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Synonymous Codon Usage Controls Various Molecular Aspects.

Eu-Hyun Im1, Sun Shim Choi1

  • 1Division of Biomedical Convergence, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Korea.

Genomics & Informatics
|January 9, 2018
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Summary
This summary is machine-generated.

Synonymous sites, often deemed neutral, may have functional roles. This review explores functions of synonymous codons beyond regulating gene expression levels.

Keywords:
optimal codonsingle nucleotide polymorphismsynonymous codon usage bias

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Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Synonymous sites are traditionally viewed as functionally neutral in genomes.
  • Recent studies challenge this notion, indicating functional roles for synonymous alleles.
  • Synonymous codon usage bias (SCUB) is observed across species, prompting investigation into its causes.

Purpose of the Study:

  • To review and discuss the diverse functional roles of synonymous codons.
  • To explore mechanisms beyond expression level regulation.
  • To highlight the non-neutrality of synonymous mutations.

Main Methods:

  • Literature review of existing research on synonymous codon usage.
  • Analysis of studies investigating the functional impact of synonymous single nucleotide polymorphisms (SNPs).
  • Examination of the correlation between SCUB and gene expression levels.

Main Results:

  • Synonymous SNPs can exhibit effect sizes comparable to nonsynonymous SNPs in disease association studies.
  • Highly expressed genes show a preference for optimal codons, correlating with tRNA abundance.
  • Evidence suggests synonymous codons have functions beyond modulating gene expression.

Conclusions:

  • Synonymous sites are not universally neutral and possess functional significance.
  • SCUB is influenced by natural selection, not just nucleotide composition.
  • Further research is needed to fully elucidate the multifaceted roles of synonymous codons.