ArticleNature chemical biology2019
Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling.
Article in Nature chemical biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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Who cites it
93 citing papers in PubMed, 137 citations in OpenAlex.
- Multiomic proximity labeling in vivo by D-amino-acid-activated peroxidase reaction.Nature chemical biology · 2026Article
- Article
- Mechanisms and Applications of Photocatalytic Proximity Labeling.Chemical & biomedical imaging · 2026Review
- Quantitative profiling of RNA modifications enriched in non-membrane-bound cellular structures using APEX-RNA-MS.Cell chemical biology · 2026Article
- Directed evolution of Lantern enables rapid RNA and protein proximity labeling.Nature chemical biology · 2026Article
- Evolving faster proximity chemistry.Nature chemical biology · 2026Article
- LipoID profiles lipid droplet interactions and identifies interorganelle regulators.Nature chemical biology · 2026Article
- Kinetic Control of Nuclear-encoded Mitochondrial mRNA Localization and Local Translation.bioRxiv : the preprint server for biology · 2026Article
- Application of Proximity-Labeling Techniques in Plants: A Review of Successful Cases.International journal of molecular sciences · 2026Review
- A practical guide to investigating biomolecular condensates: a comment from the plant community.Science China. Life sciences · 2026Review
- APEX-seq maps transcriptome-wide subcellular RNA localization in living cells.Nature protocols · 2026Review
- Recent Advances in Photocatalyst-Driven Protein Labeling and Proximity Mapping.Chemical record (New York, N.Y.) · 2026Review
- Kinetic and Spatial Resolution by dSTORM of miniSOG-Mediated Proximity Labeling in Mammalian Cells.Chembiochem : a European journal of chemical biology · 2026Article
- Transcriptomics Insights into Spinal Cord Injury for Therapy Development.International journal of molecular sciences · 2026Review
- Modulating Protein Function through Genetically Encoded Oxidative Chemistry.Journal of the American Chemical Society · 2026Article
- Directed Evolution Improves the Catalytic Efficiency of APEX2-Mediated Proximity-Dependent RNA Labeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Programmable RNA acetylation with CRISPR-Cas13.Nature chemical biology · 2026Article
- HNature chemical biology · 2026Article
- The choreography of development: RNA localization across time and space.Development (Cambridge, England) · 2026Review
- Simultaneous profiling of native-state proteomes and transcriptomes of neural cell types using proximity labeling.Nature communications · 2026Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA molecules are highly compartmentalized in eukaryotic cells, with their localizations intimately linked to their functions. Despite the importance of RNA targeting, our current knowledge of the spatial organization of the transcriptome has been limited by a lack of analytical tools. In this study, we develop a chemical biology approach to label RNAs in live cells with high spatial specificity. Our method, called CAP-seq, capitalizes on light-activated, proximity-dependent photo-oxidation of RNA nucleobases, which could be subsequently enriched via affinity purification and identified by high-throughput sequencing. Using this technique, we investigate the local transcriptomes that are proximal to various subcellular compartments, including the endoplasmic reticulum and mitochondria. We discover that messenger RNAs encoding for ribosomal proteins and oxidative phosphorylation pathway proteins are highly enriched at the outer mitochondrial membrane. Due to its specificity and ease of use, CAP-seq is a generally applicable technique to investigate the spatial transcriptome in many biological systems.
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Registered trials
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.