ArticleBMC genomics2017
Bicodon bias can determine the role of synonymous SNPs in human diseases.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 57 citations in OpenAlex.
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- Phylogenetic and Genomic Characterization of Whole Genome Sequences of Ocular Herpes Simplex Virus Type 1 Isolates Identifies Possible Virulence Determinants in Humans.Investigative ophthalmology & visual science · 2023Article
- Dicodon-based measures for modeling gene expression.Bioinformatics (Oxford, England) · 2023Article
- Distal nucleotides affect the rate of stop codon read-through.Quantitative biology (Beijing, China) · 2023Article
- Novel compound heterozygous variants inFrontiers in molecular neuroscience · 2023Article
- Analysis of nested alternate open reading frames and their encoded proteins.NAR genomics and bioinformatics · 2022Article
- Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance.Blood advances · 2022Article
- Innate immune suppression by SARS-CoV-2 mRNA vaccinations: The role of G-quadruplexes, exosomes, and MicroRNAs.Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association · 2022Article
- Large-scale analysis of SARS-CoV-2 synonymous mutations reveals the adaptation to the human codon usage during the virus evolution.Virus evolution · 2022Article
- Identification ofFrontiers in genetics · 2022Article
- Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality.Computational and structural biotechnology journal · 2022Article
- The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA.International journal of molecular sciences · 2021Article
- Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population.GigaScience · 2021Article
- Association analysis of genetic variants in the ghrelin and tumor necrosis factor α genes and the risk for non-Hodgkin's lymphoma in Kuwaitis.Cancer biomarkers : section A of Disease markers · 2021Article
- SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi.Genomics, proteomics & bioinformatics · 2020Article
- Nanomedicines to Deliver mRNA: State of the Art and Future Perspectives.Nanomaterials (Basel, Switzerland) · 2020Review
- Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- SARS-CoV-2 Codon Usage Bias Downregulates Host Expressed Genes With Similar Codon Usage.Frontiers in cell and developmental biology · 2020Article
- Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundFor a long time synonymous single nucleotide polymorphisms were considered as silent mutations. However, nowadays it is well known that they can affect protein conformation and function, leading to altered disease susceptibilities, differential prognosis and/or drug responses, among other clinically relevant genetic traits. This occurs through different mechanisms: by disrupting the splicing signals of precursor mRNAs, affecting regulatory binding-sites of transcription factors and miRNAs, or by modifying the secondary structure of mRNAs.
resultsIn this paper we considered 22 human genetic diseases or traits, linked to 35 synonymous single nucleotide polymorphisms in 27 different genes. We performed a local sequence context analysis in terms of the ribosomal pause propensity affected by synonymous single nucleotide polymorphisms. We found that synonymous mutations related to the above mentioned mechanisms presented small pause propensity changes, whereas synonymous mutations that were not related to those mechanisms presented large pause propensity changes. On the other hand, we did not observe large variations in the codon usage of codons associated with these mutations. Furthermore, we showed that the changes in the pause propensity associated with benign sSNPs are significantly lower than the pause propensity changes related to sSNPs associated to diseases.
conclusionsThese results suggest that the genetic diseases or traits related to synonymous mutations with large pause propensity changes, could be the consequence of another mechanism underlying non-silent synonymous mutations. Namely, alternative protein configuration related, in turn, to alterations in the ribosome-mediated translational attenuation program encoded by pairs of consecutive codons, not codons. These findings shed light on the latter mechanism based on the perturbation of the co-translational folding process.
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