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Open Access Highly Accessed Research

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

Klaas Vandepoele, Tineke Casneuf and Yves Van de Peer*

Author Affiliations

Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark, B-9052 Ghent, Belgium

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Genome Biology 2006, 7:R103  doi:10.1186/gb-2006-7-11-r103

Published: 7 November 2006

Abstract

Background

Transcriptional regulation plays an important role in the control of many biological processes. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity and are organized into separable cis-regulatory modules, each defining the cooperation of several transcription factors required for a specific spatio-temporal expression pattern. Consequently, the discovery of novel TFBSs in promoter sequences is an important step to improve our understanding of gene regulation.

Results

Here, we applied a detection strategy that combines features of classic motif overrepresentation approaches in co-regulated genes with general comparative footprinting principles for the identification of biologically relevant regulatory elements and modules in Arabidopsis thaliana, a model system for plant biology. In total, we identified 80 TFBSs and 139 regulatory modules, most of which are novel, and primarily consist of two or three regulatory elements that could be linked to different important biological processes, such as protein biosynthesis, cell cycle control, photosynthesis and embryonic development. Moreover, studying the physical properties of some specific regulatory modules revealed that Arabidopsis promoters have a compact nature, with cooperative TFBSs located in close proximity of each other.

Conclusion

These results create a starting point to unravel regulatory networks in plants and to study the regulation of biological processes from a systems biology point of view.