Direct observation of coordinated DNA movements on the nucleosome during chromatin remodelling

Nat Commun. 2019 Apr 12;10(1):1720. doi: 10.1038/s41467-019-09657-1.

Abstract

ATP-dependent chromatin remodelling enzymes (remodellers) regulate DNA accessibility in eukaryotic genomes. Many remodellers reposition (slide) nucleosomes, however, how DNA is propagated around the histone octamer during this process is unclear. Here we examine the real-time coordination of remodeller-induced DNA movements on both sides of the nucleosome using three-colour single-molecule FRET. During sliding by Chd1 and SNF2h remodellers, DNA is shifted discontinuously, with movement of entry-side DNA preceding that of exit-side DNA. The temporal delay between these movements implies a single rate-limiting step dependent on ATP binding and transient absorption or buffering of at least one base pair. High-resolution cross-linking experiments show that sliding can be achieved by buffering as few as 3 bp between entry and exit sides of the nucleosome. We propose that DNA buffering ensures nucleosome stability during ATP-dependent remodelling, and provides a means for communication between remodellers acting on opposite sides of the nucleosome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / metabolism*
  • Adenosine Triphosphate / chemistry
  • Animals
  • Buffers
  • Chromatin / chemistry*
  • Chromosomal Proteins, Non-Histone / metabolism*
  • DNA / analysis*
  • DNA Helicases / chemistry
  • DNA-Binding Proteins / metabolism*
  • Fluorescence Resonance Energy Transfer
  • Histones / chemistry
  • Humans
  • Nucleosomes / chemistry*
  • Protein Binding
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Xenopus

Substances

  • Buffers
  • CHD1 protein, S cerevisiae
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • DNA-Binding Proteins
  • Histones
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • Adenosine Triphosphate
  • DNA
  • Adenosine Triphosphatases
  • SMARCA5 protein, human
  • DNA Helicases