Unravelling RNA Structure / Function Relationships Via Novel Next-Generation Sequencing Techniques

The functionality of RNA in the cell is deeply related to its structure, and methods that merge chemical probing with next generation sequencing have created breakthroughs in the throughput and scale of RNA structure characterization. In this work we use Selective 2’-Hydroxyl Acylation Analyzed by Primer Extension Sequencing (SHAPE-Seq) to begin to resolve the RNA structure / function relationship on a scale necessitated by the omics-level questions being asked today. The flexibility and accuracy of the SHAPE-Seq technique, as part of the toolbox of powerful related NGS methods, has the ability to provide us with a reference point to both validate computational RNA structural prediction algorithms and observe RNA structures as they exist and interact in their natural environment. Here, in this work, we develop and apply SHAPE-Seq to study several model RNA systems, each of which offers an opportunity to study a different type of RNA structure / function relationship, or a different biological system. This includes providing structural analysis into protein-mediated small RNA regulatory mechanisms in E. coli and further insight into the exciting field of eukaryotic lncRNAs. We anticipate that our work with the SHAPE-Seq technology will provide the scientific community with a broad yet precise set of tools, aimed at providing unprecedented characterization of cellular RNA regulatory mechanisms. This will hopefully serve to be illuminating in offering deeper insight into a whole manifest of wide-ranging biological questions.