title: Inter-chromosomal contact networks provide insights into Mammalian chromatin organization.
abstract: The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale investigation of the inter-chromosomal segment and gene contact networks in embryonic stem cells of two mammalian organisms: humans and mice. Both interaction networks are characterized by a high degree of clustering of genome regions and the existence of hubs. Both genomes exhibit similar structural characteristics such as increased flexibility of certain Y chromosome regions and co-localization of centromere-proximal regions. Spatial proximity is correlated with the functional similarity of genes in both species. We also found a significant association between spatial proximity and the co-expression of genes in the human genome. The structural properties of chromatin are also species specific, including the presence of two highly interactive regions in mouse chromatin and an increased contact density on short, gene-rich human chromosomes, thereby indicating their central nuclear position. Trans-interacting segments are enriched in active marks in human and had no distinct feature profile in mouse. Thus, in contrast to interactions within individual chromosomes, the inter-chromosomal interactions in human and mouse embryonic stem cells do not appear to be conserved.
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Kaufmann
authors.affiliation: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany; Technical University Munich, Institute for Mathematical Sciences, Garching, Germany.
authors.forename: Christiane
authors.initials: C
authors.lastname: Fuchs
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany; Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, Munich, Germany.
authors.forename: Mariya
authors.initials: M
authors.lastname: Gonik
authors.affiliation: Research and Training Center on Bioinformatics, Institute for Information Transmission Problems, RAS, Moscow, Russia.
authors.forename: Ekaterina E
authors.initials: EE
authors.lastname: Khrameeva
authors.affiliation: Department of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Mironov
authors.affiliation: Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, Freising, Germany; Institute for Bioinformatics and Systems Biology, HMGU German Research Center for Environmental Health, Neuherberg, Germany; Department of Bioinformatics, St Petersburg State Polytechnical University, St Petersburg, Russia.
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
mesh_terms: D000465:Algorithms; D000818:Animals; D002843:Chromatin / Q000235:genetics*; D033481:Chromosomes, Mammalian / Q000235:genetics*; D016000:Cluster Analysis; D053595:Embryonic Stem Cells; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D018740:Genetic Heterogeneity; D023281:Genomics / Q000379:methods; D006801:Humans; D051379:Mice; D008957:Models, Genetic; D005810:Multigene Family
chemical_list: D002843:Chromatin