Genome-Scale Predictions of the Transcription Factor Binding Sites of Cys 2 His 2 Zinc Finger Proteins in Yeast June 17 th, 2005

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1 Genome-Scale Predictions of the Transcription Factor Binding Sites of Cys 2 His 2 Zinc Finger Proteins in Yeast June 17 th, 2005 John Brothers II 1,3 and Panayiotis V. Benos 1,2 1 Bioengineering and Bioinformatics Summer Institute, 2 Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA 15213, 3 Bioinformatics, Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY Introduction Cell expression and regulation of genes is still not very well understood except for a few deeply studied processes (Doniger et al., 2005). The challenge to discover a clear deterministic model for gene regulation is considered one of the greater challenges of modern computation biology and bioinformatics (Benos et al., 2002). With the combined experimental and computational data that has been discovered about regulatory motifs in Saccharomyces cerevisiae, it has become possible to pursue not only the identification of functioning transcription factor binding sites (Doniger et al., 2005), but to aim for that goal of discovering a deterministic model for the prediction of TFBSs in entire yeast genomes. By finding all of the possible TFBSs and evaluating the possible DNA interactions of the Cys 2 Hys 2 zinc finger protein domains (the domain most found on transcription factors) to discover which DNA sequences they bind to, we would be able to help expand and assess the accuracy of the model developed by Benos et al for the

2 prediction of binding sites and further improve the overall understanding of the processes behind cell regulation (Benos et al, 2002). Methodology: The DNA binding preferences of yeast Cys 2 His 2 zinc finger proteins, composed of only two or three fingers, will be determined by using position specific scoring matrices (PSSM) (Stormo, 2000). For Saccharomyces cerevisiae, a program entitled C2H2-enoLOGOS will be used to directly ascertain the PSSM models for any of the yeast Cys 2 His 2 zinc finger proteins with only two or three fingers (Workman et al., 2005). To determine the PSSM models for any other species of yeast, members of the Cys 2 Hys 2 zinc finger protein family will be extracted from the Pfam database ( By doing comparisons to the human or mouse EGR1 protein, the crucial amino acids that bind to positions 1, +3, and +6 on the DNA helix will be determined (see Figure 1). Those amino acid identities will be used to determine the position-specific base Figure 1. The DNA-binding of the EGR1 protein. preferences of the protein using the three contact model developed by Benos et all (Benos et al., 2002). Once the PSSM models for all 2- and 3-finger S. cerevisiae proteins have been calculated, the orthologues of these proteins in other yeast species will be

3 determined using Basic Local Alignment Search Tools (BLAST). For this experiment, a protein of another yeast species will be considered an orthologous protein to a S. cerevisiae protein if said protein is the top hit in the BLAST search with the amino acid sequence of the S. cerevisiae protein. Those proteins that are found to have no orthologues in other yeast species will be excluded from further analysis. Since yeast species usually have short 5 UTRs, the 1.5kb upstream of the translation start site should contain all of the important DNA regulatory elements, therefore for this experiment, that section upstream of the yeast gene will be considered the promoter region. All of the promoter regions of all the yeast genes of the multiple yeast genomes will then be identified. Those sequences will be derived from publicly available datasets or from published genomes. The promoters of the orthologous genes will then be searched for possible binding sites of each of the zinc finger proteins using a strategy similar to the FOOTER algorithm, which is where the position of the site and the PSSM score are used to decide whether a possible site is conserved between two species. Since there are multiple species and genomes available, the FOOTER algorithm may be expanded to work with multiple species comparisons. The predictions made using the above techniques will help to discover and assess further the accuracy of the Cys 2 Hys 2 zinc finger model developed by Benos et al (Benos et al., 2002). The final determination of the accuracy of this developing model for the genome-scale predictions of the binding sites of the Cys 2 Hys 2 zinc finger proteins in yeast will be assessed by evaluation of the

4 above predictions with publicly available gene microarray data and chromatin immunoprecipitation (ChIP) data (Lee et al., 2002). Other ways to assess the computed predictions may also be used. Expected Results 1. To improve the understanding of the gene regulation through the mathematical modeling of the transcription-factor binding sites using zinc finger proteins. 2. To expand the FOOTER algorithm in such a way that it can be used to do multiple comparisons between more than two species of yeast. 3. To assess and improve the current model for predicting genome-scale binding sites used by Benos, et al. References Benos, P.V., A.S. Lapedes, and G.D. Stormo Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol 323: Doniger, S.W., J. Huh, and J.C. Fay Identification of functional transcription factor binding sites using closely related Saccharomyces species. Genome Res 15: Lee, T.I., N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L. Murray, D.B. Gordon, B. Ren, J.J.

5 Wyrick, J.B. Tagne, T.L. Volkert, E. Fraenkel, D.K. Gifford, and R.A. Young Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: Stormo, G.D DNA binding sites: representation and discovery. Bioinformatics 16: Workman, C.T., Y. Yin, D.L. Corcoran, T. Ideker, G.D. Stormo, and P.V. Benos EnoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res 000: