Highlight talk – Theme: Data
Abstract
Transcriptional regulation requires the binding of transcription factors (TFs) to short sequence-specific DNA motifs. Interestingly, only a small fraction of consensus motifs in the genome are actually bound by the corresponding TF. By analysing high throughput in-vitro and in-vivo binding data for hundreds of TFs, we demonstrate that the “environment” surrounding the bound sites, far beyond the core motif, is characterized by unique sequence compositions and DNA shape features, specific to each TF. We show that these preferences are inherent binding properties of each TF and can be used for accurate prediction of TF-binding even without accounting for the motif information. We propose that these unique environmental features facilitate in guiding TFs to their cognate binding sites during the TF search process. Under this hypothesis, TF-DNA recognition is dictated not only by the motif but is also strongly influenced by the environment in which the motif resides.
Authors
Yael Mandel-Gutfreund, Faculty of Biology, Technion-Israel Institute of Technology, Haifa Israel 32000, Israel
Iris Dror, Technion-Israel Institute of Technology, Israel
Tamar Golan, Tel Aviv University, Israel
Carmit Levy, Tel Aviv University, Israel
Remo Rohs, University of South California, United States