Dynamic RNA Folding and Function

About This Grant

SUMMARY This research broadly seeks to reveal molecular principles that enable biological systems to sense and adapt to changing environments, and to understand how to use these principles to engineer synthetic biological systems that benefit humankind. A focal point of this work is RNA – a fundamental component of all living systems that enacts genetic, regulatory and catalytic functions by folding into intricate shapes within cells. As RNA folding can occur immediately during transcription, this raises a fundamental question as to how nascent RNA structures can influence many aspects of gene expression including transcription, translation, splicing, and polyadenylation. The overall vision for this proposed research program is to address aspects of this question through detailed structure-function studies of riboswitches and model eukaryotic systems, and development of technologies that can measure and model nascent RNA folding in broad RNA systems. Riboswitches are broadly distributed non- coding regulatory RNAs that bind to specific ligands and in response control gene expression. A critical feature of many riboswitches is that regulation occurs during transcription, making them ideal model systems to study the impacts of nascent RNA structure on gene expression. Principles of nascent RNA folding and function learned from riboswitches is beginning to be shown to hold true in other areas of biology including non-coding RNA biogenesis and eukaryotic RNA Pol III transcription termination. Our goal is to develop a molecular understanding of how cotranscriptional RNA folding regulates and coordinates cellular gene expression. Towards this goal, over the next five years we propose two research themes. The first uses diverse riboswitches, and eukaryotic RNA Pol III transcription termination, as model systems, to uncover general, quantitative relationships between RNA sequence, nascent folding, and transcription termination and translation initiation. We will combine high throughput cellular and in vitro functional characterization approaches to rapidly characterize model regulatory RNA sequence variants, with a hybrid experimental-computational approach called Reconstructing RNA Dynamics from Data (R2D2) to measure and model cotranscriptional RNA folding. Biophysical and data-driven modeling will be used to uncover quantitative relationships to address fundamental questions about how RNA folding kinetics and nascent RNA-RNA polymerase interactions govern transcription and translation regulation. Theme two will incorporate RNA folding energetics extracted from RNA structure chemical probing to improve R2D2’s accuracy and integrate new computational RNA folding algorithm developments to allow R2D2 to reconstruct RNA structure sub-populations of longer RNA systems. Detailed knowledge of how nascent RNA folding links to RNA regulatory function will contribute to a deeper understanding of gene expression processes, as well as numerous RNA biotechnologies such as diagnostics, RNA-targeting antibiotics and drugs, and nucleic acid therapeutics.