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Bioinformatics Advance Access originally published online on December 8, 2005
Bioinformatics 2006 22(4):392-399; doi:10.1093/bioinformatics/bti823
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae

Xiang Guo , Kay Tatsuoka and Rongxiang Liu *

GlaxoSmithKline, Bioinformatics Division 709 Swedeland Road, King of Prussia, PA 19406, USA

*To whom correspondence should be addressed.

Motivation: In eukaryotic genomes, histone acetylation and thereafter departure from the chromatin are essential for gene transcription initiation. Because gene transcription is tightly regulated by transcription factors, there are some speculations on the cooperation of histone acetylation and transcription factor binding. However, systematic statistical analyses of this relationship on a genomic scale have not been reported.

Results: We apply several statistical methods to explore this relationship on two recent genomic datasets: acetylation levels on 11 histone lysines and binding activities of 203 transcription factors, both in promoter regions across the yeast genome. By canonical correlation analysis, we find that a histone acetylation pattern is correlated with a certain profile of transcription factor binding in the genome. Furthermore, after clustering the genes by their acetylation levels on the 11 histone lysines, the genes within clusters show distinct transcription factor binding profiles, as discovered by principle component analysis. Even after applying fairly stringent statistical measurement, most of these clusters have transcription factors with binding activities significantly deviated from the overall genome. We conclude that in the yeast genome, there is a strong correlation between histone acetylation and transcription factor binding in the promoter regions.

Contact: ron.2.liu{at}gsk.com

Supplementary information: Supplementary Data are available at Bioinformatics online.

Received on August 20, 2005; revised on November 22, 2005; accepted on December 5, 2005

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