title: Integrative epigenomic mapping defines four main chromatin states in Arabidopsis.
abstract: Post-translational modification of histones and DNA methylation are important components of chromatin-level control of genome activity in eukaryotes. However, principles governing the combinatorial association of chromatin marks along the genome remain poorly understood. Here, we have generated epigenomic maps for eight histone modifications (H3K4me2 and 3, H3K27me1 and 2, H3K36me3, H3K56ac, H4K20me1 and H2Bub) in the model plant Arabidopsis and we have combined these maps with others, produced under identical conditions, for H3K9me2, H3K9me3, H3K27me3 and DNA methylation. Integrative analysis indicates that these 12 chromatin marks, which collectively cover ∼90% of the genome, are present at any given position in a very limited number of combinations. Moreover, we show that the distribution of the 12 marks along the genomic sequence defines four main chromatin states, which preferentially index active genes, repressed genes, silent repeat elements and intergenic regions. Given the compact nature of the Arabidopsis genome, these four indexing states typically translate into short chromatin domains interspersed with each other. This first combinatorial view of the Arabidopsis epigenome points to simple principles of organization as in metazoans and provides a framework for further studies of chromatin-based regulatory mechanisms in plants.
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS) UMR8197, Institut National de la Santé et de la Recherche Médicale (INSERM) U1024, Paris, France. roudier@biologie.ens.fr
authors.forename: François
authors.initials: F
authors.lastname: Roudier
authors.forename: Ikhlak
authors.initials: I
authors.lastname: Ahmed
authors.forename: Caroline
authors.initials: C
authors.lastname: Bérard
authors.forename: Alexis
authors.initials: A
authors.lastname: Sarazin
authors.forename: Tristan
authors.initials: T
authors.lastname: Mary-Huard
authors.forename: Sandra
authors.initials: S
authors.lastname: Cortijo
authors.forename: Daniel
authors.initials: D
authors.lastname: Bouyer
authors.forename: Erwann
authors.initials: E
authors.lastname: Caillieux
authors.forename: Evelyne
authors.initials: E
authors.lastname: Duvernois-Berthet
authors.forename: Liza
authors.initials: L
authors.lastname: Al-Shikhley
authors.forename: Laurène
authors.initials: L
authors.lastname: Giraut
authors.forename: Barbara
authors.initials: B
authors.lastname: Després
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Drevensek
authors.forename: Frédy
authors.initials: F
authors.lastname: Barneche
authors.forename: Sandra
authors.initials: S
authors.lastname: Dèrozier
authors.forename: Véronique
authors.initials: V
authors.lastname: Brunaud
authors.forename: Sébastien
authors.initials: S
authors.lastname: Aubourg
authors.forename: Arp
authors.initials: A
authors.lastname: Schnittger
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Martin-Magniette
authors.forename: Stéphane
authors.initials: S
authors.lastname: Robin
authors.forename: Michel
authors.initials: M
authors.lastname: Caboche
authors.forename: Vincent
authors.initials: V
authors.lastname: Colot
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000502:physiology*; D029681:Arabidopsis Proteins / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism*; D002875:Chromosomes / Q000378:metabolism; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D006657:Histones / Q000378:metabolism; D011499:Protein Processing, Post-Translational
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D006657:Histones