Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Nat Commun. 2021 May 28;12(1):3232. doi: 10.1038/s41467-021-23015-0.


Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the 'ruler' that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin Assembly and Disassembly*
  • Drosophila Proteins / genetics
  • Drosophila Proteins / isolation & purification
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster
  • Epigenesis, Genetic
  • Genome, Fungal / genetics
  • High Mobility Group Proteins / genetics
  • High Mobility Group Proteins / isolation & purification
  • High Mobility Group Proteins / metabolism
  • Histones / genetics
  • Histones / metabolism
  • Larva / genetics
  • Larva / metabolism
  • Microfilament Proteins / genetics
  • Microfilament Proteins / isolation & purification
  • Microfilament Proteins / metabolism
  • Mutagenesis
  • Nucleosomes / genetics
  • Nucleosomes / metabolism*
  • Recombinant Proteins / genetics
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism
  • Regulatory Sequences, Nucleic Acid / genetics*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / isolation & purification
  • Saccharomyces cerevisiae Proteins / metabolism
  • Whole Genome Sequencing


  • ARP8 protein, S cerevisiae
  • Drosophila Proteins
  • High Mobility Group Proteins
  • Histones
  • INO80 complex, S cerevisiae
  • Microfilament Proteins
  • NHP10 protein, S cerevisiae
  • Nucleosomes
  • Recombinant Proteins
  • Saccharomyces cerevisiae Proteins