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Proc Natl Acad Sci U S A. 2011 May 10;108(19):7799-803. doi: 10.1073/pnas.1015206108. Epub 2011 Apr 25.

Nucleosome positioning in a model of active chromatin remodeling enzymes.

Author information

1
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

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.

PMID:
21518900
PMCID:
PMC3093463
DOI:
10.1073/pnas.1015206108
[Indexed for MEDLINE]
Free PMC Article

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