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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.

SUBMITTER: Padinhateeri R 

PROVIDER: S-EPMC3093463 | biostudies-other | 2011 May

REPOSITORIES: biostudies-other

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Nucleosome positioning in a model of active chromatin remodeling enzymes.

Padinhateeri Ranjith R   Marko John F JF  

Proceedings of the National Academy of Sciences of the United States of America 20110425 19

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 nucleo  ...[more]