ArticleGenome biology2019
Codon usage optimization in pluripotent embryonic stem cells.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it, 64 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- System level identification and multidimensional analysis of hub genes reveal complex regulatory networks underlying human iPSC differentiation into motor neurons.Biochemistry and biophysics reports · 2026Article
- The Translatome of Senescent Cells Revealed by Sequencing Actively Translated mRNA.bioRxiv : the preprint server for biology · 2026Article
- ADAT2-mediated A-to-I tRNA modification promotes oncogenic translation and colorectal cancer progression and chemoresistance.Molecular cancer · 2026Article
- PUS1 Drives Renal Cancer Progression by Preventing Formation of Endogenous Double-stranded RNAs.International journal of biological sciences · 2026Article
- The tRNA Editing Complex ADAT2/3 Promotes Cancer Cell Growth and Codon-biased mRNA Translation.Journal of molecular biology · 2025Article
- ADAT3 variants disrupt the activity of the ADAT tRNA deaminase complex and impair neuronal migration.Brain : a journal of neurology · 2025Article
- Adenosine-to-inosine RNA editing in cancer: molecular mechanisms and downstream targets.Protein & cell · 2025Review
- Decoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation.International journal of molecular sciences · 2025Article
- tRNA and tsRNA: From Heterogeneity to Multifaceted Regulators.Biomolecules · 2024Review
- Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.BMC bioinformatics · 2024Article
- ADATs: roles in tRNA editing and relevance to disease.Acta biochimica et biophysica Sinica · 2024Review
- Threonine fuels glioblastoma through YRDC-mediated codon-biased translational reprogramming.Nature cancer · 2024Article
- RNA editing enzymes: structure, biological functions and applications.Cell & bioscience · 2024Review
- Molecular insights into codon usage analysis of mitochondrial fission and fusion gene: relevance to neurodegenerative diseases.Annals of medicine and surgery (2012) · 2024Article
- Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand.Science (New York, N.Y.) · 2024Article
- A snoRNA-tRNA modification network governs codon-biased cellular states.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Genetic dissection of the pluripotent proteome through multi-omics data integration.Cell genomics · 2023Article
- Rare Amyloid Precursor Protein Point Mutations Recapitulate Worldwide Migration and Admixture in Healthy Individuals: Implications for the Study of Neurodegeneration.International journal of molecular sciences · 2022Article
- Structural basis for sequence-independent substrate selection by eukaryotic wobble base tRNA deaminase ADAT2/3.Nature communications · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundThe uneven use of synonymous codons in the transcriptome regulates the efficiency and fidelity of protein translation rates. Yet, the importance of this codon bias in regulating cell state-specific expression programmes is currently debated. Here, we ask whether different codon usage controls gene expression programmes in self-renewing and differentiating embryonic stem cells.
resultsUsing ribosome and transcriptome profiling, we identify distinct codon signatures during human embryonic stem cell differentiation. We find that cell state-specific codon bias is determined by the guanine-cytosine (GC) content of differentially expressed genes. By measuring the codon frequencies at the ribosome active sites interacting with transfer RNAs (tRNA), we further discover that self-renewing cells optimize translation of codons that depend on the inosine tRNA modification in the anticodon wobble position. Accordingly, inosine levels are highest in human pluripotent embryonic stem cells. This effect is conserved in mice and is independent of the differentiation stimulus.
conclusionsWe show that GC content influences cell state-specific mRNA levels, and we reveal how translational mechanisms based on tRNA modifications change codon usage in embryonic stem cells.
Indexed as
Identifiers
What OpenQuestion holds
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.