Regulation by the RNA-binding protein Unkempt at its effector interface [iCLIP]

How RNA-binding proteins (RBPs) convey regulatory instructions to the core effectors of RNA processing is unclear. Here we document the existence and functions of a multivalent RBP–effector interface. We show that the effector interface of a conserved RBP with an essential role in metazoan development, Unkempt, is mediated by a novel type of 'dual-purpose' peptide motifs that can contact two different surfaces of interacting proteins. Unexpectedly, we find that the multivalent contacts do not merely serve effector recruitment but are required for the accuracy of RNA recognition by Unkempt. Systems analyses reveal that multivalent RBP–effector contacts can repurpose the principal activity of an effector for a different function, as we demonstrate for reuse of the central eukaryotic mRNA decay factor CCR4-NOT in translational control. Our study establishes the molecular assembly and functional principles of an RBP–effector interface. Overall design: We mapped binding sites of ectopic UNK in HeLa cells with doxycycline (Dox)-inducible expression of UNKWT, UNKdPAM2, or UNK3M at 24 hours of incubation with Dox. We separately mapped binding sites of PABPC1 in HeLa cells with Dox-inducible expression of UNKWT, UNKdPAM2, or UNK3M at 24 hours of incubation with Dox, as well as in untreated UNKWT-inducible HeLa cells. We processed four biological replicates for UNK iCLIP per condition. Two biological replicates for PABPC1 iCLIP