A statistical model of intra-chromosome contact maps.

A statistical model describing a fine structure of the intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) is proposed. The model combines hierarchical chain folding with a quenched heteropolymer structure of primary chromatin sequences. It is conjectured that the observed Hi-C maps are statistical averages over many different ways of hierarchical genome folding. It is shown that the existence of a quenched primary structure coupled with hierarchical folding induces a full range of features observed in experimental Hi-C maps: hierarchical elements, chess-board intermittency and large-scale compartmentalization.

[1]  L. Landau,et al.  statistical-physics-part-1 , 1958 .

[2]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[3]  L. Mirny,et al.  High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome , 2013, Science.

[4]  A. Tanay,et al.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture , 2011, Nature Genetics.

[5]  Mario Nicodemi,et al.  Complexity of chromatin folding is captured by the strings and binders switch model , 2012, Proceedings of the National Academy of Sciences.

[6]  Romain Koszul,et al.  Normalization of a chromosomal contact map , 2012, BMC Genomics.

[7]  D. Heermann,et al.  Spatially confined folding of chromatin in the interphase nucleus , 2009, Proceedings of the National Academy of Sciences.

[8]  G van den Engh,et al.  A random-walk/giant-loop model for interphase chromosomes. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Ralf Everaers,et al.  Ring polymers in the melt state: the physics of crumpling. , 2013, Physical review letters.

[10]  Shaheynoor Talukder,et al.  Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo , 2010, The EMBO journal.

[11]  Michael S. Becker,et al.  Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations , 2012, Cell.

[12]  Nature Genetics , 1991, Nature.

[13]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[14]  L. Mirny,et al.  Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data , 2013, Nature Reviews Genetics.

[15]  Kurt Kremer,et al.  From a melt of rings to chromosome territories: the role of topological constraints in genome folding , 2013, Reports on progress in physics. Physical Society.

[16]  Christian Münkel,et al.  Chromosome structure predicted by a polymer model , 1998 .

[17]  Eugene I. Shakhnovich,et al.  Frozen states of a disordered globular heteropolymer , 1989 .

[18]  L. Mirny,et al.  Effects of topological constraints on globular polymers. , 2014, Soft matter.

[19]  G. Schroth,et al.  Cohesin-mediated interactions organize chromosomal domain architecture , 2013, The EMBO journal.

[20]  A. Grosberg.  Annealed lattice animal model and Flory theory for the melt of non-concatenated rings: towards the physics of crumpling. , 2013, Soft matter.

[21]  Shakhnovich,et al.  Phase diagram of random copolymers. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[22]  E. Shakhnovich,et al.  The role of topological constraints in the kinetics of collapse of macromolecules , 1988 .

[23]  L. Mirny.  The fractal globule as a model of chromatin architecture in the cell , 2011, Chromosome Research.

[24]  Kurt Kremer,et al.  Molecular dynamics simulation study of nonconcatenated ring polymers in a melt. II. Dynamics. , 2011, The Journal of chemical physics.

[25]  Guillaume J. Filion,et al.  Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells , 2010, Cell.

[26]  R. Rosenfeld.  Nature , 2009, Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery.

[27]  Lattice animal model of chromosome organization. , 2012, Physical review. E, Statistical, nonlinear, and soft matter physics.

[28]  J. Langowski,et al.  Chromosome dynamics, molecular crowding, and diffusion in the interphase cell nucleus: a Monte Carlo lattice simulation study , 2010, Chromosome Research.

[29]  Ralf Everaers,et al.  Structure and Dynamics of Interphase Chromosomes , 2008, PLoS Comput. Biol..

[30]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[31]  A. Tanay,et al.  Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome , 2012, Cell.

[32]  J. Ostashevsky.  A polymer model for the structural organization of chromatin loops and minibands in interphase chromosomes. , 1998, Molecular biology of the cell.

[33]  A. Scialdone,et al.  Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus , 2013 .

[34]  Shlomo Havlin,et al.  Crumpled globule model of the three-dimensional structure of DNA , 1993 .