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Methylation Variation Documented Between Human Populations

NEW YORK (GenomeWeb) – A team from the US and Canada has started to document the epigenetic variation that exists across human populations from different parts of the world.

As they reported in Nature Ecology and Evolution today, the researchers did array-based methylation profiling on lymphoblastoid cell lines produced for nearly three dozen individuals from five distinct human populations. When they considered these methylation profiles alongside SNP and gene expression patterns from the same cell lines, the investigators found evidence for methylation variation levels that were on par with between-population genetic differences.

Nevertheless, from the methylation variation detected in the five populations profiled so far, the team suspects that these epigenetic marks may be relatively stable in human populations over time — at least compared to plant species such as Arabidopsis thaliana, where epigenetic divergence between populations has been considered in the past.

"This study provides a deeper understanding of worldwide patterns of human epigenetic diversity, as well as initial estimates of the rate of epigenetic divergence in recent human evolution," corresponding author Oana Carja, a biology researcher affiliated with Stanford University and the University of Pennsylvania, and her co-authors wrote.

For their analysis, Carja and her colleagues used Illumina 450K methylation arrays to assess genome-wide CpG DNA methylation in lymphoblastoid cell lines from 34 individuals: six Yakut individuals, seven individuals from Cambodia, seven individuals from the Pathan population, seven Mozabite individuals, and seven Mayan individuals.

"We chose these five populations to span the breadth of human worldwide migrations," they wrote, "and also capture differences in genetic diversity that stem from serial founder effects throughout human evolutionary history."

Using existing genotyping and RNA sequence data for these individuals, the team was able to characterize DNA methylation variation within and between populations within the broader context of genetic variation and gene expression. As expected, individuals from the same populations clustered together when it came to SNP profiles.

But the investigators also narrowed in on thousands of sites in the genome where population-specific methylation patterns occurred. By looking at these methylation variants in more detail, the team started to unravel the drivers, consequences, and rates of epigenetic variation. The data pointed to ties between local gene expression and nearby DNA methylation marks, for example, while local genetic variants often appeared to be better predictors of methylation variation in that population itself.

"Our analysis of five worldwide populations revealed a strong correspondence between population-specific DNA methylation, [messenger RNA] levels, and genotypes," the authors wrote. "The correlation with genetic divergence was stronger for DNA methylation, and, consistent with this, our results suggest stronger local genetic control of population-specific DNA methylation levels than of mRNA expression levels."