title: How chromatin looping and nuclear envelope attachment affect genome organization in eukaryotic cell nuclei.
abstract: To understand how interphase chromatin is organized in eukaryotic cell nuclei, it is essential to understand what kind of interactions influence the nuclear architecture and to what extent. Using a mesoscale model that incorporates chromatin-chromatin interactions as well as binding of chromatin to the nuclear envelope, we can show that chromatin loops and envelope bonds are major players in genome organization because they largely affect the entropy of the chromatin fibres. The model allows us to consistently reproduce multiple characteristic chromatin parameters in agreement with experimental data. We focus on the question of how an inversion of the nuclear architecture, in the course of which the highly active euchromatin changes its preferential position from the nuclear center to the periphery, can be achieved. We find that the transition between the common and inverted organization is driven by the strength of the envelope interaction and the nuclear chromatin density.
authors.affiliation: Institute for Theoretical Physics, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany.
authors.forename: Hansjoerg
authors.initials: H
authors.lastname: Jerabek
authors.affiliation: Institute for Theoretical Physics, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg, Germany; The Jackson Laboratory, Bar Harbor, Maine, USA; Shanghai Center for Bioinformation Technology (SCBIT), Shanghai, PR China. Electronic address: heermann@tphys.uni-heidelberg.de.
authors.forename: Dieter W
authors.initials: DW
authors.lastname: Heermann
mesh_terms: D000818:Animals; D022041:Euchromatin / Q000378:metabolism*; D015894:Genome, Human / Q000502:physiology*; D006801:Humans; D008954:Models, Biological; D009685:Nuclear Envelope / Q000378:metabolism*
chemical_list: D022041:Euchromatin
keywords: Cell nucleus; Chromatin; Chromatin looping; Entropy; Monte-Carlo simulations; Nuclear envelope; Polymer models