ArticleBMC genomics2016
Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 36 citations in OpenAlex.
- Translation of a small upstream open reading frame functions as a rheostat for the regulation ofbioRxiv : the preprint server for biology · 2026Article
- Halting translation by the letter with sequence-selective small molecules.Nature chemical biology · 2026Review
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Advances in ribosome profiling technologies.Biochemical Society transactions · 2025Review
- DMDA-PatA mediates RNA sequence-selective translation repression by anchoring eIF4A and DDX3 to GNG motifs.Nature communications · 2024Article
- Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.Nature communications · 2024Article
- mTOR pathway occupies a central role in the emergence of latent cancer cells.Cell death & disease · 2024Review
- Micropeptides translated from putative long non-coding RNAs.Acta biochimica et biophysica Sinica · 2022Review
- Translational control of stem cell function.Nature reviews. Molecular cell biology · 2021Review
- Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards.Methods in molecular biology (Clifton, N.J.) · 2021Article
- When Long Noncoding Becomes Protein Coding.Molecular and cellular biology · 2020Review
- The computational approaches of lncRNA identification based on coding potential:Computational and structural biotechnology journal · 2020Review
- Long Non-coding RNA in Plants in the Era of Reference Sequences.Frontiers in plant science · 2020Review
- Ribosome Profiling: Global Views of Translation.Cold Spring Harbor perspectives in biology · 2019Review
- Altered translation initiation ofMolecular biology of the cell · 2018Article
- Transcriptome-wide measurement of translation by ribosome profiling.Methods (San Diego, Calif.) · 2017Article
- The Growing Toolbox for Protein Synthesis Studies.Trends in biochemical sciences · 2017Review
- Insights into the mechanisms of eukaryotic translation gained with ribosome profiling.Nucleic acids research · 2017Review
- Bioinformatics and Drug Discovery.Current topics in medicinal chemistry · 2017Review
- RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing.F1000Research · 2016Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOpen reading frames are common in long noncoding RNAs (lncRNAs) and 5'UTRs of protein coding transcripts (uORFs). The question of whether those ORFs are translated was recently addressed by several groups using ribosome profiling. Most of those studies concluded that certain lncRNAs and uORFs are translated, essentially based on computational analysis of ribosome footprints. However, major discrepancies remain on the scope of translation and the translational status of individual ORFs. In consequence, further criteria are required to reliably identify translated ORFs from ribosome profiling data.
resultsWe examined the effect of the translation inhibitors pateamine A, harringtonine and puromycin on murine ES cell ribosome footprints. We found that pateamine A, a drug that targets eIF4A, allows a far more accurate identification of translated sequences than previously used drugs and computational scoring schemes. Our data show that at least one third but less than two thirds of ES cell lncRNAs are translated. We also identified translated uORFs in hundreds of annotated coding transcripts including key pluripotency transcripts, such as dicer, lin28, trim71, and ctcf.
conclusionPateamine A inhibition data clearly increase the precision of the detection of translated ORFs in ribosome profiling experiments. Our data show that translation of lncRNAs and uORFs in murine ES cells is rather common although less pervasive than previously suggested. The observation of translated uORFs in several key pluripotency transcripts suggests that translational regulation by uORFs might be part of the network that defines mammalian stem cell identity.
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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.