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


CONCLUSIONS
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.
Vandepoele
Klaas
K
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark, B-9052 Ghent, Belgium.
Casneuf
Tineke
T
Van de Peer
Yves
Y
D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D032107:Populus / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism
D014157:Transcription Factors