Signal or noise? RNA-binding proteins and the challenges of binding site assignments

A significant body of research has been devoted to pinpointing and cataloguing the binding sites of RNA-binding proteins (RBPs) on target transcripts. The most common techniques involve crosslinking and immunoprecipitation (CLIP) followed by high-throughput sequencing. In this review, we provide a comprehensive summary of the major advancements in CLIP-based techniques and state-of-the-art data analysis methods designed for identifying and analysing the binding sites of RBPs. We also brief on methods used to determine the functional relevance of these binding sites and, in addition, delve into the major hurdles faced in the detection and elucidation of the binding sites of RBPs. Finally, we explore reproducibility concerns in the CLIP field, and conclude by suggesting potential avenues for future improvements.