title: Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.
abstract: The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
authors.forename: Congmao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; chang.liu@tuebingen.mpg.de weigel@weigelworld.org.
authors.forename: Chang
authors.initials: C
authors.lastname: Liu
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany.
authors.forename: Damian
authors.initials: D
authors.lastname: Roqueiro
authors.affiliation: Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany.
authors.forename: Dominik
authors.initials: D
authors.lastname: Grimm
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
authors.forename: Rebecca
authors.initials: R
authors.lastname: Schwab
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
authors.forename: Claude
authors.initials: C
authors.lastname: Becker
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
authors.forename: Christa
authors.initials: C
authors.lastname: Lanz
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; chang.liu@tuebingen.mpg.de weigel@weigelworld.org.
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism*; D042002:Chromatin Assembly and Disassembly; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D044127:Epigenesis, Genetic; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D006657:Histones / Q000378:metabolism; D038101:Insulator Elements
chemical_list: D002843:Chromatin; D006657:Histones