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RBPscan: A quantitative in vivo tool for profiling RNA-binding protein interactions.

Dmitry A Kretov1, Owen Sanborn2, Thora McIsaac2

  • 1Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA; Department of Molecular Biology, Medical Biochemistry, and Pathology, Faculty of Medicine, Université Laval, Québec, QC G1V 0A6, Canada; Oncology Division, CHU de Québec - Université Laval Research Center, Québec, QC G1J 0J9, Canada; Université Laval Cancer Research Center, Québec, QC G1J 0J9, Canada.

Molecular Cell
|February 7, 2026
PubMed
Summary
This summary is machine-generated.

A new method, RBPscan, uses RNA editing to profile RNA-binding protein (RBP) interactions in vivo. This tool quantifies RBP binding strength and identifies binding motifs across species.

Keywords:
ADARRBP-binding specificityRBPsRNA editingRNA motif discoveryRNA-binding proteinsadenosine deaminase acting on RNAdose-response analysismassively parallel reporter assaysmicroRNAsprotein-RNA interactions

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • RNA-binding proteins (RBPs) regulate gene expression post-transcriptionally.
  • Quantitative analysis of RBP-RNA interactions in vivo is challenging.

Purpose of the Study:

  • To develop a novel method for profiling RBP-RNA interactions in vivo.
  • To quantify RBP binding strength, dissociation constants, and binding motifs.

Main Methods:

  • Developed RBP specificity and contextual analysis via nucleotide editing (RBPscan).
  • Integrated RNA editing with massively parallel reporter assays.
  • Fused RBPs to the adenosine deaminase acting on RNA (ADAR) catalytic domain.

Main Results:

  • RBPscan successfully quantified RBP binding strength and dissociation constants.
  • Identified RBP binding motifs and mapped Pumilio-binding sites in NORAD.
  • Demonstrated utility in zebrafish, human cells, and yeast.

Conclusions:

  • RBPscan is a versatile tool for studying RBP-RNA interactions.
  • Complements existing methods for post-transcriptional regulatory network analysis.
  • Enables quantitative insights into RBP function across diverse systems.