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-MagnietteStéphane Robin, Michel Caboche, Vincent Colot

Research output: Contribution to journalArticle

366 Citations (Scopus)


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
Issue number10
Publication statusPublished - 18 May 2011
Externally publishedYes



  • 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., 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., ... Colot, V. (2011). Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO Journal, 30(10), 1928-1938.