Nucleosome hopping and sliding kinetics determined from dynamics of single chromatin fibers in Xenopus egg extracts

Padinhateeri Ranjith*, Jie Yan, John F. Marko

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

39 Scopus citations

Abstract

Chromatin function in vivo is intimately connected with changes in its structure: a prime example is occlusion or exposure of regulatory sequences via repositioning of nucleosomes. Cell extracts used in concert with single-DNA micromanipulation can control and monitor these dynamics under in vivo-like conditions. We analyze a theory of the assembly-disassembly dynamics of chromatin fiber in such experiments, including effects of lateral nucleosome diffusion (''sliding'') and sequence positioning. Experimental data determine the force-dependent on- and off-rates as well as the nucleosome sliding diffusion rate. The resulting theory simply explains the very different nucleosome displacement kinetics observed in constant-force and constant-pulling velocity experiments. We also show that few-piconewton tensions comparable to those generated by polymerases and helicases drastically affect nucleosome positions in a sequence-dependent manner and that there is a long-lived structural "memory" of force-driven nucleosome rearrangement events.

Original languageEnglish (US)
Pages (from-to)13649-13654
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume104
Issue number34
DOIs
StatePublished - Aug 21 2007

Keywords

  • Chromatin assembly
  • Chromatin disassembly

ASJC Scopus subject areas

  • General

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