Forced unraveling of chromatin fibers with nonuniform linker DNA lengths

Gungor Ozer, Rosana Collepardo-Guevara, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

The chromatin fiber undergoes significant structural changes during the cell's life cycle to modulate DNA accessibility. Detailed mechanisms of such structural transformations of chromatin fibers as affected by various internal and external conditions such as the ionic conditions of the medium, the linker DNA length, and the presence of linker histones, constitute an open challenge. Here we utilize Monte Carlo (MC) simulations of a coarse grained model of chromatin with nonuniform linker DNA lengths as found in vivo to help explain some aspects of this challenge. We investigate the unfolding mechanisms of chromatin fibers with alternating linker lengths of 26-62bp and 44-79bp using a series of end-to-end stretching trajectories with and without linker histones and compare results to uniform-linker-length fibers. We find that linker histones increase overall resistance of nonuniform fibers and lead to fiber unfolding with superbeads-on-a-string cluster transitions. Chromatin fibers with nonuniform linker DNA lengths display a more complex, multi-step yet smoother process of unfolding compared to their uniform counterparts, likely due to the existence of a more continuous range of nucleosome-nucleosome interactions. This finding echoes the theme that some heterogeneity in fiber component is biologically advantageous.

Original languageEnglish (US)
Article number064113
JournalJournal of Physics Condensed Matter
Volume27
Issue number6
DOIs
StatePublished - Feb 18 2015

Keywords

  • Monte Carlo
  • alternating linker DNA length
  • chromatin
  • coarse-grained modeling
  • force pulling
  • nonuniform NRL

ASJC Scopus subject areas

  • Materials Science(all)
  • Condensed Matter Physics

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