Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

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. By deploying the exoribonuclease XRN1, ePRINT allows precise mapping of the 5’ end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons. Given its versatility, ePRINT has vast application potential as an investigative tool for RNA regulation in development, health and disease. The following are sequencing data for an enhanced crosslinking immunoprecipitation-seq experiments. The sets contain the RNAs directly crosslinked to FUS with a size-matched control used as an input.