Transcriptome-wide mapping of RNA-RNA interactions by CLASH

Pairwise interactions between RNA molecules are fundamental to many biological processes, including translation, splicing, and gene regulation. Traditionally, RNA-RNA interactions have been mapped experimentally one at a time, or predicted computationally. To facilitate the study of RNA interactomes, we have recently developed CLASH (Cross-linking, Ligation and Sequencing of Hybrids), an experimental technique that captures RNA-RNA interactions by physically joining two RNA molecules into a single chimeric RNA molecule, followed by next-generation sequencing. I will discuss the applications of this approach in the study of ribosome biogenesis, gene regulation by microRNAs, and splicing. I will also present a new experimental approach that will allow comprehensive mapping of genetic interactions within and between genes, at a single nucleotide resolution.