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Published Online June 16, 2005
Science DOI: 10.1126/science.1112178

Reports

Submitted on March 14, 2005
Accepted on June 2, 2005

Genome-Scale Identification of Nucleosome Positions in S. Cerevisiae

Guo-Cheng Yuan 1, Yuen-Jong Liu 2, Michael F. Dion 1, Michael D. Slack 3, Lani F. Wu 1, Steven J. Altschuler 1, Oliver J. Rando 1*

1 Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.
2 Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA; Present address: Department of Molecular Biophysics and Biochemistry, Yale University, PO Box 208114, New Haven, CT 06520, USA.
3 Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA; BAE Systems Advanced Information Technologies, 9655 Granite Ridge Dr., San Diego, CA 92123, USA.

* To whom correspondence should be addressed.
Oliver J. Rando , E-mail: orando{at}cgr.harvard.edu

The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, as 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 yeast 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 ~200 basepairs upstream of the start codon, flanked on both sides by positioned nucleosomes. The nucleosome-free sequences were evolutionarily conserved, and were enriched in Poly(dA-dT) sequences. Most occupied transcription factor binding motifs were devoid of nucleosomes, strongly suggesting that nucleosome positioning is a global determinant of transcription factor access.


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