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Open Access Research article

Nucleosome-coupled expression differences in closely-related species

Yuanfang Guan12, Victoria Yao1, Kyle Tsui34, Marinella Gebbia34, Maitreya J Dunham5, Corey Nislow367* and Olga G Troyanskaya18*

Author Affiliations

1 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA

2 Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA

3 Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada

4 Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada

5 Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA

6 Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada

7 Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada

8 Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA

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BMC Genomics 2011, 12:466  doi:10.1186/1471-2164-12-466

Published: 26 September 2011

Abstract

Background

Genome-wide nucleosome occupancy is negatively related to the average level of transcription factor motif binding based on studies in yeast and several other model organisms. The degree to which nucleosome-motif interactions relate to phenotypic changes across species is, however, unknown.

Results

We address this challenge by generating nucleosome positioning and cell cycle expression data for Saccharomyces bayanus and show that differences in nucleosome occupancy reflect cell cycle expression divergence between two yeast species, S. bayanus and S. cerevisiae. Specifically, genes with nucleosome-depleted MBP1 motifs upstream of their coding sequence show periodic expression during the cell cycle, whereas genes with nucleosome-shielded motifs do not. In addition, conserved cell cycle regulatory motifs across these two species are more nucleosome-depleted compared to those that are not conserved, suggesting that the degree of conservation of regulatory sites varies, and is reflected by nucleosome occupancy patterns. Finally, many changes in cell cycle gene expression patterns across species can be correlated to changes in nucleosome occupancy on motifs (rather than to the presence or absence of motifs).

Conclusions

Our observations suggest that alteration of nucleosome occupancy is a previously uncharacterized feature related to the divergence of cell cycle expression between species.