ArticlePLoS genetics2016
Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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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
57 citing papers in PubMed, 1 synthesis or guideline pooled it, 98 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer.Scientific reports · 2026Article
- Essentiality and dynamic expression of the human tRNA pool during viral infection.Molecular systems biology · 2026Article
- RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.Nucleic acids research · 2026Article
- Species-specific AAVR dominates species-tropism of adeno-associated virus (AAV) vectors.Research square · 2025Article
- Compensatory tRNA Modification by DUS3L Confers Resistance to METTL1 Loss in Oesophageal Cancer.bioRxiv : the preprint server for biology · 2025Article
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- Ageing-related decline of translation as a consequence of transcription dysregulation.Journal of the Royal Society, Interface · 2025Article
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- Viral codon usage and the virus-host interactions.Frontiers in microbiology · 2025Review
- SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.International journal of molecular sciences · 2024Article
- The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer.Human genomics · 2024Review
- tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.Nucleic acids research · 2024Article
- Article
- Intrinsic deletion at 10q23.31, including theLife science alliance · 2024Article
- Selective gene expression maintains human tRNA anticodon pools during differentiation.Nature cell biology · 2024Article
- Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line.RNA (New York, N.Y.) · 2023Article
- Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells.Genome research · 2022Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- CCT3-Gut · 2022Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Whether codon usage fine-tunes mRNA translation in mammals remains controversial, with recent papers suggesting that production of proteins in specific Gene Ontological (GO) pathways can be regulated by actively modifying the codon and anticodon pools in different cellular conditions. In this work, we compared the sequence content of genes in specific GO categories with the exonic genome background. Although a substantial fraction of variability in codon usage could be explained by random sampling, almost half of GO sets showed more variability in codon usage than expected by chance. Nevertheless, by quantifying translational efficiency in healthy and cancerous tissues in human and mouse, we demonstrated that a given tRNA pool can equally well translate many different sets of mRNAs, irrespective of their cell-type specificity. This disconnect between variations in codon usage and the stability of translational efficiency is best explained by differences in GC content between gene sets. GC variation across the mammalian genome is most likely a result of the interplay between genome repair and gene duplication mechanisms, rather than selective pressures caused by codon-driven translational rates. Consequently, codon usage differences in mammalian transcriptomes are most easily explained by well-understood mutational biases acting on the underlying genome.
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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.