ArticleJournal of molecular evolution2005
Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes.
Article in Journal of molecular evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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Who cites it
27 citing papers in PubMed, 63 citations in OpenAlex.
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- Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species.Functional & integrative genomics · 2024Article
- Codon usage bias.Molecular biology reports · 2022Review
- Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells.Nucleic acids research · 2021Article
- Disrupting upstream translation in mRNAs is associated with human disease.Nature communications · 2021Article
- Sensing through Non-Sensing Ocular Ion Channels.International journal of molecular sciences · 2020Review
- Selection Shapes Synonymous Stop Codon Use in Mammals.Journal of molecular evolution · 2020Article
- Enabling large-scale genome editing at repetitive elements by reducing DNA nicking.Nucleic acids research · 2020Article
- Evaluation and optimisation of unnatural amino acid incorporation and bioorthogonal bioconjugation for site-specific fluorescent labelling of proteins expressed in mammalian cells.Biochemistry and biophysics reports · 2019Article
- The novel aminoglycoside, ELX-02, permits CTNSW138X translational read-through and restores lysosomal cystine efflux in cystinosis.PloS one · 2019Article
- Forces acting on codon bias in malaria parasites.Scientific reports · 2018Article
- Humanin Prevents Age-Related Cognitive Decline in Mice and is Associated with Improved Cognitive Age in Humans.Scientific reports · 2018Article
- Eukaryotic translational termination efficiency is influenced by the 3' nucleotides within the ribosomal mRNA channel.Nucleic acids research · 2018Article
- Running the Stop Sign: Readthrough of a Premature UAG Termination Signal in the Translation of a Zebrafish (Danio rerio) Taurine Biosynthetic Enzyme.Marine drugs · 2017Article
- Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.BMC genomics · 2016Article
- A flow cytometry-based reporter assay identifies macrolide antibiotics as nonsense mutation read-through agents.Journal of molecular medicine (Berlin, Germany) · 2016Article
- Clinical potential of ataluren in the treatment of Duchenne muscular dystrophy.Degenerative neurological and neuromuscular disease · 2016Review
- High-level expression of a novel liver-targeting fusion interferon with preferred Escherichia coli codon preference and its anti-hepatitis B virus activity in vivo.BMC biotechnology · 2015Article
- A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data.International journal of molecular sciences · 2015Article
- Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance.The Journal of biological chemistry · 2014Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is well known that stop codons play a critical role in the process of protein synthesis. However, little effort has been made to investigate whether stop codon usage exhibits biases, such as widely seen for synonymous codon usage. Here we systematically investigate stop codon usage bias in various eukaryotes as well as its relationships with its context, GC3 content, gene expression level, and secondary structure. The results show that there is a strong bias for stop codon usage in different eukaryotes, i.e., UAA is overrepresented in the lower eukaryotes, UGA is overrepresented in the higher eukaryotes, and UAG is least used in all eukaryotes. Different conserved patterns for each stop codon in different eukaryotic classes are found based on information content and logo analysis. GC3 contents increase with increasing complexity of organisms. Secondary structure prediction revealed that UAA is generally associated with loop structures, whereas UGA is more uniformly present in loop and stem structures, i.e., UGA is less biased toward having a particular structure. The stop codon usage bias, however, shows no significant relationship with GC3 content and gene expression level in individual eukaryotes. The results indicate that genomic complexity and GC3 content might contribute to stop codon usage bias in different eukaryotes. Our results indicate that stop codons, like synonymous codons, exhibit biases in usage. Additional work will be needed to understand the causes of these biases and their relationship to the mechanism of protein termination.
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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.