The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States  . Issue 6 (16th June 2014)

• Record Type: Journal Article
• Authors: Sequeira-Mendes, Joana; Aragüez, Irene; Peiró, Ramón; Mendez-Giraldez, Raul; Zhang, Xiaoyu; Jacobsen, Steven E.; Bastolla, Ugo; Gutierrez, Crisanto
• Is Part Of: The Plant Cell. Volume 26:Issue 6(2014)
• Page Start: 2351
• Page End: 2366
• Publication Date: 2014-06-16
• DOI: 10.1105/tpc.114.124578
• Languages: English
• ISSNs: 1040-4651

Abstract

Abstract : A computational study of combinations of histone modifications and DNA features was developed to determine a high-resolution landscape of Arabidopsis chromatin states. The linear topography across the genome revealed the existence of chromatin motifs. This work provides a basis for studies on gene expression, e.g., bivalent H3K27me3/H3K4me3-containing regions, DNA replication, and epigenetics. Abstract: Chromatin is of major relevance for gene expression, cell division, and differentiation. Here, we determined the landscape of Arabidopsis thaliana chromatin states using 16 features, including DNA sequence, CG methylation, histone variants, and modifications. The combinatorial complexity of chromatin can be reduced to nine states that describe chromatin with high resolution and robustness. Each chromatin state has a strong propensity to associate with a subset of other states defining a discrete number of chromatin motifs. These topographical relationships revealed that an intergenic state, characterized by H3K27me3 and slightly enriched in activation marks, physically separates the canonical Polycomb chromatin and two heterochromatin states from the rest of the euchromatin domains. Genomic elements are distinguished by specific chromatin states: four states span genes from transcriptional start sites (TSS ) to termination sites and two contain regulatory regions upstream of TSS . Polycomb regions and the rest of the euchromatin can be connected by two major chromatin paths. Sequential chromatin immunoprecipitation experiments demonstrated the occurrence of H3K27me3 and H3K4me3 in the same chromatin fiber, within a two to three nucleosome size range. Our data provide insight into the Arabidopsis genome topography and the establishment of gene expression patterns, specification of DNA replication origins, and definition of chromatin domains.