Integrative epigenomic mapping defines four main chromatin states in Arabidopsis
2011
Roudier, François | Ahmed, Ikhlak, I. | Berard, Caroline, C. | Sarazin, Alexis, A. | Mary-Huard, Tristan | Cortijo, Sandra, S. | Bouyer, Daniel, D. | Caillieux, Erwann, E. | Duvernois-Berthet, Evelyne, E. | Liza, Al-Shikhley, A.-S. | Giraut, Laurene, L. | Després, Barbara, B. | Drevensek, Stéphanie, S. | Barneche, Frédy, F. | Derozier, Sandra, S. | Brunaud, Veronique, V. | Aubourg, Sebastien, S. | Schnittger, Arp, A. | Bowler, Chris, C. | Magniette, Marie-Laure, M.-L. | Robin, Stephane, S. | Caboche, Michel, M. | Colot, Vincent, V. | Institut de biologie de l'ENS Paris (IBENS) ; Département de Biologie - ENS-PSL (IBENS) ; École normale supérieure - Paris (ENS-PSL) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS) | Mathématiques et Informatique Appliquées (MIA-Paris) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Institut de Biologie Moléculaire des Plantes (IBMP) ; Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS) | Institut Jean-Pierre Bourgin (IJPB) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Unité de recherche en génomique végétale (URGV) ; Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) | Unité Mathématique Informatique et Génome (MIG) ; Institut National de la Recherche Agronomique (INRA) | French National Research Agency (ANR) | European Commission
Italiano. 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 similar to 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.
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