title: The Functional Topography of the Arabidopsis Genome Is Organized in a Reduced Number of Linear Motifs of Chromatin States.
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.
authors.affiliation: Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Joana
authors.initials: J
authors.lastname: Sequeira-Mendes
authors.affiliation: Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Aragüez
authors.affiliation: Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Ramón
authors.initials: R
authors.lastname: Peiró
authors.affiliation: Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Raul
authors.initials: R
authors.lastname: Mendez-Giraldez
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, California 90095.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California, Los Angeles, California 90095.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.affiliation: Bioinformatics Unit, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain.
authors.forename: Ugo
authors.initials: U
authors.lastname: Bastolla
authors.affiliation: Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, 28049 Madrid, Spain cgutierrez@cbm.csic.es.
authors.forename: Crisanto
authors.initials: C
authors.lastname: Gutierrez