Abstract
Epigenetic modifications are alterations that regulate gene expression without modifying the underlying DNA sequence. DNA methylation and histone modifications, for example, are capable of spatial and temporal regulation of expression—with several studies demonstrating that these epigenetic marks are heritable. Thus, like DNA sequence, epigenetic marks are capable of storing information and passing it from one generation to the next. Because the epigenome is dynamic and epigenetic modifications can respond to external environmental stimuli, such changes may play an important role in adaptive evolution. While recent studies provide strong evidence for species-specific signatures of epigenetic marks, little is known about the mechanisms by which such modifications evolve. In order to address this question, we analyze the genome wide distribution of an epigenetic histone mark (H3K4me3) in prefrontal cortex neurons of humans, chimps and rhesus macaques. We develop a novel statistical framework to quantify within- and between-species variation in histone methylation patterns, using an ANOVA-based method and defining an FST -like measure for epigenetics (termed epi- FST), in order to develop a deeper understanding of the evolutionary pressures acting on epigenetic variation. Results demonstrate that genes with high epigenetic FST values are indeed significantly overrepresented among genes that are differentially expressed between species, and we observe only a weak correlation with SNP density.
Highlights
Elucidating the relationship between genotypes and phenotypes remains an important challenge
Correlating Epigenetic FST with Differences in Gene Expression between Humans and Chimps We evaluated whether our H3K4me3 epigenetic FST values for genes correlate with differences in gene expression between humans and chimps, using the data for differential gene expression between human and chimps published in Cain et al (2011)
It is important to note that we review only one histone mark in this study (H3K4me3); in order to capture the full extent of how epigenetic divergence correlates to differences in gene expression between species, it would be helpful to consider several different epigenetic marks
Summary
Elucidating the relationship between genotypes and phenotypes remains an important challenge. Epi-population genetics alter the expression of genes without altering the underlying DNA sequence (Bird, 2007; Goldberg et al, 2007) These “epi-allele” modifications may provide an important source of variation within a population on which selection may act upon an environmental change. Studies in mice have shown that genetically identical parents having different methylated states at Agouti can produce offspring with different coat colors (Morgan et al, 1999). Another recent study demonstrated that when mice were taught to fear an odor, this response was transmissible for up to two generations and was linked to changes in the DNA methylation status of a gene in the germline (Dias and Ressler, 2014)
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