Integrative epigenomic mapping defines four main chromatin states in Arabidopsis


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.

DOI: 10.1038/emboj.2011.103

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@inproceedings{Roudier2011IntegrativeEM, title={Integrative epigenomic mapping defines four main chromatin states in Arabidopsis}, author={François 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{\`e}ne Giraut and B. Despres 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 Marie-Laure Martin-Magniette and St{\'e}phane Robin and Michel Caboche and Vincent Colot}, booktitle={The EMBO journal}, year={2011} }