The RNA Binding Protein EWS Is Broadly Involved in the Regulation of Pri-miRNA Processing in Mammalian Cells

The Ewing Sarcoma protein (EWS) is a multifaceted RNA binding protein (RBP) with established roles in transcription, pre-mRNA processing, and DNA damage response. By generating high quality EWS-RNA interactome, we uncovered its specific and prevalent interaction with a large subset of primary microRNAs (pri-miRNA). Depletion of EWS reduced, while overexpression enhanced, the expression of its target miRNAs. Biochemical analysis revealed that multiple elements in target pri-miRNAs, including the sequences flanking the stem-loop region, contribute to EWS binding and sequence swap between target and non-target demonstrated that the flanking sequences provide the specificity for enhanced pri-miRNA processing by the Microprocessor Drosha/DGCR8. Interestingly, as previously reported and we confirmed, EWS appears to repress Drosha expression, and we further demonstrated that EWS is able to enhance the recruitment of Drosha to the chromatin. Together, these findings suggest that EWS may positively and negatively regulate miRNA biogenesis, but via distinct mechanisms, thus providing a new foundation to understand the function of EWS in development and disease. EWS CLIP-seq