Beyond CLIP: advances and opportunities to measure RBP–RNA and RNA–RNA interactions

RNA is an essential player in almost all biological processes, and has an ever-growing number of roles in regulating cellular growth and organization. RNA functions extend far beyond just coding for proteins and RNA has been shown to function in signaling events, chromatin organization and transcriptional regulation. Dissecting how the complex network of RNA-binding proteins (RBPs) and regulatory RNAs interact with their substrates within the cell is a real, but exciting, challenge for the RNA community. Investigating these biological questions has fueled the development of new quantitative technologies to measure how RNA and RBPs interact both locally and on a global scale. In this review, we provide an assessment of available approaches to enable researchers to select the protocol most applicable for their experimental question.