Finding and folding novel RNA structures

PROJECT SUMMARY/ABSTRACT Investigating the functional aspects of RNA structure is significant as it provides fundamental knowledge of RNA biology and advances emergent technologies that seek to use, and target, RNA therapeutically. Major obstacles to such efforts arise from our limited knowledge of the extent of functional RNA structure encoded within human pathogenic viral genomes. This renewal seeks to advance upon our previous work that developed a methodological pipeline for structured RNA discovery. This approach divides the discovery process into two parts: a scanning step, where long sequences are decomposed into overlapping analysis windows from which structure-related metrics are predicted and a folding step, where consensus structures across overlapping windows are generated revealing the most sequence-ordered, thermodynamically stable structures (an indication of an evolved property). Our approach has been very successful at identifying highly ordered and functional structures across an array of human pathogens, e.g., SARS-CoV-2, where discovered motifs were used to develop therapeutic leads. Our overarching hypothesis is that many regulatory RNA structures remain to be found in the highly restricted space of viral genomes and that they can be uncovered using a holistic research approach that combines computational and experimental methods. In this renewal, our goal is to make improvements to our discovery pipeline to overcome its current limitations (most significantly to address higher order RNA structure) and apply it to medically important viral genomes. The outcomes of this proposal will be: (i) the generation of a robust methodological pipeline for functional RNA 2D and 3D structure discovery; (ii) insight into novel regulatory features of pathogenic human viruses; and (iii) leads for future work to therapeutically target RNA structure.