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

GSE311748 Homo sapiens Expression profiling by high throughput sequencing 6 samples Submitted 2026/01/12 Platform GPL34284
Summary
RNA-binding proteins (RBPs) orchestrate post-transcriptional gene regulatory (PTGR) processes through specific interactions with RNA molecules, which are tightly regulated in both space and time, including through the subcellular compartmentalization of RBPs and their target RNAs. To characterize these interactions in specific subcellular compartments, we developed RBProximity-CLIP, an approach that integrates targeted APEX2-based proximity labeling with 4-thiouridine–enhanced RNA–protein crosslinking to enable the isolation and profiling of target sites of individual RBPs in a compartment-specific manner . Using this approach, we profiled three RBPs—AGO2, YBX1, and ELAVL1—within the cytoplasmic, nuclear, and nucleolar compartments. RBProximity-CLIP enabled robust isolation of compartment specific RBP-RNA interactome and new insights of compartmental specific gene regulation of distinct RBPs.
Published in
RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution
Nowak I, Polash AH, Huynh HT et al. · bioRxiv : the preprint server for biology 2025 · PMID 41473311 · doi:10.64898/2025.12.12.693770
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Also filed as BioProject PRJNA1370872 and SRA study SRP649669. Searching any of these in the dataset finder brings you back here.

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