ArticleNature biotechnology2019
RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 56 citations in OpenAlex.
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- CircTarget: a comprehensive database of circRNA-target RNA interactions across multiple cell types.Nucleic acids research · 2026Article
- Applications of single-cell analysis in immunotherapy for lung cancer: Current progress, new challenges and expectations.Journal of advanced research · 2025Review
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA Interactions through TaDRIM-seq.Nature communications · 2025Article
- Spatial omics advances for in situ RNA biology.Molecular cell · 2024Review
- The selective sponging of miRNAs by OIP5-AS1 regulates metabolic reprogramming of pyruvate in adenoma-carcinoma transition of human colorectal cancer.BMC cancer · 2024Article
- lhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK.PLoS genetics · 2023Article
- Article
- Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets.Functional & integrative genomics · 2023Review
- Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations.Journal of autoimmunity · 2023Review
- An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.PLoS computational biology · 2022Article
- A global high-density chromatin interaction network reveals functional long-range and trans-chromosomal relationships.Genome biology · 2022Article
- The nucleolus is the site for inflammatory RNA decay during infection.Nature communications · 2022Article
- Detecting TAD-like domains from RNA-associated interactions.Nucleic acids research · 2022Article
- MiRNA fine tuning for crop improvement: using advance computational models and biotechnological tools.Molecular biology reports · 2022Review
- RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation.Nucleic acids research · 2022Article
- Methods to Analyze the Non-Coding RNA Interactome-Recent Advances and Challenges.Frontiers in genetics · 2022Review
- A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly.RNA (New York, N.Y.) · 2022Review
- Three-dimensional genome organization via triplex-forming RNAs.Nature structural & molecular biology · 2021Article
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Authors and funding
13 authors at 6 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The global, three-dimensional organization of RNA molecules in the nucleus is difficult to determine using existing methods. Here we introduce Proximity RNA-seq, which identifies colocalization preferences for pairs or groups of nascent and fully transcribed RNAs in the nucleus. Proximity RNA-seq is based on massive-throughput RNA barcoding of subnuclear particles in water-in-oil emulsion droplets, followed by cDNA sequencing. Our results show RNAs of varying tissue-specificity of expression, speed of RNA polymerase elongation and extent of alternative splicing positioned at varying distances from nucleoli. The simultaneous detection of multiple RNAs in proximity to each other distinguishes RNA-dense from sparse compartments. Application of Proximity RNA-seq will facilitate study of the spatial organization of transcripts in the nucleus, including non-coding RNAs, and its functional relevance.
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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.