Project description:In bacteria, adaptive regulation of gene expression occurs through the precise interactions of hundreds of DNA binding proteins across the chromosome. Decades of research has revealed the identity and functions of many of these regulators. However, a systems-level understanding of gene expression requires simultaneous, comprehensive monitoring of these interactions as a function of genetic and environmental perturbations. Here we present a high-resolution in vivo protein occupancy display (IPOD-HR) technology that enables quantitative and comprehensive monitoring of DNA-protein interactions across a bacterial chromosome. The global nature of IPOD-HR permits simultaneous activity profiling of all known sequence specific transcription factors and discovery of novel condition-dependent DNA-binding proteins. We show that global IPOD-HR profiles can be used for de novo discovery of sequence specificity motifs for active transcription factors. IPOD-HR also reveals many large domains of extended protein occupancy that define relatively stable, transcriptionally silent regions with unique sequence and gene functional features. IPOD-HR thus provides a unique form of systems-level access to transcriptional regulatory states that will allow rapid profiling and characterization of both known and novel regulatory logic in bacteria. We provide here IPOD-HR occupancy results across a range of genetic and physiological perturbations, as detailed in the accompanying manuscript.
