Positive selection for unpreferred codon usage in eukaryotic genomes
Author Information
Author(s): Neafsey Daniel E, Galagan James E
Primary Institution: Broad Institute of MIT and Harvard
Hypothesis
Is there evidence of directional selection resulting in increased unpreferred codon usage in eukaryotic genomes?
Conclusion
The study finds recent selection for unpreferred codon usage at approximately 1% of genetic loci in Cryptococcus and several genes in Drosophila, suggesting that translational efficiency may be suppressed to reduce stochastic noise in gene expression.
Supporting Evidence
- Natural selection is responsible for causing accelerated unpreferred codon substitution in some genes.
- Many genes in Cryptococcus and Drosophila show a statistically significant signal of selection for unpreferred codon usage.
- Functional enrichment analysis reveals that genes in regulatory roles are particularly subject to this type of selection.
Takeaway
Some genes in certain organisms are changing to use less common codons, which can slow down how quickly proteins are made, possibly to help control how much noise there is in gene expression.
Methodology
Genome-wide scans for selection for inefficient translation using a metric based on synonymous codon substitutions.
Potential Biases
Potential biases in codon preference assignments across different growth conditions.
Limitations
The study may overlook species-specific selection due to averaging across multiple species.
Statistical Information
P-Value
≤ 0.01
Statistical Significance
p ≤ 0.01
Digital Object Identifier (DOI)
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