title: Nucleosome positioning in a model of active chromatin remodeling enzymes.
abstract: Accounting for enzyme-mediated active sliding, disassembly, and sequence-dependent positioning of nucleosomes, we simulate nucleosome occupancy over cell-cycle-scale times using a stochastic kinetic model. We show that ATP-dependent active nucleosome sliding and nucleosome removal processes are essential to obtain in vivo-like nucleosome positioning. While active sliding leads to dense nucleosome filling, sliding events alone cannot ensure sequence-dependent nucleosome positioning: Active nucleosome removal is the crucial remodeling event that drives positioning. We also show that remodeling activity changes nucleosome dynamics from glassy to liquid-like, and that remodeling dramatically influences exposure dynamics of promoter regions.
authors.affiliation: Department of Biosciences and Bioengineering and Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India. ranjithp@iitb.ac.in
authors.forename: Ranjith
authors.initials: R
authors.lastname: Padinhateeri
authors.forename: John F
authors.initials: JF
authors.lastname: Marko
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D055592:Biophysical Phenomena; D042002:Chromatin Assembly and Disassembly / Q000235:genetics / Q000502:physiology*; D015825:Chromosomes, Fungal / Q000235:genetics / Q000378:metabolism; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D007700:Kinetics; D008954:Models, Biological; D009068:Movement / Q000502:physiology; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D013269:Stochastic Processes
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D000255:Adenosine Triphosphate