[1] Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA
[2] Stanford Genome Technology Center, 855 California Avenue, Palo Alto, California 94304, USA
[3] Department of Molecular and Medical Genetics, University of Toronto, Canada
[4] Wadsworth Center P.O. Box 22001, Albany, NY 12054, USA
[5] Terrence Donnelly Centre for Cellular & Biomolecular Research, 160 College Street, Toronto, Ontario, Canada M5S 3E1
[6] Banting and Best Department of Medical Research
[7] Author for correspondence: corey -dot- nislow -at- utoronto -dot- ca

Summary

We present the first complete high-resolution map of nucleosome occupancy across the whole Saccharomyces cerevisiae genome, identifying over 70,000 positioned nucleosomes occupying 81% of the genome. On a genome-wide scale, the persistent nucleosome depeleted region identified previously in a subset of genes demarcates the transcription start site. Both nucleosome occupancy signatures and overall occupancy correlate with transcript abundance and transcription rate. In addition, functionally related genes can be clustered on the basis of the nucleosome occupancy patterns observed at their promoters. A quantitative model of nucleosome occupancy indicates that DNA structural features may account for much of the global nucleosome occupancy.

Supplementary figures and datasets:

Can be downloaded here: http://chemogenomics.stanford.edu/supplements/03nuc/index.html
Note: Tiling array coordinates correspond to February 2006 SGD build. Genomic sequence can be found here: [link to directory]

HMM nucleosome calls:

Download HMM inferred nucleosome positions: [gff, tar.gz, README]

Nucleosome sequence model:

Download yeast structural features: [tar.gz, README] Updated 24 Sept 2007 - chr10_struct_75.tab coordinates now correspond to Feb 2006 SGD build
Download table of dinucleotide measures: [xls]
Download binary transcription factor binding site data: [tar.gz, README]
Download Lasso selected motifs (4-mer copy number, other excluding motifs): [txt, 48MB]
Download Lasso model score (Chromosomes 1-16): [txt, 34MB]

Genome browser tracks:

http://hugheslab.ccbr.utoronto.ca/supplementary-data/tillo/nucleosomes/gtracks/lee_2007_hyb_plus_model.wig
http://hugheslab.ccbr.utoronto.ca/supplementary-data/tillo/nucleosomes/gtracks/lee_2007_nucs.gff
http://hugheslab.ccbr.utoronto.ca/supplementary-data/tillo/nucleosomes/gtracks/structural_features.wig

To view all tracks in the UCSC genome browser (for quick display purposes only due to differences in genome versions, but none which will affect graphical representation), copy and paste the above links here. For quick display purposes only (genome versions are slightly different - this does not significantly affect the visual representation on the browser).

Download genome browser tracks: [link to directory]

Updated 6 January 2008
email: desiree -dot- tillo -at- utoronto -dot- ca