Integrative epigenomic mapping defines four main chromatin states in Arabidopsis
By F. Roudier, Ikhlak Ahmed, Caroline Bérard, A. Sarazin, T. Mary-Huard, S. Cortijo, D. Bouyer, E. Caillieux, Evelyne Duvernois-Berthet, Liza Al-Shikhley and 13 more. EMBO Journal, 2011
683 citations recorded by the source corpus.
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.
View Paper: https://www.semanticscholar.org/paper/93e26f7d1ff274e6178b690c3c089b3c32b90d2c
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Citations in the corpus
- Regulation of nucleosome dynamics by histone modifications (2013, unknown): “…advent of genome-wide chromatin immunoprecipitation (ChIP)-based techniques such as ChIP with tiled microarray analysis (ChIP-chip) or high-throughput sequencing (ChIP-seq), mapping of global patterns of histone modifications has become commonplace and has been performed in many organisms 7–11 .”
- Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact (2012, unknown): “For example, different computational approaches have led to the determination of anywhere from four states inArabidopsis (Roudier et al., 2011) to 5–9 states in Drosophila (Kharchenko et al., 2011; Riddle et al., 2011) to up to 51 states in human cells (Ernst and Kellis, 2010).”
- Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome (2013, unknown): “Histone Modification Data Previously published histone ChIP data (Bernatavichute et al., 2008; Roudier et al., 2011; Zhang et al., 2009) were used for analyses.”
- Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, unknown): “Metal concentrations were measured by using inductively coupled plasma optical emission spectrometry SPS3000 (Seiko, Tokyo, Japan).”
- The nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin (2013, background): “The properties of nucleosomes in euchromatic genes do differ from those of heterochromatic TEs, as exemplified by different sets of posttranslational histone modifications (Roudier et al., 2011).”