ArticleNucleic acids research2022
Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 65 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
- Directed evolution of Lantern enables rapid RNA and protein proximity labeling.Nature chemical biology · 2026Article
- Subcellular localization of human long non-coding RNAs is an isoform-resolved property masked by gene-level analysis.Molecular genetics and genomics : MGG · 2026Article
- PCRD-seq: proximity crosslinking-induced RNA depletion sequencing for low-input chromatin-associated transcriptome profiling.Nucleic acids research · 2026Article
- The choreography of development: RNA localization across time and space.Development (Cambridge, England) · 2026Review
- Progress and challenges in profiling protein-RNA and protein-associated RNA-RNA interactions.RNA (New York, N.Y.) · 2026Review
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- 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
- High-throughput Screening of Sequence Elements Associated with RNA Localization.Computational and structural biotechnology journal · 2026Article
- The RNA-binding protein HNRNPA2B1 regulates neurite RNA abundance and motor-dependent cargo transport.Molecular biology of the cell · 2025Article
- Photocatalytic labelling-enabled subcellular-resolved RNA profiling and synchronous multi-omics investigation.Nature chemistry · 2025Article
- Systematic discovery of subcellular RNA patterns in the gut epithelium.Genome biology · 2025Article
- Precise andACS central science · 2025Article
- Ribosome biogenesis: A central player in liver diseases.Genes & diseases · 2025Review
- Analyzing RNA Localization Using the RNA Proximity Labeling Method OINC-seq.Bio-protocol · 2025Article
- A molecular cartographer's toolkit for mapping RNA's uncharted realms.Cell reports · 2025Review
- Quantification of subcellular RNA localization through direct detection of RNA oxidation.Nucleic acids research · 2025Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.
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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.