ArticlePloS one2007
Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.
Article in PloS one, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed, 107 citations in OpenAlex.
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- Interrogating nucleotide sequences with AI to understand codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Predicting gene sequences with AI to study codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease.Molecular neurobiology · 2024Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias.Acta biochimica Polonica · 2024Article
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- Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.Molecular neurobiology · 2023Article
- Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria.bioRxiv : the preprint server for biology · 2023Article
- Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts.Pathogens (Basel, Switzerland) · 2023Article
- Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation.Vaccines · 2022Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy.Cells · 2022Article
- Zinc-finger antiviral protein-mediated inhibition of porcine epidemic diarrhea virus growth is antagonized by the coronaviral nucleocapsid protein.Frontiers in microbiology · 2022Article
- Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris.Microbial cell factories · 2021Article
- A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.Gene reports · 2021Article
- The Use of the Rare TTA Codon inIndian journal of microbiology · 2021Article
- Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects.Scientific reports · 2021Article
- A Codon-Pair Bias Associated With Network Interactions in Influenza A, B, and C Genomes.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCodon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL
findingsWe have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context.
conclusionsThe data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.
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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.