ArticleGenetics2004
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence.
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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Who cites it
116 citing papers in PubMed.
- Article
- Genome-Wide Identification and Characterization of Heat Shock Proteins in the Stored-Product PestInsects · 2025Article
- Codon-Usage Bias and Genomic Architecture of 79 Psoriasis-Susceptibility Genes: Implications for Expression Efficiency and Therapeutic Targeting.Psoriasis (Auckland, N.Z.) · 2025Article
- Compositional Features and Codon Usage Pattern of Genes Associated with Parkinson's Disease.Molecular neurobiology · 2024Article
- Codon Usage Provide Insights into the Adaptation of Rice Genes under Stress Condition.International journal of molecular sciences · 2023Article
- The regulation of inhibitor of apoptosis proteins (IAPs) during the apoptosis ofFrontiers in physiology · 2023Article
- Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution.Virus evolution · 2022Article
- Article
- Context-dependent and -independent selection on synonymous mutations revealed by 1,135 genomes of Arabidopsis thaliana.BMC ecology and evolution · 2021Article
- Cost-efficiency tradeoff is optimized in various cancer types revealed by genome-wide analysis.Molecular genetics and genomics : MGG · 2021Article
- Genome-wide role of codon usage on transcription and identification of potential regulators.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Proximity to the Promoter and Terminator Regions Regulates the Transcription Enhancement Potential of an Intron.Frontiers in molecular biosciences · 2021Article
- Article
- A code within the genetic code: codon usage regulates co-translational protein folding.Cell communication and signaling : CCS · 2020Review
- Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape.PLoS genetics · 2020Article
- Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome.Journal of molecular evolution · 2020Article
- Characterization of an inducible HSP70 gene in Chilo suppressalis and expression in response to environmental and biological stress.Cell stress & chaperones · 2020Article
- Hijacking tRNAs From Translation: Regulatory Functions of tRNAs in Mammalian Cell Physiology.Frontiers in molecular biosciences · 2020Review
- Selection On synonymous Mutations Revealed by 1135 Genomes ofEvolutionary bioinformatics online · 2020Article
- Correlation between gene expression levels under drought stress and synonymous codon usage in rice plant by in-silico study.PloS one · 2020Article
56 more citing papers are in PubMed but not listed here.
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1 author.
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Abstract
We report the results of a comprehensive study of the influence of gene expression on synonymous codons, amino acid composition, and intron presence and size in human protein-coding genes. First, in addition to a strong effect of isochores, we have detected the influence of transcription-associated mutational biases (TAMB) on gene composition. Genes expressed in different tissues show diverse degrees of TAMB, with genes expressed in testis showing the greatest influence. Second, the study of tissues with no evidence of TAMB reveals a consistent set of optimal synonymous codons favored in highly expressed genes. This result exposes the consequences of natural selection on synonymous composition to increase efficiency of translation in the human lineage. Third, overall amino acid composition of proteins closely resembles tRNA abundance but there is no difference in amino acid composition in differentially expressed genes. Fourth, there is a negative relationship between expression and CDS length. Significantly, this is observed only among genes with introns, suggesting that the cause for this relationship in humans cannot be associated only with costs of amino acid biosynthesis. Fifth, we show that broadly and highly expressed genes have more, although shorter, introns. The selective advantage for having more introns in highly expressed genes is likely counterbalanced by containment of transcriptional costs and a minimum exon size for proper splicing.
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