title: Genome-scale identification of nucleosome positions in S. cerevisiae.
abstract: The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. We developed a tiled microarray approach to identify at high resolution the translational positions of 2278 nucleosomes over 482 kilobases of Saccharomyces cerevisiae DNA, including almost all of chromosome III and 223 additional regulatory regions. The majority of the nucleosomes identified were well-positioned. We found a stereotyped chromatin organization at Pol II promoters consisting of a nucleosome-free region approximately 200 base pairs upstream of the start codon flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved and were enriched in poly-deoxyadenosine or poly-deoxythymidine sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.
authors.affiliation: Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
authors.forename: Guo-Cheng
authors.initials: GC
authors.lastname: Yuan
authors.forename: Yuen-Jong
authors.initials: YJ
authors.lastname: Liu
authors.forename: Michael F
authors.initials: MF
authors.lastname: Dion
authors.forename: Michael D
authors.initials: MD
authors.lastname: Slack
authors.forename: Lani F
authors.initials: LF
authors.lastname: Wu
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Altschuler
authors.forename: Oliver J
authors.initials: OJ
authors.lastname: Rando
mesh_terms: D001665:Binding Sites; D015825:Chromosomes, Fungal / Q000737:chemistry / Q000235:genetics*; D017124:Conserved Sequence; D004271:DNA, Fungal / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics; D015870:Gene Expression; D016681:Genome, Fungal; D008390:Markov Chains; D015233:Models, Statistical; D009707:Nucleosomes / Q000648:ultrastructure; D020411:Oligonucleotide Array Sequence Analysis; D011061:Poly A / Q000032:analysis; D011071:Poly T / Q000032:analysis; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D021901:DNA, Intergenic; D009707:Nucleosomes; D014157:Transcription Factors; D011061:Poly A; D011071:Poly T; C015465:poly(dA)