RNA-protein interaction techniques - A historical and comparative analysis

RNAs intricately orchestrate a myriad of molecular and cellular processes. This includes mRNAs which serve as the essential blueprints for protein synthesis and the non-coding RNAs which act as versatile regulators, influencing gene expression, RNA stability, and even protein function. Over the past few decades, a diverse array of RNA- and protein-centric methodologies have emerged to discern and elucidate the identities of RNA binding proteins (RBPs) and RNAs engaged in RNA-Protein interactions (RPI). The selection of an appropriate method is paramount, given the distinctive advantages and limitations inherent to each technique, in order to effectively address specific biological inquiries. This review spans the spectrum of techniques employed in RNA-Protein interaction studies, ranging from time-honored methods like Electrophoretic Mobility Shift Assay (EMSA) to contemporary approaches such as CRISPR-based RNA-Protein interaction profiling (CBRIP). This review aims not only to list methods but also to provide historical background, discuss the strengths and weaknesses of each approach, and highlight their current applications. Furthermore, it consolidates methodologies tailored to characterize RNA-protein interactions based on their distinct purposes.