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MBE Advance Access originally published online on March 3, 2009
Molecular Biology and Evolution 2009 26(6):1299-1307; doi:10.1093/molbev/msp040
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Evolutionary Forces Act on Promoter Length: Identification of Enriched Cis-Regulatory Elements

Erik Kristiansson*,{dagger},{ddagger},§, Michael Thorsen||, Markus J. Tamás and Olle Nerman{ddagger},§

* Department of Zoology, University of Gothenburg, Göteborg, Sweden
{dagger} Department of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Göteborg, Sweden
{ddagger} Department of Mathematical Statistics, Chalmers University of Technology, Göteborg, Sweden
§ Department of Mathematical Statistics, University of Gothenburg, Göteborg, Sweden
|| Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, Denmark
Department of Cell and Molecular Biology/Microbiology, University of Gothenburg, Göteborg, Sweden

E-mail: erik.kristiansson{at}zool.gu.se.

Accepted for publication February 24, 2009.

Transcription factors govern gene expression by binding to short DNA sequences called cis-regulatory elements. These sequences are typically located in promoters, which are regions of variable length upstream of the open reading frames of genes. Here, we report that promoter length and gene function are related in yeast, fungi, and plants. In particular, the promoters for stress-responsive genes are in general longer than those of other genes. Essential genes have, on the other hand, relatively short promoters. We utilize these findings in a novel method for identifying relevant cis-regulatory elements in a set of coexpressed genes. The method is shown to generate more accurate results and fewer false positives compared with other common procedures. Our results suggest that genes with complex transcriptional regulation tend to have longer promoters than genes responding to few signals. This phenomenon is present in all investigated species, indicating that evolution adjust promoter length according to gene function. Identification of cis-regulatory elements in Saccharomyces cerevisiae can be done with the web service located at http://enricher.zool.gu.se.

Key Words: gene regulation • transcription factor • promoter • cis-regulatory element

Douglas Crawford, Associate Editor


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