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The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

ABSTRACT: Chromatin is of major relevance for gene expression, cell division and differentiation, among other processes. Here we have used 16 chromatin features, including DNA sequence, CG methylation, histone modifications and variants, to obtain a high-resolution landscape of the Arabidopsis chromatin states. The combinatorial complexity of chromatin features can be reduced to 9 states defined by their distinct signatures. These chromatin states preferentially associate with certain genomic elements, gene expression levels, and DNase I accessibility. Each chromatin state has strong propensity to associate with only a subset of other states defining a small number of chromatin motifs. These topographical relationships revealed that Polycomb chromatin physically separates the two heterochromatin states from active chromatin domains. Two paths that mainly differ in their GC content and gene density join active and Polycomb chromatin. The remaining states are associated with active genes: four of them spanning gene bodies and two located upstream of transcription start sites. Our data provide a ground for better understanding the Arabidopsis genome topography and for obtaining new insights into establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE54489 | GEO | 2014/06/01

SECONDARY ACCESSION(S): PRJNA236623

REPOSITORIES: GEO

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The Functional Topography of the Arabidopsis Genome is Defined by Nine Chromatin States that Associate in a Small Number of Motifs

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