Genome-scale identification of nucleosome positions in S. cerevisiae

Science. 2005 Jul 22;309(5734):626-30. doi: 10.1126/science.1112178. Epub 2005 Jun 16.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Binding Sites
  • Chromosomes, Fungal / chemistry
  • Chromosomes, Fungal / genetics*
  • Conserved Sequence
  • DNA, Fungal / genetics
  • DNA, Intergenic / genetics
  • Gene Expression
  • Genome, Fungal*
  • Markov Chains
  • Models, Statistical
  • Nucleosomes* / ultrastructure
  • Oligonucleotide Array Sequence Analysis
  • Poly A / analysis
  • Poly T / analysis
  • Promoter Regions, Genetic
  • Regulatory Sequences, Nucleic Acid
  • Saccharomyces cerevisiae / genetics*
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Transcription, Genetic


  • DNA, Fungal
  • DNA, Intergenic
  • Nucleosomes
  • Transcription Factors
  • Poly A
  • Poly T
  • poly(dA)