Experimental and computational studies of the in vivo genomic repertoire of DNA -protein interactions in Escherichia coli

The ability to monitor the occupancy of transcription-factor binding sites in vivo is an important pre-requisite to modeling and understanding regulatory network dynamics. To this end, we have developed a technology for whole genome identification and monitoring of protein-DNA "footprints" in bacterial genomes. Unlike chromatin immunoprecipitation, which allows genome-wide mapping of a single transcription factor's binding sites, our approach aims to identify all protein occupancies without a priori knowledge of the factors involved. The details of this new methodology are presented in Chapter 2.;We employed the power of genome-wide analyses to detect underlying complex patterns connecting the set of DNA-protein interactions and the transcription regulatory network. In Chapter 3, genome-level views of these connections are presented. We examined local protein occupancy under changing genotypic and environmental conditions in Chapter 4. As a proof-of-principle, we considered the cellular responses mediated by the carbon catabolite repression regulon and by the entry into stationary phase of growth.;In addition to monitoring the occupancy dynamics of sequence-specific transcription factors, we are using this technology to gain a better understanding of the structural organization of the bacterial genome in terms of nucleoid proteins and the domains they help to organize. Chapter 5 contains detailed analyses of many computational and experimental data sets to explore the contribution of "bacterial heterochromatin" to overall genomic architecture.