RNA-Centric Methods: Toward the Interactome of Specific RNA Transcripts

Highlights

• RNA–protein interactions play a role in various cellular processes, and methods to study these interactions are expanding.

• RNA–protein complexes can be isolated, after which bound proteins can be identified by western blot or mass spectrometry.

• Despite the variety of existing methods, it remains challenging to characterize the global interactome of a specific RNA transcript in their native context and upon cellular perturbations.

• Promising technologies use RNA-targeting systems coupled with proximity-dependent biotinylation to identify RNA–protein interactions in vivo.

RNA–protein interactions play an important role in numerous cellular processes in health and disease. In recent years, the global RNA-bound proteome has been extensively studied, uncovering many previously unknown RNA-binding proteins. However, little is known about which particular proteins bind to which specific RNA transcript. In this review, we provide an overview of methods to identify RNA–protein interactions, with a particular focus on strategies that provide insights into the interactome of specific RNA transcripts. Finally, we discuss challenges and future directions, including the potential of CRISPR-RNA targeting systems to investigate endogenous RNA–protein interactions.