ArticleDevelopment (Cambridge, England)2013
Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs.
Article in Development (Cambridge, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers.
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
161 citing papers in PubMed.
- Real-time single-molecule imaging in zebrafish embryos uncovers noncanonical translation.Science advances · 2026Article
- Ribo-ITP enables identification of translons from limited input samples.Nature communications · 2026Article
- Benchmarking reveals the superiority of nucleic acid foundation models in predicting lncRNA coding potential.Genome biology · 2026Article
- Human SRD5A1 as a case of gene expression indel-resistance in triple-coding region.Genome biology · 2026Article
- Genome-wide ribosome profiling reveals a dynamic translational landscape in Arabidopsis seedling roots under simulated microgravity.Communications biology · 2026Article
- How tailored Ribo-seq methods probe unique translation events.RNA (New York, N.Y.) · 2026Review
- Ribo-Seq Analysis-Based Elucidation of the Dynamic Translation Landscape of Yak Ovarian Tissues in Different Reproductive Stages.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Finding functional microproteins.Trends in genetics : TIG · 2025Review
- Pervasiveness of Microprotein Function AmongstCells · 2024Article
- Tiny but mighty: Diverse functions of uORFs that regulate gene expression.Computational and structural biotechnology journal · 2024Review
- The dynamics and functional impact of tRNA repertoires during early embryogenesis in zebrafish.The EMBO journal · 2024Article
- The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.Genome biology · 2024Article
- Noncanonical microprotein regulation of immunity.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Review
- Cell-type-specific mRNA transcription and degradation kinetics in zebrafish embryogenesis from metabolically labeled single-cell RNA-seq.Nature communications · 2024Article
- Non-coding RNAs in disease: from mechanisms to therapeutics.Nature reviews. Genetics · 2024Review
- Forward genetic screen using a gene-breaking trap approach identifies a novel role ofFrontiers in cell and developmental biology · 2024Article
- Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer.Cancer medicine · 2023Review
- Review
- Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants.International journal of molecular sciences · 2023Review
- Discovering microproteins: making the most of ribosome profiling data.RNA biology · 2023Review
101 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Large-scale genomics and computational approaches have identified thousands of putative long non-coding RNAs (lncRNAs). It has been controversial, however, as to what fraction of these RNAs is truly non-coding. Here, we combine ribosome profiling with a machine-learning approach to validate lncRNAs during zebrafish development in a high throughput manner. We find that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble the 5' leaders of coding RNAs. Analysis of ribosome profiling data from embryonic stem cells reveals similar properties for mammalian lncRNAs. These results clarify the annotation of developmental lncRNAs and suggest a potential role for translation in lncRNA regulation. In addition, our computational pipeline and ribosome profiling data provide a powerful resource for the identification of translated open reading frames during zebrafish development.
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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.