Mapping In Situ RNA–RNA Interactions with RIC-seq

Abstract

Mammalian genomes encode large amounts of noncoding RNAs (ncRNAs), which tend to form intricate structures and interact with their target RNA molecules through complementary base pairing with the help of proteins. Mapping of intra- and inter-molecular RNA–RNA interactions (RRIs) is required to unravel the structure and targets of ncRNAs which are two essential aspects for understanding the molecular mechanisms of ncRNAs in various biological processes. At this frontiers, we recently invented RNA in situ conformation sequencing (RIC-seq) technology to profile protein-mediated RNA–RNA spatial interactions at single-nucleotide resolution in an unbiased manner. We have demonstrated that RIC-seq-identified RRIs are helpful for simultaneously deducing ncRNA structures and targets. Here, we summarize methods for probing RRIs and describe a step-by-step protocol for generating a successful RIC-seq library.