ArticleBMC genomics2016
Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.
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, 35 citations in OpenAlex.
- Glutamine codon-driven translational readthrough reveals context-dependent stop codon decoding fidelity.bioRxiv : the preprint server for biology · 2026Article
- A predictive framework for stop-loss variants with C-terminal extensions.Nucleic acids research · 2026Article
- Therapeutic Potential of Translational Readthrough at Disease-Associated Premature Termination Codons From Tumor Suppressor Genes.IUBMB life · 2025Review
- Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations.Nucleic acids research · 2024Article
- Extended stop codon context predicts nonsense codon readthrough efficiency in human cells.Nature communications · 2024Article
- Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.PLoS computational biology · 2023Article
- Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts.Nucleic acids research · 2023Article
- Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox.Genome biology and evolution · 2022Article
- Tissue-specific regulation of translational readthrough tunes functions of the traffic jam transcription factor.Nucleic acids research · 2022Article
- Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection.PLoS biology · 2022Article
- Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage.Molecular biology and evolution · 2022Article
- Article
- Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines.Vaccines · 2021Article
- Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells.Nucleic acids research · 2021Article
- Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.Molecular biology and evolution · 2021Article
- Selection Shapes Synonymous Stop Codon Use in Mammals.Journal of molecular evolution · 2020Article
- The Role ofGenetics · 2020Article
- Forces acting on codon bias in malaria parasites.Scientific reports · 2018Article
- Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints.BMC genomics · 2018Article
- Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel.Nucleic acids research · 2018Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies.
resultsIn this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences.
conclusionsIn human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.
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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.