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RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution.

Iwona Nowak1,2, Ahsan H Polash3, Hang T Huynh1,2

  • 1Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden.

Biorxiv : the Preprint Server for Biology
|December 31, 2025
PubMed
Summary
This summary is machine-generated.

Researchers developed RBProximity-CLIP to map RNA-binding protein (RBP) interactions within specific cellular compartments. This method reveals how RBP-RNA interactions change across the cytoplasm, nucleus, and nucleolus, offering new insights into gene regulation.

Keywords:
AGO2APEX2ELAVL1Proximity labelingRNA binding proteinsYBX1fPAR-CLIP

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Area of Science:

  • Molecular Biology
  • Genetics
  • Cell Biology

Background:

  • RNA-binding proteins (RBPs) are crucial regulators of gene expression at the post-transcriptional level.
  • Subcellular localization of RBPs determines their access to RNA targets and the regulatory outcomes.
  • Understanding RBP-RNA interactions within specific cellular compartments is essential for deciphering spatial gene regulation.

Purpose of the Study:

  • To develop a novel method, RBProximity-CLIP, for characterizing RBP-RNA interactions at subcellular resolution.
  • To profile the compartment-specific RNA interactomes of key RBPs, including AGO2, YBX1, and ELAVL1.
  • To investigate how subcellular compartmentalization influences RBP-RNA binding and gene regulation.

Main Methods:

  • RBProximity-CLIP combines APEX2-based proximity labeling and 4-thiouridine-enhanced RNA-protein crosslinking.
  • Sequential RBP- and biotin-affinity purifications enable compartment-specific isolation of RBP-RNA complexes.
  • The method allows for sensitive and specific detection of RBP-RNA interactomes within defined subcellular locations.

Main Results:

  • RBProximity-CLIP successfully profiled RNA targets of AGO2, YBX1, and ELAVL1 across cytoplasmic, nuclear, and nucleolar compartments.
  • Nucleus-specific, miRNA-mediated targets for AGO2 were identified.
  • Distinct subsets of YBX1 and ELAVL1 targets were found in different compartments, despite sharing identical binding motifs.

Conclusions:

  • RBProximity-CLIP provides a powerful tool for mapping compartment-specific RBP-RNA interactions.
  • The findings reveal novel insights into the spatial regulation of gene expression by RBPs.
  • Understanding the subcellular dynamics of RBP-RNA interactions is key to comprehending PTGR.