title: DNA looping facilitates targeting of a chromatin remodeling enzyme.
abstract: ATP-dependent chromatin remodeling enzymes are highly abundant and play pivotal roles regulating DNA-dependent processes. The mechanisms by which they are targeted to specific loci have not been well understood on a genome-wide scale. Here, we present evidence that a major targeting mechanism for the Isw2 chromatin remodeling enzyme to specific genomic loci is through sequence-specific transcription factor (TF)-dependent recruitment. Unexpectedly, Isw2 is recruited in a TF-dependent fashion to a large number of loci without TF binding sites. Using the 3C assay, we show that Isw2 can be targeted by Ume6- and TFIIB-dependent DNA looping. These results identify DNA looping as a mechanism for the recruitment of a chromatin remodeling enzyme and define a function for DNA looping. We also present evidence suggesting that Ume6-dependent DNA looping is involved in chromatin remodeling and transcriptional repression, revealing a mechanism by which the three-dimensional folding of chromatin affects DNA-dependent processes.
authors.affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors.forename: Adam N
authors.initials: AN
authors.lastname: Yadon
authors.forename: Badri Nath
authors.initials: BN
authors.lastname: Singh
authors.forename: Michael
authors.initials: M
authors.lastname: Hampsey
authors.forename: Toshio
authors.initials: T
authors.lastname: Tsukiyama
mesh_terms: D000251:Adenosine Triphosphatases / Q000378:metabolism*; D001665:Binding Sites; D042002:Chromatin Assembly and Disassembly; D004271:DNA, Fungal / Q000737:chemistry / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D009690:Nucleic Acid Conformation; D012097:Repressor Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D035581:Transcription Factor TFIIB / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; C086468:ISWI protein; D012097:Repressor Proteins; C073680:SUA7 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D035581:Transcription Factor TFIIB; D014157:Transcription Factors; C089979:UME6 protein, S cerevisiae; D000251:Adenosine Triphosphatases