Modeling regulatory complexes using both TF-DNA and TF-TF interactions
Esko Ukkonen
Department of Computer Science, University of Helsinki, Finland

Transcription factors (TFs) not only bind to DNA but also to each other. The individual interactions between TFs are often weak. However, the complexes formed by both TF-DNA and TF-TF interactions are much more stable than those based on similar TF-DNA interactions alone. Thus, the dimerization mediated by DNA gives a much richer regulatory machinery that has a potentially stronger capability to explain the regulation of gene expression. The talk will describe recent developments in modeling and predicting such regulatory complexes, using data from high-throughput SELEX experiments, and applying this to explain observed binding patterns in DNA.

Joint work with J. Taipale, T. Kivioja, P. Rastas, A. Jolma and J. Toivonen.