ReviewThe international journal of biochemistry & cell biology2015
Decoding mechanisms by which silent codon changes influence protein biogenesis and function.
Review in The international journal of biochemistry & cell biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
70 citing papers in PubMed, 1 synthesis or guideline pooled it, 131 citations in OpenAlex.
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- Trial
- Multilayered nucleotide organization reveals purifying selection and host-driven adaptation in CPV and FPV.BMC veterinary research · 2026Article
- Multidomain DNA-Protein Mining Reveals Polymorphic Variations in RhlB Enhancing Monorhamnolipid Biosynthesis.ACS synthetic biology · 2026Article
- Immortalization and characterization of Schwann cell lines derived from NF1-associated cutaneous neurofibromas.PloS one · 2026Article
- Implementation of Apriori Algorithm to Biomedical Data: Silent Mutations in GWAS-GAD Edition.Advances in experimental medicine and biology · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Assessing Splicing Variants in the PAX6 Gene: A Comprehensive Minigene Approach.Journal of cellular and molecular medicine · 2025Article
- Uncovering codon usage patterns during murine embryogenesis and tissue-specific developmental diseases.Frontiers in genetics · 2025Article
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- Scarless genome editing technology and its application to crop improvement.Breeding science · 2024Article
- A modular inquiry-based semester theme that integrates data science education and bioinformatics in protein structure function courses.FEMS microbiology letters · 2024Article
- Nonsynonymous Synonymous Variants Demand for a Paradigm Shift in Genetics.Current genomics · 2023Review
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Reading Frame Retrieval of Genes: A New Parameter of Codon Usage Based on the Circular Code Theory.Bulletin of mathematical biology · 2023Article
- Novel compound heterozygous synonymous and missense variants in the MYO7A gene identified by next-generation sequencing in a Chinese family with nonsyndromic hearing loss.Journal of clinical laboratory analysis · 2022Article
- Analysis of the Compositional Features and Codon Usage Pattern of Genes Involved in Human Autophagy.Cells · 2022Article
- Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance.Blood advances · 2022Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
scopeSynonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health. PURPOSE: This synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics. PHYSIOLOGICAL AND MEDICAL RELEVANCE: Understanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies.
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Registered trials
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.