The Impact of the Nucleosome Code on Protein-Coding Sequence Evolution in Yeast
Author Information
Author(s): Warnecke Tobias, Batada Nizar N., Hurst Laurence D., Petrov Dmitri A.
Primary Institution: Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
Hypothesis
Does the way DNA is organized impose constraints on coding sequence evolution?
Conclusion
Nucleosome positioning impacts codon choice, amino acid choice, and rates of evolution in coding sequences.
Supporting Evidence
- Nucleosome-free linker sequences evolve slower at synonymous sites.
- Reduced rates of evolution in linker are especially evident at the 5′ end of genes.
- Codons that are unfavorable for nucleosome formation are enriched in linker sequences.
- Amino acid content is skewed based on nucleosome occupancy.
- Selection on DNA to maintain nucleosome positioning impacts coding sequence evolution.
Takeaway
The way DNA is wrapped around proteins in cells can affect how genes change over time, making some parts of genes evolve slower than others.
Methodology
High-resolution microarray data in yeast was used to compare the evolution of coding sequences bound to or free from nucleosomes.
Potential Biases
The sample may not represent all genes due to the focus on longer genes for within-gene analysis.
Limitations
The within-gene comparisons were biased towards very long genes, limiting the generalizability of the findings.
Participant Demographics
Yeast (Saccharomyces cerevisiae) genes were analyzed.
Statistical Information
P-Value
p<0.0001
Statistical Significance
p<0.0001
Digital Object Identifier (DOI)
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