Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant

Marnie E. Gelbart, Nurjana Bachman, Jeffrey Delrow, Jef D. Boeke, Toshio Tsukiyama

    Research output: Contribution to journalArticle

    Abstract

    Isw2 ATP-dependent chromatin-remodeling activity is targeted to early meiotic and MATa-specific gene promoters in Saccharomyces cerevisiae. Unexpectedly, preferential cross-linking of wild-type Isw2p was not detected at these loci. Instead, the catalytically inactive Isw2p-K215R mutant is enriched at Isw2 targets, suggesting that Isw2p-K215R, but not wild-type Isw2p, is a sensitive chromatin immunoprecipitation (ChIP) reagent for marking sites of Isw2 activity in vivo. Genome-wide ChIP analyses confirmed this conclusion and identified tRNA genes (tDNAs) as a new class of Isw2 targets. Loss of Isw2p disrupted the periodic pattern of Ty1 integration upstream of tDNAs, but did not affect transcription of tDNAs or the associated Ty1 retrotransposons. In addition to identifying new Isw2 targets, our localization studies have important implications for the mechanism of Isw2 association with chromatin in vivo. Target-specific enrichment of Isw2p-K215R, not wild-type Isw2p, suggests that Isw2 is recruited transiently to remodel chromatin structure at these sites. In contrast, we found no evidence for Isw2 function at sites preferentially enriched by wild-type Isw2p, leading to our proposal that wild-type Isw2p cross-linking reveals a scanning mode of the complex as it surveys the genome for its targets.

    Original languageEnglish (US)
    Pages (from-to)942-954
    Number of pages13
    JournalGenes and Development
    Volume19
    Issue number8
    DOIs
    StatePublished - Apr 15 2005

    Keywords

    • ATP-dependent chromatin remodeling
    • Chromatin
    • Genome-wide localization
    • ISWI
    • Retrotransposon
    • tRNA

    ASJC Scopus subject areas

    • Genetics
    • Developmental Biology

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