Mechanistic Problems in Eukaryotic Gene Regulation

Northwestern University, Evanston IL

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Abstract

DESCRIPTION (provided by applicant): The long-term aim of my research program is to develop a quantitative understanding of gene regulation in vivo. This project focuses on the earliest steps in gene regulation, namely, how gene regulatory proteins gain access to their DNA target sites in chromatin. Access to target sites inside nucleosomes can occur spontaneously, and can be catalyzed by ATP-dependent nucleosome remodeling factors. We are studying both of these mechanisms. Studies in Aim 1 will characterize the equilibria and kinetics for spontaneous invasion of nucleosomes by site-specific DNA binding proteins, in model chromatin fibers. Studies in Aim 2 seek to elucidate the detailed molecular mechanisms by which the Snf2 class of ATP-dependent remodeling machines act to alter the structure of protein-DNA complexes including nucleosomes. We focus on the yeast Snf2 family member Mot1 because we believe its activity- the displacement of TBP from DNA - to be the simplest of any of the Snf2 family members, and thus the most amenable to detailed mechanistic analysis at this time. Mot1 is also of great importance in its own right, since TBP occupancy at both TATA-containing and TATA-less promoters can be rate-limiting for gene expression. Studies in this aim will advance our understanding of Mot1 domain organization and function, and define the mechanism of mechanochemical coupling in Mot1 action PUBLIC HEALTH RELEVANCE: The proper regulation of genes is essential for the development and health of all organisms. Our expectation is that understanding how regulatory proteins find and bind to their DNA target sites will lead, over the long term, to a better understanding of fundamental mechanisms in disease processes, and from there, to new diagnostics. We also expect that progress in the aims of this project will lead to an improved ability to engineer artificial transgenes for applications in biotechnology and gene therapy. Studies of ATP-dependent nucleosome remodeling factors have a specific relevance to human development and health, as mutations in these factors are responsible for a wide range of human developmental diseases and cancers, including: Williams syndrome, Schimke immunoosseous dysplasia, Cockayne syndrome, X-linked 1 thalassaemia, mental retardation, malignant rhabdoid tumors, chronic myeloid leukemia, and prostate and lung carcinomas.