Genome-wide nucleosome specificity and directionality of chromatin remodelers

Cell. 2012 Jun 22;149(7):1461-73. doi: 10.1016/j.cell.2012.04.036.


How chromatin remodelers cooperate to organize nucleosomes around the start and end of genes is not known. We determined the genome-wide binding of remodeler complexes SWI/SNF, RSC, ISW1a, ISW1b, ISW2, and INO80 to individual nucleosomes in Saccharomyces, and determined their functional contributions to nucleosome positioning through deletion analysis. We applied ultra-high-resolution ChIP-exo mapping to Isw2 to determine its subnucleosomal orientation and organization on a genomic scale. Remodelers interacted with selected nucleosome positions relative to the start and end of genes and produced net directionality in moving nucleosomes either away or toward nucleosome-free regions at the 5' and 3' ends of genes. Isw2 possessed a subnucleosomal organization in accord with biochemical and crystallographic-based models that place its linker binding region within promoters and abutted against Reb1-bound locations. Together, these findings reveal a coordinated position-specific approach taken by remodelers to organize genic nucleosomes into arrays.

Publication types

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

MeSH terms

  • Adenosine Triphosphatases / metabolism
  • Chromatin Assembly and Disassembly*
  • DNA-Binding Proteins / metabolism
  • Exodeoxyribonucleases
  • Genetic Techniques
  • Genome, Fungal*
  • Genome-Wide Association Study*
  • Nucleosomes / metabolism*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Transcription Factors / metabolism


  • DNA-Binding Proteins
  • ISWI protein
  • Nucleosomes
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • Exodeoxyribonucleases
  • Adenosine Triphosphatases
  • ISW1 protein, S cerevisiae