The solution structure of Dead End bound to AU-rich RNA reveals an unprecedented mode of tandem RRM-RNA recognition required for mRNA repression

Abstract Dead End (DND1) is an RNA-binding protein essential for germline development through its role in the clearance of AU-rich mRNAs. Here, we present the solution structure of its tandem RNA Recognition Motifs (RRMs) bound to AU-rich RNA. The structure reveals how an NYAYUNN element is recognized in agreement with recent genome-wide studies. RRM1 acts as a main binding platform, including unusual helical and β-hairpin extensions to the canonical RRM fold. RRM2 acts cooperatively with RRM1, capping the RNA in an unprecedented mode of tandem RRM-RNA recognition. We show that mutation of the RNA-binding interface of the RRMs weakens affinity and repression of a reporter gene by DND1 depends on its double-stranded RNA binding domain (dsRBD). Our results point to a model where RNA recognition by DND1 is mediated by an uncanonical mode of binding by the tandem RRMs and a role for the dsRBD in the recruitment of repressing factors.