title: Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast.
abstract: The packaging of eukaryotic DNA into chromatin has profound consequences for gene regulation, as well as for other DNA transactions such as recombination, replication and repair. Understanding how this packaging is determined is consequently a pressing problem in molecular genetics. DNA sequence, chromatin remodelers and transcription factors affect chromatin structure, but the scope of these influences on genome-wide nucleosome occupancy patterns remains uncertain. Here, we use high resolution tiling arrays to examine the contributions of two general regulatory factors, Abf1 and Rap1, to nucleosome occupancy in Saccharomyces cerevisiae. These factors have each been shown to bind to a few hundred promoters, but we find here that thousands of loci show localized regions of altered nucleosome occupancy within 1 h of loss of Abf1 or Rap1 binding, and that altered chromatin structure can occur via binding sites having a wide range of affinities. These results indicate that DNA-binding transcription factors affect chromatin structure, and probably dynamics, throughout the genome to a much greater extent than previously appreciated.
authors.affiliation: Laboratory of Molecular Genetics, New York State Department of Health, Wadsworth Center, Albany, NY 12201-0509, USA.
authors.forename: Mythily
authors.initials: M
authors.lastname: Ganapathi
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Palumbo
authors.forename: Suraiya A
authors.initials: SA
authors.lastname: Ansari
authors.forename: Qiye
authors.initials: Q
authors.lastname: He
authors.forename: Kyle
authors.initials: K
authors.lastname: Tsui
authors.forename: Corey
authors.initials: C
authors.lastname: Nislow
authors.forename: Randall H
authors.initials: RH
authors.lastname: Morse
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000032:analysis / Q000502:physiology*; D016681:Genome, Fungal; D009707:Nucleosomes / Q000737:chemistry; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis / Q000502:physiology*; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins / Q000032:analysis / Q000502:physiology*; D014157:Transcription Factors / Q000032:analysis / Q000502:physiology*
chemical_list: C061886:ABF1 protein, S cerevisiae; D002843:Chromatin; D004268:DNA-Binding Proteins; D009707:Nucleosomes; C440829:RAP1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins; D014157:Transcription Factors