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Schneider, T.* ; Hung, L.H.* ; Aziz, M. ; Wilmen, A.* ; Thaum, S.* ; Wagner, J.* ; Janowski, R. ; Müller, S.* ; Schreiner, S.* ; Friedhoff, P.* ; Hüttelmaier, S.* ; Niessing, D. ; Sattler, M. ; Schlundt, A. ; Bindereif, A.*

Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3.

Nat. Commun. 10:2266 (2019)

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How multidomain RNA-binding proteins recognize their specific target sequences, based on a combinatorial code, represents a fundamental unsolved question and has not been studied systematically so far. Here we focus on a prototypical multidomain RNA-binding protein, IMP3 (also called IGF2BP3), which contains six RNA-binding domains (RBDs): four KH and two RRM domains. We establish an integrative systematic strategy, combining single-domain-resolved SELEX-seq, motif-spacing analyses, in vivo iCLIP, functional validation assays, and structural biology. This approach identifies the RNA-binding specificity and RNP topology of IMP3, involving all six RBDs and a cluster of up to five distinct and appropriately spaced CA-rich and GGC-core RNA elements, covering a >100 nucleotide-long target RNA region. Our generally applicable approach explains both specificity and flexibility of IMP3-RNA recognition, allows the prediction of IMP3 targets, and provides a paradigm for the function of multivalent interactions with multidomain RNA-binding proteins in gene regulation.

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