Part IX: Unraveling the interplay between transcription and RNA folding

RNA mediates essential biological processes in all organisms. These functions include catalysis of crucial biochemical reactions such as peptidyl transfer during translation and transesterification during RNA splicing, regulation of gene expression, and defense against foreign nucleic acids. A unifying characteristic of RNA-mediated cellular activities is that their function and specificity frequently depend on RNA secondary and tertiary structures which begin to fold during transcription. RNA sequence can therefore be constrained by its coding potential, by the architecture of its biochemically active folds, and by the requirements of co-transcriptional structure formation. Consequently, understanding the interdependence of these constraints is fundamental to predicting how changes in an RNA sequence affect its structure and biological function. As an Arnold O. Beckman Postdoctoral Fellow, my research has focused on addressing this fundamental challenge through the development and application of systematic in vitro methods for assessing cotranscriptional RNA structure and function. These studies have begun to expose the molecular details of cotranscriptional gene regulation in bacteria and have established a foundation for the continued development of quantitative experimental tools to understand how transcription and RNA folding are coordinated in biological systems.