A large part of the regulation of gene expression occurs through control of transcription. Factors that influence transcription thus play a pivotal role in the expression of all human genes, and are relevant to a wide range of human health related subjects including embryology, virology, and oncogenesis. A complete understanding of the process of transcription will require detailed descriptions of the structures at each stage of transcription. The research described in this application will characterize the solution structure of transcription-related DNA protein complexes using a number of approaches that are generally based on measuring the topological properties of the DNA in these complexes. A new method, termed rotational variant analysis, will be used to measure changes in the bend and duplex winding angles in the DNA of prokaryotic transcription complexes at various stages of transcription initiation and elongation. The resulting description of DNA architecture in these complexes will test current mechanistic models for transcription initiation.
A second aim will quantify topological changes to characterize the structure of a looped structure of DNA proposed to be involved in regulation of transcription.
A third aim will measure changes in topology induced in the DNA when a eukaryotic promoter is bound by transcription factors in a preinitiation complex, as well as when RNA polymerase binds to this complex. This information will bear upon the question of how closely eukaryotic and prokaryotic transcription mechanisms are related. The specific, quantitative information available from these studies will improve our understanding of the basic mechanism of transcription and its control in prokaryotes and eukaryotes. An understanding of this fundamental cellular function is an essential step in addressing malfunctions of this process, such as occurs in cancer, diabetes, and metabolic diseases, as well as during viral and bacterial infection.