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A high-resolution atlas of nucleosome occupancy in yeast | Nature Genetics
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A high-resolution atlas of nucleosome occupancy in yeast

Nature Genetics volume 39, pages 1235–1244 (2007)Cite this article

Abstract

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-depleted 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.

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Figure 1: Distribution of nucleosomes around the CHA1 and HIS3 promoters.
Figure 2: TSSs are demarcated by NDRs.
Figure 3: NDRs align with TSSs and not with translation start sites.
Figure 4: Clustering promoter nucleosome signatures.
Figure 5: Relative nucleosome occupancy of promoters is related to presence of TFBSs of nuclear transcription factors, and correlates with enrichment of TFBSs near −100 bp.
Figure 6: Correlations between nucleosome occupancy measurements and local DNA properties.

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Acknowledgements

We thank G. Giaever for scientific advice; members of the HIP-HOP labs at Stanford and Toronto for advice and encouragement; C. Palm for help with data analysis; S.J. Altschuler (Univ. Texas Southwester Medical Center) and G.-C. Yuan (Harvard Univ.) for software for the HMM; and Z. Zhang, Q. Morris and E. Chan for discussions. W.L. is supported by a training grant from the US National Institutes of Health, and the work was supported by grants from the National Human Genome Research Institute (R.W.D. and C.N.), the National Science Foundation (R.H.M.), Genome Canada and the Ontario Genomics Institute (N.B., D.T. and T.R.H.).

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Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, 94305-5120, California, USA

    William Lee & Ronald W Davis

  2. Stanford Genome Technology Center, 855 California Avenue, Palo Alto, 94304, California, USA

    William Lee & Ronald W Davis

  3. Department of Molecular and Medical Genetics, University of Toronto, Toronto, M5S 1A8, Ontario, Canada

    Desiree Tillo, Nicolas Bray, Timothy R Hughes & Corey Nislow

  4. New York State Department of Health, Wadsworth Center, Albany, 12201-2002, New York, USA

    Randall H Morse

  5. Terrence Donnelly Centre for Cellular & Biomolecular Research, 160 College Street, Toronto, M5S 3E1, Ontario, Canada

    Timothy R Hughes & Corey Nislow

  6. Banting and Best Department of Medical Research, 112 College St., Toronto, M5S 1L6, Ontario, Canada

    Timothy R Hughes & Corey Nislow

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Contributions

W.L. preformed experiments, collected and analyzed the data, prepared figures and co-wrote the paper. R.W.D. provided essential input into the study design and interpretation. D.T. designed the Lasso model, analyzed all of the data, ran the HMM, and prepared figures. N.B. did data analysis on TFBSs. R.H.M. contributed to the initial study design, provided essential experimental advice, and contributed text. T.R.H. directed the detailed data analysis, and contributed figures and text. C.N. designed the study, directed the work and wrote the paper.

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Correspondence to Corey Nislow.

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Lee, W., Tillo, D., Bray, N. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39, 1235–1244 (2007). https://doi.org/10.1038/ng2117

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