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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 implicatedin the regulation of gene expression in eukaryotic cells, aspackaging DNA into nucleosomes affects sequence accessibility.We developed a tiled microarray approach to identify at highresolution the translational positions of 2278 nucleosomes over482 kilobases of yeast DNA, including almost all of chromosomeIII and 223 additional regulatory regions. The majority of thenucleosomes identified were well-positioned. We found a stereotypedchromatin organization at Pol II promoters consisting of a nucleosome-freeregion 200 basepairs upstream of the start codon, flanked onboth sides by positioned nucleosomes. The nucleosome-free sequenceswere evolutionarily conserved, and were enriched in Poly(dA-dT)sequences. Most occupied transcription factor binding motifswere devoid of nucleosomes, strongly suggesting that nucleosomepositioning is a global determinant of transcription factoraccess.
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