Evidence map›Paper›PMID 42681519›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

RBProximity-CLIP: A Method for Profiling the Interactome of an RNA-Binding Protein at Subcellular Resolution.

Iwona Nowak, Hang T Huynh, Mahekdeep Kaur, Orli Korchev, Veronica Moskovicz, Vivian Lobo, Michelle Fong, Aishe A Sarshad, Daniel Benhalevy

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Iwona Nowak *Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
Hang T Huynh *Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
Mahekdeep Kaur *The Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Orli Korchev *The Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Veronica Moskovicz *The Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Vivian LoboDepartment of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
Michelle FongDepartment of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
Aishe A SarshadDepartment of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden. aishe.sarshad@gu.se.
Daniel BenhalevyThe Lab for Cellular RNA Biology, Shmunis School of Biomedicine and Cancer Research, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel. benhalevyd@tauex.tau.ac.il.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

RNA-binding proteins (RBPs) are central players in post-transcriptional gene regulation (PTGR), and their mode of action often depends on subcellular localization. Conventional crosslinking and immunoprecipitation (CLIP) methods map the RNA targets of RBPs with nucleotide resolution but lack spatial specificity, making it impossible to distinguish how one RBP can contribute to biological processes across distinct compartments simultaneously. Here, we present RBProximity-CLIP, an extension of Proximity-CLIP that integrates APEX2-mediated proximity labeling with UV crosslinking of 4-thiouridine-labeled RNAs, followed by sequential biotin- and RBP-specific immunoprecipitations, to capture RBP-RNA complexes with both spatial and protein specificity. RBProximity-CLIP generates nucleotide-resolution maps of RBP-RNA interactions and enables proteomic characterization of complete ribonucleoprotein (RNP) compositions. Using Y-box binding protein 1 (YBX1) as a model RBP, we provide a detailed protocol for RBProximity-CLIP.

Indexed as

ImmunoprecipitationProteomicsRNARNA-Binding ProteinsCross-Linking ReagentsHumansProtein BindingRibonucleoproteinsY-Box-Binding Protein 1Cross-Linking ReagentsRibonucleoproteinsRNARNA-Binding ProteinsY-Box-Binding Protein 1YBX1 protein, humanAPEX2Crosslinking and immunoprecipitation (CLIP)Multifunctional RBPsMultilocalized RBPsPost-transcriptional gene regulationProtein–RNA interactionsProximity-biotinylationRNA-binding proteins (RBPs)Spatial transcriptomicsSubcellular resolutionYBX1

Identifiers

PMID42681519

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.