ArticleNature methods2018
Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 91 citations in OpenAlex.
- LipoID profiles lipid droplet interactions and identifies interorganelle regulators.Nature chemical biology · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Repurposed hnRNPC binds mature mRNAs and safeguards the mitotic transcriptome.Nucleic acids research · 2026Article
- Single-cell profiling reveals pervasive heterogeneity in subcellular RNA localization.bioRxiv : the preprint server for biology · 2026Article
- Proximity labeling in neuroscience: decoding molecular landscapes for precision neurology.Translational neurodegeneration · 2026Review
- RBProximity-CLIP: A Method for Profiling the Interactome of an RNA-Binding Protein at Subcellular Resolution.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RBProximity-CLIP Enables Subcellular Mapping of RNA-Binding Protein Interactions at Nucleotide Resolution.bioRxiv : the preprint server for biology · 2025Article
- A molecular cartographer's toolkit for mapping RNA's uncharted realms.Cell reports · 2025Review
- Review
- Dissecting the stress granule RNA world: dynamics, strategies, and data.RNA (New York, N.Y.) · 2025Review
- CRISPR/Cas13 sgRNA-Mediated RNA-RNA Interaction Mapping in Live Cells with APOBEC RNA Editing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Decoding protein-RNA interactions using CLIP-based methodologies.Nature reviews. Genetics · 2024Review
- Spatial omics advances for in situ RNA biology.Molecular cell · 2024Review
- Mapping subcellular RNA localization with proximity labeling.Acta biochimica et biophysica Sinica · 2024Review
- Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology.Cell chemical biology · 2024Review
- Mapping RNA-protein interactions with subcellular resolution using colocalization CLIP.RNA (New York, N.Y.) · 2024Article
- Creative approaches using proximity labeling to gain new biological insights.Trends in biochemical sciences · 2024Review
- Spatiotemporal control of RNA metabolism and CRISPR-Cas functions using engineered photoswitchable RNA-binding proteins.Nature protocols · 2024Review
- Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction.Nature communications · 2024Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Methods for the systematic study of subcellular RNA localization are limited, and their development has lagged behind that of proteomic tools. We combined APEX2-mediated proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced crosslinking to simultaneously profile the proteome and the transcriptome bound by RNA-binding proteins in any given subcellular compartment. Our approach is fractionation independent and allows study of the localization of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied by proteins, in a cellular-compartment-specific manner. We used our method, Proximity-CLIP, to profile RNA and protein in the nucleus, in the cytoplasm, and at cell-cell interfaces. Among other insights, we observed frequent transcriptional readthrough continuing for several kilobases downstream of the canonical cleavage and polyadenylation site and a differential RBP occupancy pattern for mRNAs in the nucleus and cytoplasm. We observed that mRNAs localized to cell-cell interfaces often encoded regulatory proteins and contained protein-occupied CUG sequence elements in their 3' untranslated region.
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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.