Theory of Active Chromatin Remodeling

Zhongling Jiang and Bin Zhang
Phys. Rev. Lett. 123, 208102 – Published 13 November 2019
PDFHTMLExport Citation

Abstract

Nucleosome positioning controls the accessible regions of chromatin and plays essential roles in DNA-templated processes. ATP driven remodeling enzymes are known to be crucial for its establishment in vivo, but their nonequilibrium nature has hindered the development of a unified theoretical framework for nucleosome positioning. Using a perturbation theory, we show that the effect of these enzymes can be well approximated by effective equilibrium models with rescaled temperatures and interactions. Numerical simulations support the accuracy of the theory in predicting both kinetic and steady-state quantities, including the effective temperature and the radial distribution function, in biologically relevant regimes. The energy landscape view emerging from our study provides an intuitive understanding for the impact of remodeling enzymes in either reinforcing or overwriting intrinsic signals for nucleosome positioning, and may help improve the accuracy of computational models for its prediction in silico.

  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Received 14 April 2019

DOI:https://doi.org/10.1103/PhysRevLett.123.208102

© 2019 American Physical Society

Physics Subject Headings (PhySH)

Physics of Living SystemsInterdisciplinary PhysicsStatistical Physics & Thermodynamics

Authors & Affiliations

Zhongling Jiang and Bin Zhang*

  • Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

  • *binz@mit.edu

Article Text (Subscription Required)

Click to Expand

Supplemental Material (Subscription Required)

Click to Expand

References (Subscription Required)

Click to Expand
Issue

Vol. 123, Iss. 20 — 15 November 2019

Reuse & Permissions
Access Options
CHORUS

Article Available via CHORUS

Download Accepted Manuscript
Author publication services for translation and copyediting assistance advertisement

Authorization Required


×
×

Images

×

Sign up to receive regular email alerts from Physical Review Letters

Log In

Cancel
×

Search


Article Lookup

Paste a citation or DOI

Enter a citation
×