ArticleNature methods2024
Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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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.
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Who cites it
29 citing papers in PubMed.
- Mapping subcellular microenvironments using oligonucleotide-directed proximity labeling.Current opinion in chemical biology · 2026Review
- Accurate RNA-Ligand Binding Site Prediction Based on a Multi-Channel Graph Neural Network.Interdisciplinary sciences, computational life sciences · 2026Article
- Epistemological parameters in the recent era of nuclear organization and function.Molecular biology of the cell · 2026Review
- Review
- Scanning transcriptomes for nonlinear, domain-level similarities using hmSEEKR.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide mapping of RNA-protein associations through sequencing.Nature biotechnology · 2026Article
- Correlated protein-RNA associations and a requirement for HNRNPU in the long-range recruitment of Polycomb Repressive Complexes by the lncRNAs Airn and Kcnq1ot1.PLoS genetics · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- Widespread DNA off-targeting confounds RNA chromatin occupancy studies.Nature biotechnology · 2026Article
- A unified photosensitizer platform forbioRxiv : the preprint server for biology · 2026Article
- Inherent Specificity and Variation Sensitivity as Quantitative Metrics for RBP Binding.bioRxiv : the preprint server for biology · 2026Article
- Article
- Recent Advances in Proximity Labeling-Based Subcellular Proteomic Mapping.Molecular & cellular proteomics : MCP · 2026Review
- HCR-Proxy resolves site-specific proximal RNA microenvironments at subcompartmental resolution.Nucleic acids research · 2026Article
- Long noncoding RNA regulation of immunity.Nature immunology · 2026Review
- RNA-stabilized coat proteins for sensitive and simultaneous imaging of distinct single mRNAs in live cells.Nature methods · 2026Article
- Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq).Nature communications · 2025Article
- Impact of somatic XIST deletions on ongoing XIST expression and inactive X silencing and heterochromatin.Human molecular genetics · 2025Article
- The emerging roles of long non-coding RNAs in the nervous system.Nature reviews. Neuroscience · 2025Review
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
RNA molecules form complex networks of molecular interactions that are central to their function and to cellular architecture. But these interaction networks are difficult to probe in situ. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a method for elucidating the biomolecules near an RNA of interest, within its native context. O-MAP uses RNA-fluorescence in situ hybridization-like oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA in situ, enabling nearby molecules to be enriched by streptavidin pulldown. This induces exceptionally precise biotinylation that can be easily optimized and ported to new targets or sample types. Using the noncoding RNAs 47S, 7SK and Xist as models, we develop O-MAP workflows for discovering RNA-proximal proteins, transcripts and genomic loci, yielding a multiomic characterization of these RNAs' subcellular compartments and new regulatory interactions. O-MAP requires no genetic manipulation, uses exclusively off-the-shelf parts and requires orders of magnitude fewer cells than established methods, making it accessible to most laboratories.
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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.