Synonymous Codon Usage Controls Various Molecular Aspects
Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphism...
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BioMed Central
2017-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2017-15-4-123.pdf |
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| author | Eu-Hyun Im Sun Shim Choi |
| author_facet | Eu-Hyun Im Sun Shim Choi |
| author_sort | Eu-Hyun Im |
| collection | DOAJ |
| description | Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels. |
| format | Article |
| id | doaj-art-e1776a363299413d8518a4e7c09a446e |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2017-12-01 |
| publisher | BioMed Central |
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| series | Genomics & Informatics |
| spelling | doaj-art-e1776a363299413d8518a4e7c09a446e2025-02-02T08:55:27ZengBioMed CentralGenomics & Informatics2234-07422017-12-0115412312710.5808/GI.2017.15.4.123494Synonymous Codon Usage Controls Various Molecular AspectsEu-Hyun ImSun Shim ChoiSynonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.http://genominfo.org/upload/pdf/gi-2017-15-4-123.pdfoptimal codonsingle nucleotide polymorphismsynonymous codon usage bias |
| spellingShingle | Eu-Hyun Im Sun Shim Choi Synonymous Codon Usage Controls Various Molecular Aspects Genomics & Informatics optimal codon single nucleotide polymorphism synonymous codon usage bias |
| title | Synonymous Codon Usage Controls Various Molecular Aspects |
| title_full | Synonymous Codon Usage Controls Various Molecular Aspects |
| title_fullStr | Synonymous Codon Usage Controls Various Molecular Aspects |
| title_full_unstemmed | Synonymous Codon Usage Controls Various Molecular Aspects |
| title_short | Synonymous Codon Usage Controls Various Molecular Aspects |
| title_sort | synonymous codon usage controls various molecular aspects |
| topic | optimal codon single nucleotide polymorphism synonymous codon usage bias |
| url | http://genominfo.org/upload/pdf/gi-2017-15-4-123.pdf |
| work_keys_str_mv | AT euhyunim synonymouscodonusagecontrolsvariousmolecularaspects AT sunshimchoi synonymouscodonusagecontrolsvariousmolecularaspects |