on histone H3 (H3K9me). A puzzling feature of H3K9me is that this modification localizes not only in promoters but also in internal regions (bodies) of silent transcription units. Despite its prevalence, the biological significance of gene-body H3K9me remains enigmatic. Here we show that H3K9me-associated removal of H3K4 monomethylation (H3K4me1) in gene bodies mediates transcriptional silencing. Mutations in anArabidopsisH3K9 demethylase geneIBM1induce ectopic H3K9me2 accumulation in gene bodies, with accompanying severe developmental defects. Through suppressor screening of theibm1-induced developmental defects, we identified theLDL2gene, which encodes a homolog of conserved H3K4 demethylases. Theldl2mutation suppressed the developmental defects, without suppressing theibm1-induced ectopic H3K9me2. The ectopic H3K9me2 mark directed removal of gene-body H3K4me1 and caused transcriptional repression in an LDL2-dependent manner. Furthermore, mutations of H3K9 methylases increased the level of H3K4me1 in the gene bodies of various transposable elements, and this H3K4me1 increase is a prerequisite for their transcriptional derepression. Our results uncover an unexpected role of gene-body H3K9me2/H3K4me1 dynamics as a mediator of heterochromatin silencing and epigenome differentiation.
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan soinagak@nig.ac.jp tkakutan@nig.ac.jp.|Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.
authors.forename: Soichi
authors.identifier: 0000-0003-4090-826X
authors.initials: S
authors.lastname: Inagaki
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Mayumi
authors.initials: M
authors.lastname: Takahashi
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan.|Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.
authors.forename: Aoi
authors.initials: A
authors.lastname: Hosaka
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan.|Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Tasuku
authors.initials: T
authors.lastname: Ito
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan.|Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Tarutani
authors.affiliation: National Institute of Genetics, Mishima, Shizuoka, Japan soinagak@nig.ac.jp tkakutan@nig.ac.jp.|Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.|Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
authors.forename: Tetsuji
authors.identifier: 0000-0002-6137-4474
authors.initials: T
authors.lastname: Kakutani
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D020868:Gene Silencing; D006570:Heterochromatin / Q000378:metabolism; D006657:Histones / Q000235:genetics; D056484:Jumonji Domain-Containing Histone Demethylases / Q000235:genetics / Q000378:metabolism; D008745:Methylation; D009154:Mutation; D011499:Protein Processing, Post-Translational
chemical_list: D029681:Arabidopsis Proteins; D006570:Heterochromatin; D006657:Histones; C526313:IBM1 protein, Arabidopsis; D056484:Jumonji Domain-Containing Histone Demethylases
keywords: gene body; heterochromatin; histone demethylase; histone methylation