Guan Lab

Department of Computational Medicine & Bioinformatics
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TitleNucleosome-coupled expression differences in closely-related species.
Publication TypeJournal Article
Year of Publication2011
AuthorsGuan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG
JournalBMC Genomics
Volume12
Pagination466
Date Published2011
ISSN1471-2164
KeywordsCell Cycle Proteins, Fungal Proteins, Gene Expression Regulation, Fungal, Nucleosomes, Saccharomyces, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Species Specificity, Transcription Factors
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.

DOI10.1186/1471-2164-12-466
Alternate JournalBMC Genomics
PubMed ID21942931
PubMed Central IDPMC3209474
Grant ListMOP-86705 / / Canadian Institutes of Health Research / Canada
P41-RR011823 / RR / NCRR NIH HHS / United States
P50 GM071508 / GM / NIGMS NIH HHS / United States
R01 GM071966 / GM / NIGMS NIH HHS / United States
R01 GM071966-07 / GM / NIGMS NIH HHS / United States
R01HG005998 / HG / NHGRI NIH HHS / United States