ArticleGenetics2004
Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 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
50 citing papers in PubMed.
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Position-dependent codon occurrence is associated with patterns of translational efficiency and ribosomal occupancy in the human transcriptome.PLoS computational biology · 2026Article
- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Chloroplast genome analysis and evolutionary insights in the versatile medicinal plant Calendula officinalis L.Scientific reports · 2024Article
- Fitness benefits of a synonymous substitution in an ancient EF-Tu gene depend on the genetic background.Journal of bacteriology · 2024Article
- Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina.BMC genomic data · 2024Article
- Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa.Microorganisms · 2023Article
- Analysis of Codon Usage Bias in Xyloglucan Endotransglycosylase (XET) Genes.International journal of molecular sciences · 2023Article
- Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus.BMC genomic data · 2022Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach.BMC genomics · 2022Article
- The Codon Usage Bias Analysis of Free-Living Ciliates' Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction ofFrontiers in microbiology · 2022Article
- A single synonymous nucleotide change impacts the male-killing phenotype of prophage WO geneeLife · 2021Article
- Insights into Comparative Genomics, Codon Usage Bias, and Phylogenetic Relationship of Species from Biebersteiniaceae and Nitrariaceae Based on Complete Chloroplast Genomes.Plants (Basel, Switzerland) · 2020Article
- Improving the Expression of Human Granulocyte Colony Stimulating Factor in Escherichia coli by Reducing the GC-content and Increasing mRNA Folding Free Energy at 5'-Terminal End.Advanced pharmaceutical bulletin · 2020Article
- Corticotropin-Releasing Hormone (CRH) Gene Family Duplications in Lampreys Correlate With Two Early Vertebrate Genome Doublings.Frontiers in neuroscience · 2020Article
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5 authors.
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Abstract
To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.
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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.