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

Nat Commun. 2019 May 22;10(1):2266. 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Gene Expression Regulation / physiology
  • High-Throughput Nucleotide Sequencing / methods
  • Models, Molecular*
  • Protein Binding / physiology
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • RNA-Binding Motifs / physiology*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / isolation & purification
  • RNA-Binding Proteins / metabolism*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / isolation & purification
  • Recombinant Proteins / metabolism
  • SELEX Aptamer Technique
  • Sequence Analysis, DNA / methods


  • IGF2BP3 protein, human
  • RNA, Messenger
  • RNA-Binding Proteins
  • Recombinant Proteins