75 OnTheFly database – structural basis to study TF’s DNA-binding specificity

Abstract

We describe a systematic determination of Drosophila melanogaster transcription factor DNA-binding specificities. We annotated and classified all transcription factors (TFs) predicted in the Drosophila melanogaster genome (Pfreundt, U. et al. 2009) and collected the known preferred DNA binding sites of the TFs based on the B1H (Zhu, L.J. et al. 2011), DNaseI (Bergman C.M. et al. 2005), and SELEX (Slattery, M. et al. 2011) methods. Then, we identified the sequence and shape preferences for all DNA-binding proteins (Kuziemko A et al. 2011) and also characterized the shapes of their preferred DNA binding sites using structural models. The identification of the preferred DNA binding sites, and their shapes, for all DNA binding proteins will provide an unprecedented and extremely valuable database for anyone attempting to decipher noncoding regulatory DNA. Specifically, we showed that using structural criteria such as the width of the minor groove (Rohs R. et al. 2010), we distinguished DNA sequences bound by proteins which possess a Homeodomain from other proteins that possess a ZNF-C2H2 domain or ETS domains (pictured bellow from right to left). Furthermore, based on key TF–DNA interactions from the template structure stored in PDB, we superpose query DNA structure onto the template. Therefore, we obtain a homology model, where TF is from the template and DNA is from the query. This model will provide potential structural basis to study TF’s DNA-binding specificity. The insights from such a study could help in selecting the best DNA candidates to be bound by a certain TF for experimental testing. Finding such pairs will help to characterize the unique properties of protein–DNA interfaces and identify new drug target sites.