Genome-scale identification of nucleosome positions in S. cerevisiae.
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.
Yuan
Guo-Cheng
GC
Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
Liu
Yuen-Jong
YJ
Dion
Michael F
MF
Slack
Michael D
MD
Wu
Lani F
LF
Altschuler
Steven J
SJ
Rando
Oliver J
OJ
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
D004271:DNA, Fungal; D021901:DNA, Intergenic; D009707:Nucleosomes; D014157:Transcription Factors; D011061:Poly A; D011071:Poly T; C015465:poly(dA)