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

• DOI: 10.1038/s41467-019-09769-8
• Publication Date: 2019-05-22T10:04:48Z
• Authors: Tim Schneider; Lee-Hsueh Hung; Masood Aziz; Anna Wilmen; Stephanie Thaum; Jacqueline Wagner; Robert Janowski; Simon Müller; Silke Schreiner; Peter Friedhoff; Stefan Hüttelmaier; Dierk Niessing; Michael Sattler; Andreas Schlundt; Albrecht Bindereif
• Keywords: Riboswitch; Binding selectivity; Nucleic acid structure

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