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Originally published in Science Express on 16 June 2005
Science 22 July 2005:
Vol. 309. no. 5734, pp. 626 - 630
DOI: 10.1126/science.1112178
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Genome-Scale Identification of Nucleosome Positions in S. cerevisiae

Guo-Cheng Yuan, Yuen-Jong Liu,* Michael F. Dion, Michael D. Slack,{dagger} Lani F. Wu, Steven J. Altschuler, Oliver J. Rando{ddagger}

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 ~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.

Bauer Center for Genomics Research, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138, USA.

Published online 16 June 2005

Include this information when citing this paper.

* Present address: Department of Molecular Biophysics and Biochemistry, Yale University, Post Office Box 208114, New Haven, CT 06520, USA.

{dagger} Present address: BAE Systems Advanced Information Technologies, 9655 Granite Ridge Drive, San Diego, CA 92123, USA.

{ddagger} To whom correspondence should be addressed. E-mail: orando{at}cgr.harvard.edu

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