title: Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes.
abstract: Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of ∼1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland, Vital-IT Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland and Laboratory of Particle Physics and Cosmology, Institute of Theoretical Physics, Ecole polytechnique fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland.
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Benedetti
authors.forename: Julien
authors.initials: J
authors.lastname: Dorier
authors.forename: Yannis
authors.initials: Y
authors.lastname: Burnier
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
mesh_terms: D002843:Chromatin / Q000737:chemistry*; D002875:Chromosomes / Q000737:chemistry*; D003198:Computer Simulation; D004278:DNA, Superhelical / Q000737:chemistry; D007399:Interphase / Q000235:genetics*; D008958:Models, Molecular
chemical_list: D002843:Chromatin; D004278:DNA, Superhelical