RNA binding proteins are dynamically interacting with cellular RNA transcripts to regulate their stability, degradation rate, cellular localization, and interaction propensity. Protein-RNA interactions are at the basis of key biological processes such as transcription, RNA splicing, RNA nuclear export, and translation. Specific methods have been developed to study protein-RNA interactions in vitro, in cell, and in vivo models. Especially in the last few years, a particular emphasis has been given to the development of specific methodologies that allows the identification of RNA-protein interactions through OMICS-technologies. In particular, protein-centric and RNA-centric strategies have been coupled to next-generation sequencing and mass spectrometry-based approaches, respectively. This methodology has enhanced the detection of transient interactions as well as the identification of low abundant interactors. In addition, it has been possible to identify and characterize the role that posttranscriptional and posttranslational modifications are playing within RNA and protein interactions.

The aim of this Methods Collection is to include the current methods used to identify, quantify, and characterize RNA-protein interactions occurring both in prokaryotic and eukaryotic cells. Specifically, methods that can determine the dynamics of the interaction of a specific protein and an RNA, such as ITC, BLI, switchSENSE, and the fluorescence-based methods (FRET, FRAP); the structural characteristics of protein-RNA interactions as assessed by NMR, CD, DLS; the global and unbiased identification of RNA-proteins interactions obtained by the adoption of antisense oligos used as probes (RNA-pulldowns, ChIRP, RAP, iDRIP), RNA immunoprecipitation strategies (RIP, CLIP), proximity-ligation techniques (APEX2, RaPID, CaRPID, TRIBE) and organic: aqueous phase separation methods (XRNAX, OOPS, PTEx).