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 non-coding regulatory DNA. Specifically we showed that using structural criteria such as the width of minor groove (Rohs R. et al. 2010) we distinguished, DNA sequences bound by proteins which possess a Homeodomain from other proteins that possess 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.

References

Pfreundt, U. et al. FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res 38, D443-447 (2009).

Bergman, C.M., Carlson, J.W. & Celniker, S.E. Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster. Bioinformatics 21, 1747-1749 (2005).

Zhu, L.J. et al. FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system. Nucleic Acids Res 39, D111-117 (2011).

Slattery M, et al. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. Vol. 147, Issue 6, pp. 1270-1282 (2011).

Kuziemko A, Honig B, Petrey D. (2011). Using structure to explore the sequence alignment space of remote homologs. PLoS Comput Biol. 2011 Oct;7(10):e1002175.

Rohs, R., et al., Origins of specificity in protein-DNA recognition. Annu Rev Biochem. 79: p. 233-69 (2010).