ArticleGenome research2012
Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 248 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
248 citing papers in PubMed, 1 synthesis or guideline pooled it, 473 citations in OpenAlex.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- Global translational reprogramming inVirulence · 2026Article
- Codon optimality predicts mRNA half-life but does not transfer to lncRNAs.Molecular genetics and genomics : MGG · 2026Article
- An lncRNA-aware single-cell framework with donor-level validation identifies reproducible MEG3 enrichment in human liver sinusoidal endothelial cells.Functional & integrative genomics · 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
- Single-cell proteomic landscape of the developing human brain.Nature biotechnology · 2026Article
- Half-Life as a Therapeutic Design Axis: Targeting Short-Lived lncRNAs With Antisense Oligonucleotides.IUBMB life · 2026Review
- Cell size-dependent mRNA transcription drives proteome remodeling.Cell reports · 2026Article
- RNA-Binding Protein Occupancy Composition Predicts Long Noncoding RNA Subcellular Localization.International journal of molecular sciences · 2026Article
- Ribosome biogenesis bottlenecks reveal vulnerabilities in cancer.bioRxiv : the preprint server for biology · 2026Article
- circTGFBR2(3-6) acts as an assembly platform for RNA-binding protein IGF2BP3 and TGFBR1 mRNA to enhance breast cancer cell plasticity.Cell death and differentiation · 2026Article
- Systematic identification of variant-specific RNA structure-small molecule interactions exemplified by RNA G-quadruplexes.Nature communications · 2026Article
- The Kinetic Intron Hypothesis.bioRxiv : the preprint server for biology · 2026Article
- Analysis of coding gene expression from small RNA sequencing.Genome research · 2026Article
- In vivo RNA structure influences the translation and stability of plant long non-coding RNAs.Plant communications · 2026Article
- Comprehensive analysis of differential mRNA, lncRNA and circRNA and their ceRNA network in the Longissimus Dorsi Muscle of Jerseyyak in response to dietary protein levels.Frontiers in veterinary science · 2026Article
- Molecular Analysis of miRNA Stability and Decay Dynamics by Northern Blot.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Nonsense-mediated mRNA decay: a key regulatory system engaged in cancer.Cell communication and signaling : CCS · 2025Review
- Key Considerations on CITE-Seq for Single-Cell Multiomics.Proteomics · 2025Review
- The emerging roles of long non-coding RNAs in the nervous system.Nature reviews. Neuroscience · 2025Review
188 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mammalian genomes produce huge numbers of noncoding RNAs (ncRNAs). However, the functions of most ncRNAs are unclear, and novel techniques that can distinguish functional ncRNAs are needed. Studies of mRNAs have revealed that the half-life of each mRNA is closely related to its physiological function, raising the possibility that the RNA stability of an ncRNA reflects its function. In this study, we first determined the half-lives of 11,052 mRNAs and 1418 ncRNAs in HeLa Tet-off (TO) cells by developing a novel genome-wide method, which we named 5'-bromo-uridine immunoprecipitation chase-deep sequencing analysis (BRIC-seq). This method involved pulse-labeling endogenous RNAs with 5'-bromo-uridine and measuring the ongoing decrease in RNA levels over time using multifaceted deep sequencing. By analyzing the relationship between RNA half-lives and functional categories, we found that RNAs with a long half-life (t(1/2) ≥ 4 h) contained a significant proportion of ncRNAs, as well as mRNAs involved in housekeeping functions, whereas RNAs with a short half-life (t(1/2) < 4 h) included known regulatory ncRNAs and regulatory mRNAs. The stabilities of a significant set of short-lived ncRNAs are regulated by external stimuli, such as retinoic acid treatment. In particular, we identified and characterized several novel long ncRNAs involved in cell proliferation from the group of short-lived ncRNAs. We designated this novel class of ncRNAs with a short half-life as Short-Lived noncoding Transcripts (SLiTs). We propose that the strategy of monitoring RNA half-life will provide a powerful tool for investigating hitherto functionally uncharacterized regulatory RNAs.
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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.