CHD4 slides nucleosomes by decoupling entry- and exit-side DNA translocation

Nat Commun. 2020 Mar 23;11(1):1519. doi: 10.1038/s41467-020-15183-2.

Abstract

Chromatin remodellers hydrolyse ATP to move nucleosomal DNA against histone octamers. The mechanism, however, is only partially resolved, and it is unclear if it is conserved among the four remodeller families. Here we use single-molecule assays to examine the mechanism of action of CHD4, which is part of the least well understood family. We demonstrate that the binding energy for CHD4-nucleosome complex formation-even in the absence of nucleotide-triggers significant conformational changes in DNA at the entry side, effectively priming the system for remodelling. During remodelling, flanking DNA enters the nucleosome in a continuous, gradual manner but exits in concerted 4-6 base-pair steps. This decoupling of entry- and exit-side translocation suggests that ATP-driven movement of entry-side DNA builds up strain inside the nucleosome that is subsequently released at the exit side by DNA expulsion. Based on our work and previous studies, we propose a mechanism for nucleosome sliding.

Publication types

  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Chromatin Assembly and Disassembly*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • HEK293 Cells
  • Histones / genetics
  • Histones / metabolism
  • Humans
  • Intravital Microscopy*
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex / genetics
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex / metabolism*
  • Microscopy, Fluorescence
  • Nucleosomes / metabolism*
  • Protein Domains
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Single Molecule Imaging
  • Translocation, Genetic*

Substances

  • CHD1 protein, S cerevisiae
  • CHD4 protein, human
  • DNA-Binding Proteins
  • Histones
  • Nucleosomes
  • Recombinant Proteins
  • Saccharomyces cerevisiae Proteins
  • Mi-2 Nucleosome Remodeling and Deacetylase Complex