Nucleosome positioning in a model of active chromatin remodeling enzymes

Ranjith Padinhateeri*, John F. Marko

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)7799-7803
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume108
Issue number19
DOIs
StatePublished - May 10 2011

Keywords

  • ATP-dependent nucleosome removal
  • ATP-dependent nucleosome sliding
  • Chromatin dynamics
  • Protein-DNA interactions

ASJC Scopus subject areas

  • General

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