Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning

Science. 2025 Jul 17;389(6757):eadr3831. doi: 10.1126/science.adr3831. Epub 2025 Jul 17.

Abstract

Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.

MeSH terms

  • Adenosine Triphosphatases* / chemistry
  • Adenosine Triphosphatases* / genetics
  • Chromatin Assembly and Disassembly*
  • Cryoelectron Microscopy
  • DNA, Fungal / chemistry
  • DNA, Fungal / metabolism
  • Microfilament Proteins
  • Nucleosomes* / chemistry
  • Nucleosomes* / metabolism
  • Nucleosomes* / ultrastructure
  • Protein Conformation
  • Saccharomyces cerevisiae Proteins* / chemistry
  • Saccharomyces cerevisiae Proteins* / genetics
  • Saccharomyces cerevisiae Proteins* / metabolism
  • Saccharomyces cerevisiae* / genetics

Substances

  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • INO80 complex, S cerevisiae
  • ARP8 protein, S cerevisiae
  • DNA, Fungal
  • Adenosine Triphosphatases
  • Microfilament Proteins