Experimental and theoretical investigations of gene regulation by chromosomal topological domains in E. coli

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Bacteria are one of the simplest forms of life on Earth. Despite their relative simplicity, each single bacterial cell is still a sophisticated living system capable of precisely responding to changes in its environment. Over the last 70 years details describing of how this regulation occurs have been uncovered, however there is still gaps in our understanding. New research is uncovering evidence of a novel mechanism employed by bacterial cells to globally control the regulation of genes using the structure of chromosomal DNA. This mechanism was long thought to be missing from bacterial life forms. Investigators will explore this previously unknown regulatory mechanism using an integrated experimental and computational modeling approach. Successful completion of the project goals will contribute to the understanding of the evolution of gene regulation in bacterial systems. As part of the broader impacts of the project, investigators will engage in interdisciplinary training of graduate students, research experience for high school students, and summer programs for elementary students within inner city communities in the Baltimore area.The objective of the project is to investigate the role of chromosomal topological domains in regulating gene expression in E. coli. The project will combine single-cell imaging, biochemical analysis, and theoretical modeling of these topological domains to uncover their global regulatory effect on gene expression. The classic dogma of bacterial genetic information processing focuses on the regulation of a gene's transcriptional activity only through the mechanism of DNA and/or RNA sequence recognition by proteins such as RNA polymerase and transcription factors. In recent years an increasing number of studies have shown that the supercoiling state of chromosomal DNA is another fundamental factor impacting gene expression in bacteria. The topological organization of chromosomal DNA into individual domains, between which the diffusion of supercoiling is prohibited, must play an important role in gene regulation. However, knowledge of how chromosomal topological domains are organized in E. coli, and how they impact gene expression, remains elusive. In this project the two principal investigators will combine their expertise in the experimental analyses of E. coli chromosomal organization and theoretical modeling of bacterial gene regulatory networks to address three specific aims: (1) Investigate whether and how the expression of multiple genes within the same topological domain is coordinated using single cell mRNA and protein production imaging methods; (2) Model gene regulation by chromosomal topological domains at the genome scale; and (3) Determine the correlation between chromosomal topological organization and gene expression profile. Results of the proposed work will result in the development of a topologically-informed gene regulatory network model.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.