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. Methods to identify transcriptome wide binding of RBPs without purifying individual RBPs are gaining interest. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale in an RBP agnostic manner. Our method allows precise mapping of the 5' end of the RBP binding site and uncovers RBPs that are differentially activated during cell fate transitions. Overall design: ePRINT analysis of HEK293T cells transfected with an siRNA against FUS or a scrambled control siRNA. ePRINT analysis of motor neuron progenitors and differentiated motor neurons.