Nucleosome Occupancy and Transcription Factor Binding Sites in Yeast
Author Information
Author(s): Swamy Krishna BS, Chu Wen-Yi, Wang Chun-Yi, Tsai Huai-Kuang, Wang Daryi
Primary Institution: Academia Sinica, Taipei, Taiwan
Hypothesis
How does nucleosome positioning influence the evolution of transcription factor binding sites in yeast?
Conclusion
Nucleosome occupied regions have different selection constraints and higher evolution rates for binding sites compared to nucleosome depleted regions.
Supporting Evidence
- Nucleosome occupied regions accommodate greater binding site variations than nucleosome depleted regions.
- Binding sites at nucleosome occupied regions exhibit a higher evolution rate than those at nucleosome depleted regions.
- Site-directed mutagenesis confirmed that binding site changes at nucleosome depleted regions cause more expression differences.
Takeaway
This study shows that where DNA is wrapped around proteins in yeast affects how genes are turned on and off, and how quickly those instructions can change over time.
Methodology
The study analyzed transcription factor binding sites in nucleosome occupied and depleted regions across different yeast species, using statistical tests to compare their frequencies and evolution rates.
Potential Biases
Potential biases in estimates due to the methods used for determining nucleosome positions and TFBS.
Limitations
The study may be limited by experimental errors in determining nucleosome positions and TFBS predictions.
Participant Demographics
Yeast species from the Saccharomyces sensu stricto clade.
Statistical Information
P-Value
p<0.05
Statistical Significance
p<0.05
Digital Object Identifier (DOI)
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