| Understanding how genes are regulated is pivotal for understanding many cellular processes. Regulation of gene expression through transcription is complicated, involving interplay between gene-specific transcription factors, DNA packaged into chromatin, chromatin remodelers/modifiers, elongation and RNA processing factors. Intricate signal transduction pathways control these components through modifications such as phosphorylation, ubiquitination and acetylation. Past studies have yielded many details on how a minority of genes are regulated. This knowledge is too fragmented to form complete models of the entire system. Comprehensive knowledge is lacking about which genes are controlled by which regulatory proteins, how these factors are themselves regulated, which cooperate, how and on which genes. Such information, systematically generated, would result in genome control maps: genomic wiring-diagrams that describe in molecular detail how each gene is controlled by each regulatory component. My long-term aim is to develop such genome control maps since this would have wide-ranging benefits for a variety of research areas. Using a robotic facility we will first finish generating DNA microarray expression-profiles of targeted mutations in virtually all known and putative components of the transcription and signaling machinery in Saccharomyces cerevisiae, an important model organism for eukaryotic transcription. The data will be analyzed in a variety of ways, including analysis as detailed molecular phenotypes to determine regulatory relationships. Analysis alongside publicly available genome-scale data will further help uncover systems-level characteristics and the nature of the regulatory interactions observed. This will lead to biochemical and genetic follow-up experiments targeting the most interesting new regulatory mechanisms. Besides objectively assessing the role of many evolutionarily conserved regulators in parallel for the first time, the project will address key questions regarding general mechanisms of transcription regulation, such as redundancy, cross-talk, recruitment and specificity. The data will be useful for a variety of other purposes and allow functional mapping of the signaling and transcription machinery onto the genome comprehensively for the first time. |
