|Beyond ATCG: “Dixel” representations of DNA-protein interactions
Principal Investigator: Curt M. Breneman
Co-Investigator: N. Sukumar
Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute
In April 2003, the sequence of the human genome was completed, and numerous other genomes have been and are now being sequenced. Although these are significant achievements, much remains to be done. While reasonable progress has been made toward finding the identities and locations of genes within the data, the identities of other functional elements encoded in the DNA sequence - such as promoters and other transcriptional regulatory sequences - remain largely unknown. The sequence-specific binding of various proteins to DNA is perhaps the most fundamental process in the utilization of these other functional elements encoded in the DNA. For example, transcription regulation, which is achieved primarily through the sequence-specific binding of transcription factors to DNA, is arguably the most important foundation of cellular function, since it exerts the most fundamental control over the abundance of virtually all of a cell’s functional macromolecules. Because of this fundamental role, the study of transcription regulation will be critical to our understanding and eventual control of growth, development, evolution and disease. As part of this proposal, we seek support to develop improved computational technologies for the identification of transcription factor binding sites (TFBS) in DNA through cheminformatic techniques and to develop a framework for generating a broad molecular understanding of the selectivity of binding of such regulatory elements to specific DNA sequences.