The Yeast INO80 Complex Operates as a Tunable DNA Length-Sensitive Switch to Regulate Nucleosome Sliding

Mol Cell. 2018 Feb 15;69(4):677-688.e9. doi: 10.1016/j.molcel.2018.01.028.

Abstract

The yeast INO80 chromatin remodeling complex plays essential roles in regulating DNA damage repair, replication, and promoter architecture. INO80's role in these processes is likely related to its ability to slide nucleosomes, but the underlying mechanism is poorly understood. Here we use ensemble and single-molecule enzymology to study INO80-catalyzed nucleosome sliding. We find that the rate of nucleosome sliding by INO80 increases ∼100-fold when the flanking DNA length is increased from 40 to 60 bp. Furthermore, once sliding is initiated, INO80 moves the nucleosome rapidly at least 20 bp without pausing to re-assess flanking DNA length, and it can change the direction of nucleosome sliding without dissociation. Finally, we show that the Nhp10 module of INO80 plays an auto-inhibitory role, tuning INO80's switch-like response to flanking DNA. Our results indicate that INO80 is a highly processive remodeling motor that is tightly regulated by both substrate cues and non-catalytic subunits.

Keywords: ATP-dependent chromatin-remodeling enzyme; DNA length sensing; INO80; enzymology; single-molecule FRET.

Publication types

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

MeSH terms

  • Chromatin Assembly and Disassembly*
  • DNA Repair
  • DNA Replication*
  • DNA, Fungal / genetics
  • DNA, Fungal / metabolism*
  • High Mobility Group Proteins / genetics
  • High Mobility Group Proteins / metabolism
  • Histones / genetics
  • Histones / metabolism
  • Nucleosomes / genetics
  • Nucleosomes / metabolism*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / growth & development
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*

Substances

  • DNA, Fungal
  • High Mobility Group Proteins
  • Histones
  • INO80 complex, S cerevisiae
  • NHP10 protein, S cerevisiae
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins