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Bioinformatics Advance Access published online on March 25, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp172
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

In silico analysis of promoter regions from cold-induced genes in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control

Angelica Lindlöf 1,*, Marcus Bräutigam 2, Aakash Chawade 3, Olof Olsson 3 and Björn Olsson 1

1 Systems Biology Research Centre, School of Life Sciences, University of Skövde, Box 408, 541 28 Skövde, Sweden
2Department of Cell and Molecular biology, Medicinaregatan 9C, Box 462, Gothenburg University, SE405 30 Göteborg
3 Department of Plant and Environmental Sciences, Box 461 Gothenburg University, SE405 30 Göteborg, Sweden

*To whom correspondence should be addressed. Dr. Angelica Lindlöf, E-mail: angelica.lindlof{at}his.se


  Abstract

Motivation: Cold acclimation involves a number of different cellular processes that together increase the freezing tolerance of an organism. The DREB1/CBFs are transcription factors that are prominent in the regulation of cold responses in Arabidopsis thaliana, rice and many other crops. We investigated if the expression of DREB1/CBFs and co-expressed genes relies on combinatorial control by several transcription factors. Our results support this notion and indicate that methods for studying the regulation of complex cellular processes should include identification of combinations of motifs, in addition to searching for individual over-represented binding sites.

Associate Editor: Dr. Limsoon Wong

Received on October 27, 2008; revised on March 4, 2009; accepted on March 21, 2009

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