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Quantifying polymorphism and divergence from epigenetic data: a framework for inferring the action of selection
Shivani Mahajan1, Jessica Crisci2, Alex Wong3
1School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland ; Swiss Institute of Bioinformatics Lausanne, Switzerland.
Frontiers in Genetics
|June 16, 2015
Summary
Epigenetic marks, like DNA sequence, store heritable information. Studying histone modifications in humans and primates reveals how these epigenetic changes evolve and influence species-specific gene expression.
Area of Science:
- Evolutionary biology
- Genetics
- Neuroscience
Background:
- Epigenetic modifications regulate gene expression without altering DNA sequence.
- Epigenetic marks, such as DNA methylation and histone modifications, are heritable and can be influenced by environmental stimuli.
- The dynamic nature of epigenetics suggests a role in adaptive evolution, but evolutionary mechanisms are not well understood.
Purpose of the Study:
- To investigate the evolutionary mechanisms of epigenetic modifications.
- To analyze the genome-wide distribution of histone mark H3K4me3 in primate prefrontal cortex neurons.
- To understand evolutionary pressures on epigenetic variation.
Main Methods:
- Analysis of H3K4me3 distribution in human, chimpanzee, and rhesus macaque prefrontal cortex neurons.
- Development of a novel statistical framework to quantify epigenetic variation (epi-FST).
- Application of an ANOVA-based method to assess within- and between-species variation.
Main Results:
- Genes with high epi-FST values are significantly overrepresented among differentially expressed genes between species.
- A weak correlation was observed between epigenetic variation and single nucleotide polymorphism (SNP) density.
- Species-specific signatures of epigenetic marks were identified.
Conclusions:
- Epigenetic modifications play a significant role in the evolution of species-specific gene expression.
- Epigenetic variation evolves under distinct pressures compared to DNA sequence variation.
- The developed epi-FST measure provides a valuable tool for studying epigenetic evolution.
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