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Updated: Jun 11, 2025

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Comprehensive Profiling of Roquin Binding Preferences for RNA Stem-Loops.

Lasse Oberstrass1, Jan-Niklas Tants2, Chiara Lichtenthaeler1

  • 1Department of Pharmacy, Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35037, Marburg, Germany.

Angewandte Chemie (International Ed. in English)
|September 30, 2024
PubMed
Summary

Roquin proteins bind specific RNA structures to control mRNA stability. This study reveals their precise binding preferences and identifies new mRNA targets, advancing our understanding of RNA regulation.

Keywords:
RNA interactomeRNA structuresRNA-binding proteinsRNA–protein interactions

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Biochemistry

Background:

  • Cellular mRNA levels are regulated post-transcriptionally by cis-regulatory elements in the 3'-untranslated region.
  • RNA-binding proteins (RBPs) interact with these elements to control mRNA stability and degradation.
  • Roquin-1 and -2 proteins recognize specific RNA stem-loop motifs (CDEs and ADEs) to initiate mRNA decay.

Purpose of the Study:

  • To rigorously characterize the RNA-binding capacity of the Roquin ROQ domain towards different stem-loop structures.
  • To clarify the exact binding preferences of Roquin proteins.
  • To identify novel Roquin target mRNAs and elucidate the biological function of RBPs.

Main Methods:

  • Development and application of sRBNS (structured RNA Bind-n-Seq), a customized workflow using pre-structured RNA libraries.
  • Nucleotide-resolution mapping of the ROQ domain's RNA-binding preference.
  • Prediction and in-cell verification of novel Roquin target mRNAs.

Main Results:

  • Roquin demonstrated a clear preference for specific RNA loop sizes.
  • Extended consensus motifs for constitutive decay elements (CDEs) and alternative decay elements (ADEs) were identified.
  • Newly identified motifs are recognized with nanomolar affinity via the canonical RNA-ROQ interface, and novel mRNA targets were validated in cells.

Conclusions:

  • The study systematically investigated Roquin's structural RNA-binding preferences using high-throughput assays.
  • The expanded understanding of Roquin-RNA interactions facilitates comprehensive identification of mRNA targets.
  • This work elucidates the biological function of RBPs in post-transcriptional gene regulation.