| The proper regulation of gene expression is an essential constituent of all life processes. We are only beginning to understand how a genome mediates, through regulatory sequences, the proper expression of the genes it encodes. The computational and experimental work discussed here is unified by the goal of furthering the understanding of the role of genome sequences in transcriptional regulation. A significant portion of this work involves GOMER, a computational tool designed for the study of transcription factor binding and consequent regulation. I discuss the theoretical basis and implementation of GOMER, and provide instructions for its use. I also describe the application of GOMER to several model transcription regulatory systems in Saccharomyces cerevisiae, including the binding site distribution of Fkh1p, cooperative interactions between Fkh2p and Mcm1p, competitive interactions between Sum1p and Ndt80p, the genome localization of Rap1p, and the role of Nrd1p and Nab3p in signaling the transcriptional termination of snRNA and snoRNA transcripts. Using GOMER it has been possible to determine models of regulation for these regulatory systems, which can identify sets of genes known to be regulated. I also describe a genetic algorithm based computational tool for refining the description of a transcription factor's binding specificity using regulatory sequences known to be bound by the transcription factor. This tool was used to refine an experimentally determined description of the binding specificity of the a1/alpha2 heterodimeric transcription factor, producing a description that was better at identifying known a1/alpha2 regulated genes than the original. Finally I present microarray based experiments comparing whole genome expression in mata1Delta, mata1Delta/matalpha2Delta, and wild-type cells. These experiments were used to determine the haploid-specific genes regulated by the a1/alpha2 heterodimer and the a-specific genes regulated by the alpha2/Mcm1 heterodimer. |
