TY - JOUR
T1 - Nucleosome-coupled expression differences in closely-related species
AU - Guan, Yuanfang
AU - Yao, Victoria
AU - Tsui, Kyle
AU - Gebbia, Marinella
AU - Dunham, Maitreya J.
AU - Nislow, Corey
AU - Troyanskaya, Olga G.
N1 - Funding Information:
We thank James Broach and Amy Caudy for discussion and suggestions on the manuscript, Lance Parsons for technical support and Lance Parsons for technical support. OGT is supported by the NIH grants R01 GM071966 and R01HG005998, NSF grant IIS-0513552 and NSF CAREER award DBI-0546275. CN is supported by the Canadian Institutes for Health Research MOP-86705. YG, MJD and OGT were partially supported by the NIGMS Center of Excellence P50 GM071508, and by donations from the A. V. Davis Foundation and Princeton University for funding of QCB301, Experimental Project Laboratory. MJD is a Rita Allen Foundation Scholar and supported by NIH-P41-RR011823. Supplementary information All nucleosome and expression data associated with this study is available at http://function.princeton.edu/cm/data/cellcycle_nucleosome/ Cell cycle expression data are available at GSE16544 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA. 2Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. 3Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada. 4Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada. 5Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA. 6Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. 7Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada. 8Department of Computer Science, Princeton University, Princeton, NJ, 08540, USA.
PY - 2011/9/26
Y1 - 2011/9/26
N2 - 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.
AB - 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.
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U2 - 10.1186/1471-2164-12-466
DO - 10.1186/1471-2164-12-466
M3 - Article
C2 - 21942931
AN - SCOPUS:80053356939
SN - 1471-2164
VL - 12
JO - BMC Genomics
JF - BMC Genomics
M1 - 466
ER -