RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution

Abstract RNA-binding proteins (RBPs) regulate gene expression through interactions with RNA molecules. Many RBPs reside in multiple compartments within cells, partitioning their accessible RNA targets and regulome. To characterize RBP-RNA interactions at subcellular resolution, we develop RBProximity-CLIP, which enables compartment-specific capture and profiling of individual RBP-RNA interactions by combining APEX2-based proximity labeling and 4-thiouridine–enhanced RBP-RNA crosslinking, with sequential RBP- and biotin-affinity purifications. Using RBProximity-CLIP, we profile subcellular RNA interactions of AGO2, YBX1, and ELAVL1. We reveal distinct, compartment-specific RNA-binding patterns by these RBPs through canonical motif recognition.

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Publication Details

Journal
Genome biology
Published
2026-09-11
DOI
https://doi.org/10.1186/s13059-026-04278-6
Primary Topic
RNA Research and Splicing
Type
article
Field-Weighted Citation Impact
0.00

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RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution

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Genome biology
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RBProximity-CLIP enables subcellular mapping of RNA-binding protein interactions at nucleotide resolution

Dimitrios G. Anastasakis, Markus Hafner, Jérémy Scutenaire, Vivian Lobo, Aishe A. Sarshad, Daniel Benhalevy, Hang T Huynh, Iwona Nowak, Michelle Fong, Ghaliah Alluhaibi, Ahsan H. Polash, Mahekdeep Kaur
article en

Abstract

Abstract RNA-binding proteins (RBPs) regulate gene expression through interactions with RNA molecules. Many RBPs reside in multiple compartments within cells, partitioning their accessible RNA targets and regulome. To characterize RBP-RNA interactions at subcellular resolution, we develop RBProximity-CLIP, which enables compartment-specific capture and profiling of individual RBP-RNA interactions by combining APEX2-based proximity labeling and 4-thiouridine–enhanced RBP-RNA crosslinking, with sequential RBP- and biotin-affinity purifications. Using RBProximity-CLIP, we profile subcellular RNA interactions of AGO2, YBX1, and ELAVL1. We reveal distinct, compartment-specific RNA-binding patterns by these RBPs through canonical motif recognition.

Genome biology
Tel Aviv University (IL), National Institute of Arthritis and Musculoskeletal and Skin Diseases (US), Institute for Biomedicine (IT), AstraZeneca (Finland) (FI), InDex Pharmaceuticals (Sweden) (SE), University of Gothenburg (SE)
Svenska Sällskapet för Medicinsk Forskning, Israel Science Foundation, Knut och Alice Wallenbergs Stiftelse, Vetenskapsrådet, Göteborgs Universitet
Openalex Percentile: Top 18%
RNA Research and Splicing
DOIOpen Access PDFOpenAlex
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