Genome-wide nucleosome specificity and directionality of chromatin remodelers

Kuangyu Yen, Vinesh Vinayachandran, Kiran Batta, R. Thomas Koerber, B. Franklin Pugh

Research output: Contribution to journalArticlepeer-review

180 Scopus citations

Abstract

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′ 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.

Original languageEnglish (US)
Pages (from-to)1461-1473
Number of pages13
JournalCell
Volume149
Issue number7
DOIs
StatePublished - Jun 22 2012

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

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