Opportunities and Challenges in Global Quantification of RNA-Protein Interaction via UV Cross-Linking

RNA-binding proteins (RBPs) are key mediators of posttranscriptional gene expression control. However, the links between cell signaling on one hand and RBP function other understudied. While thousands posttranslational modification (PTM) sites RBPs have been identified, their functional roles only poorly characterized. RNA-interactome capture (RIC) cross-linking immunoprecipitation (CLIP) attractive methods that provide information about RBP-RNA interactions a genome-wide scale. Both approaches rely in situ UV RNAs, biochemical enrichment analysis by RNA-sequencing or mass spectrometry (RIC). In principle, RIC- CLIP-like could be used to globally quantify response perturbations. several biases taken into account avoid misinterpretation results obtained. Here, we focus RIC-like discuss four aspects relevant for quantitative interpretation: (1) RNA isolation efficiency, (2) inefficient highly variable cross-linking, (3) baseline occupancy RBPs, (4) indirect factors affecting interaction. We highlight these points presenting selected examples PTMs might induce differential quantification experiments without necessarily RNA-binding. conclude quantifying via RIC should not regarded as an end itself but rather starting deeper analysis.