Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors

The processes that take place during development and differentiation are di rected through coordinated regulation of expression of a large number of ge nes. One such gene regulatory network provides cell cycle control in eukary otic organisms. Ln this work, we have studied the structural features of th e 5' regulatory regions of cell cycle-related genes. We developed a new met hod for identifying composite substructures (modules) in regulatory regions of genes consisting of a binding site for a key transcription factor and a dditional contextual motifs: potential targets for other transcription fact ors that may synergistically regulate gene transcription. Applying this met hod to cell cycle-related promoters, we created a program for context-speci fic identification of binding sites for transcription factors of the E2F fa mily which are key regulators of the cell cycle. We found that E2F composit e modules are found at a high frequency and in close proximity to the start of transcription in cell cycle-related promoters in comparison with other promoters. Using this information, we then searched for E2F sites in genomi c sequences with the goal of identifying new genes which play important rol es in controlling cell proliferation, differentiation and apoptosis. Using a chromatin immunoprecipitation assay, we then experimentally verified the binding of E2F in vivo to the promoters predicted by the computer-assisted methods. Our identification of new E2F target genes provides new insight in to gene regulatory networks and provides a framework for continued analysis of the role of contextual promoter features in transcriptional regulation. The tools described are available at http:// compel.bionet.nsc.ru/FunSite/ SiteScan.html. (C) 2001 Academic Press.