ArticleGenome biology2015
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 410 papers.
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Who cites it
410 citing papers in PubMed.
- Identification of long non-coding RNAs involved in leukemogenesis and venetoclax response in acute myeloid leukemia through functional CRISPR-dCas9 interference screens.Non-coding RNA research · 2026Article
- Exploring the Effect of Whole-Genome Duplication on Salmonid LincRNA Repertoire.International journal of molecular sciences · 2026Article
- Rebalancing the non-coding RNA research agenda: future directions for long non-coding RNA and circular RNA research.Experimental & molecular medicine · 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
- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections.Plant communications · 2026Article
- Expression Landscape and Circadian Regulation of lncRNAs in the Kidney.Acta physiologica (Oxford, England) · 2026Article
- RNA-Binding Protein Occupancy Composition Predicts Long Noncoding RNA Subcellular Localization.International journal of molecular sciences · 2026Article
- The emerging regulatory roles of non-coding RNA in Ventilator-induced Lung Injury.Non-coding RNA research · 2026Review
- Intron Retention Controls Localization of lncRNAsbioRxiv : the preprint server for biology · 2026Article
- Single-cell profiling reveals pervasive heterogeneity in subcellular RNA localization.bioRxiv : the preprint server for biology · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- High-throughput Screening of Sequence Elements Associated with RNA Localization.Computational and structural biotechnology journal · 2026Article
- Knocking Down Long Noncoding RNAs Using Antisense Oligonucleotide Gapmers.Methods in molecular biology (Clifton, N.J.) · 2026Article
- LncRNA Knockdown Using Gapmer Antisense Oligonucleotides.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RAP-RNA: A Methodological Approach to Study Base-Pairing Between Endogenous RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Long non-coding RNA in hepatocellular carcinoma: mechanistic insights and therapeutic perspectives.Cellular oncology (Dordrecht, Netherlands) · 2025Review
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Authors and funding
8 authors.
Funding
Abstract
backgroundLong non-coding RNAs (lncRNAs) have been implicated in diverse biological processes. In contrast to extensive genomic annotation of lncRNA transcripts, far fewer have been characterized for subcellular localization and cell-to-cell variability. Addressing this requires systematic, direct visualization of lncRNAs in single cells at single-molecule resolution.
resultsWe use single-molecule RNA-FISH to systematically quantify and categorize the subcellular localization patterns of a representative set of 61 lncRNAs in three different cell types. Our survey yields high-resolution quantification and stringent validation of the number and spatial positions of these lncRNA, with an mRNA set for comparison. Using this highly quantitative image-based dataset, we observe a variety of subcellular localization patterns, ranging from bright sub-nuclear foci to almost exclusively cytoplasmic localization. We also find that the low abundance of lncRNAs observed from cell population measurements cannot be explained by high expression in a small subset of 'jackpot' cells. Additionally, nuclear lncRNA foci dissolve during mitosis and become widely dispersed, suggesting these lncRNAs are not mitotic bookmarking factors. Moreover, we see that divergently transcribed lncRNAs do not always correlate with their cognate mRNA, nor do they have a characteristic localization pattern.
conclusionsOur systematic, high-resolution survey of lncRNA localization reveals aspects of lncRNAs that are similar to mRNAs, such as cell-to-cell variability, but also several distinct properties. These characteristics may correspond to particular functional roles. Our study also provides a quantitative description of lncRNAs at the single-cell level and a universally applicable framework for future study and validation of lncRNAs.
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