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

• Published in: Nature communications Vol. 10; no. 1; pp. 2266 - 18
• Main Authors: Schneider, Tim, Hung, Lee-Hsueh, Aziz, Masood, Wilmen, Anna, Thaum, Stephanie, Wagner, Jacqueline, Janowski, Robert, Müller, Simon, Schreiner, Silke, Friedhoff, Peter, Hüttelmaier, Stefan, Niessing, Dierk, Sattler, Michael, Schlundt, Andreas, Bindereif, Albrecht
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22.05.2019; Nature Publishing Group; Nature Portfolio
• Subjects: 140/131; 38; 38/91; 631/337/1645; 631/535; Combinatorial analysis; Domains; Gene expression; Gene Expression Regulation - physiology; Gene regulation; Gene sequencing; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Models, Molecular; multidisciplinary; Protein Binding - physiology; Proteins; Recombinant Proteins - chemistry; Recombinant Proteins - isolation & purification; Recombinant Proteins - metabolism; Ribonucleic acid; RNA; RNA, Messenger - chemistry; RNA, Messenger - metabolism; RNA-Binding Motifs - physiology; RNA-binding protein; RNA-Binding Proteins - chemistry; RNA-Binding Proteins - isolation & purification; RNA-Binding Proteins - metabolism; Science; Science (multidisciplinary); SELEX Aptamer Technique; Sequence Analysis, DNA - methods; Target recognition; Topology
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-09769-8

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. Multidomain RNA-binding proteins recognize specific target sequences through mechanisms that are not well understood. Here the authors present an integrated approach to define the RNA-binding specificity and RNP topology and apply it to the analysis of the prototypical multidomain RNA-binding protein IMP3.