Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

Fraņois Roudier, Ikhlak Ahmed, Caroline Bérard, Alexis Sarazin, Tristan Mary-Huard, Sandra Cortijo, Daniel Bouyer, Erwann Caillieux, Evelyne Duvernois-Berthet, Liza Al-Shikhley, Lauráne Giraut, Barbara Desprás, Stéphanie Drevensek, Frédy Barneche, Sandra Dérozier, Véronique Brunaud, Sébastien Aubourg, Arp Schnittger, Chris Bowler, Marie Laure Martin-Magniette & 3 others Stéphane Robin, Michel Caboche, Vincent Colot

Research output: Contribution to journalArticle

355 Citations (Scopus)

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 -490% 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.

Original languageEnglish
Pages (from-to)1928-1938
Number of pages11
JournalEMBO Journal
Volume30
Issue number10
DOIs
Publication statusPublished - 18 May 2011
Externally publishedYes

Fingerprint

Arabidopsis
Epigenomics
Chromatin
Genes
Genome
DNA Methylation
Histones
Histone Code
Intergenic DNA
Level control
Post Translational Protein Processing
Eukaryota

Keywords

  • Arabidopsis
  • chromatin
  • DNA methylation
  • epigenome
  • histone modifications

ASJC Scopus subject areas

  • Neuroscience(all)
  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Roudier, F., Ahmed, I., Bérard, C., Sarazin, A., Mary-Huard, T., Cortijo, S., ... Colot, V. (2011). Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO Journal, 30(10), 1928-1938. https://doi.org/10.1038/emboj.2011.103

Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. / Roudier, Fraņois; Ahmed, Ikhlak; Bérard, Caroline; Sarazin, Alexis; Mary-Huard, Tristan; Cortijo, Sandra; Bouyer, Daniel; Caillieux, Erwann; Duvernois-Berthet, Evelyne; Al-Shikhley, Liza; Giraut, Lauráne; Desprás, Barbara; Drevensek, Stéphanie; Barneche, Frédy; Dérozier, Sandra; Brunaud, Véronique; Aubourg, Sébastien; Schnittger, Arp; Bowler, Chris; Martin-Magniette, Marie Laure; Robin, Stéphane; Caboche, Michel; Colot, Vincent.

In: EMBO Journal, Vol. 30, No. 10, 18.05.2011, p. 1928-1938.

Research output: Contribution to journalArticle

Roudier, F, Ahmed, I, Bérard, C, Sarazin, A, Mary-Huard, T, Cortijo, S, Bouyer, D, Caillieux, E, Duvernois-Berthet, E, Al-Shikhley, L, Giraut, L, Desprás, B, Drevensek, S, Barneche, F, Dérozier, S, Brunaud, V, Aubourg, S, Schnittger, A, Bowler, C, Martin-Magniette, ML, Robin, S, Caboche, M & Colot, V 2011, 'Integrative epigenomic mapping defines four main chromatin states in Arabidopsis', EMBO Journal, vol. 30, no. 10, pp. 1928-1938. https://doi.org/10.1038/emboj.2011.103
Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S et al. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO Journal. 2011 May 18;30(10):1928-1938. https://doi.org/10.1038/emboj.2011.103
Roudier, Fraņois ; Ahmed, Ikhlak ; Bérard, Caroline ; Sarazin, Alexis ; Mary-Huard, Tristan ; Cortijo, Sandra ; Bouyer, Daniel ; Caillieux, Erwann ; Duvernois-Berthet, Evelyne ; Al-Shikhley, Liza ; Giraut, Lauráne ; Desprás, Barbara ; Drevensek, Stéphanie ; Barneche, Frédy ; Dérozier, Sandra ; Brunaud, Véronique ; Aubourg, Sébastien ; Schnittger, Arp ; Bowler, Chris ; Martin-Magniette, Marie Laure ; Robin, Stéphane ; Caboche, Michel ; Colot, Vincent. / Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. In: EMBO Journal. 2011 ; Vol. 30, No. 10. pp. 1928-1938.
@article{bf4db45f0ff646a3b3782374b0aa9477,
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 -490{\%} 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.",
keywords = "Arabidopsis, chromatin, DNA methylation, epigenome, histone modifications",
author = "Fraņois Roudier and Ikhlak Ahmed and Caroline B{\'e}rard and Alexis Sarazin and Tristan Mary-Huard and Sandra Cortijo and Daniel Bouyer and Erwann Caillieux and Evelyne Duvernois-Berthet and Liza Al-Shikhley and Laur{\'a}ne Giraut and Barbara Despr{\'a}s and St{\'e}phanie Drevensek and Fr{\'e}dy Barneche and Sandra D{\'e}rozier and V{\'e}ronique Brunaud and S{\'e}bastien Aubourg and Arp Schnittger and Chris Bowler and Martin-Magniette, {Marie Laure} and St{\'e}phane Robin and Michel Caboche and Vincent Colot",
year = "2011",
month = "5",
day = "18",
doi = "10.1038/emboj.2011.103",
language = "English",
volume = "30",
pages = "1928--1938",
journal = "EMBO Journal",
issn = "0261-4189",
publisher = "Nature Publishing Group",
number = "10",

}

TY - JOUR

T1 - Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

AU - Roudier, Fraņois

AU - Ahmed, Ikhlak

AU - Bérard, Caroline

AU - Sarazin, Alexis

AU - Mary-Huard, Tristan

AU - Cortijo, Sandra

AU - Bouyer, Daniel

AU - Caillieux, Erwann

AU - Duvernois-Berthet, Evelyne

AU - Al-Shikhley, Liza

AU - Giraut, Lauráne

AU - Desprás, Barbara

AU - Drevensek, Stéphanie

AU - Barneche, Frédy

AU - Dérozier, Sandra

AU - Brunaud, Véronique

AU - Aubourg, Sébastien

AU - Schnittger, Arp

AU - Bowler, Chris

AU - Martin-Magniette, Marie Laure

AU - Robin, Stéphane

AU - Caboche, Michel

AU - Colot, Vincent

PY - 2011/5/18

Y1 - 2011/5/18

N2 - 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 -490% 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.

AB - 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 -490% 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.

KW - Arabidopsis

KW - chromatin

KW - DNA methylation

KW - epigenome

KW - histone modifications

UR - http://www.scopus.com/inward/record.url?scp=79956066320&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79956066320&partnerID=8YFLogxK

U2 - 10.1038/emboj.2011.103

DO - 10.1038/emboj.2011.103

M3 - Article

VL - 30

SP - 1928

EP - 1938

JO - EMBO Journal

JF - EMBO Journal

SN - 0261-4189

IS - 10

ER -