Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Abstract

RNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale without purifying individual RBPs. ePRINT allows precise mapping of the 5 end of the RBP binding site, and can uncover direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, for instance, as neural progenitors differentiate into neurons. Given its versatility, ePRINT has vast application potential as an investigative tool for RNA regulation in development, health and disease.