The 82nd Annual Meeting of the American Association of Physical Anthropologists (2013)

Analysis of cytosine methylation in Native American ancient DNA


1Department of Anthropology, University of Texas at Austin, 2Population Research Center, University of Texas at Austin

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Cytosine methylation of CpG dinucleotides is an important epigenetic mark that regulates gene expression in humans. While methylation patterns in extant populations have been widely studied, few studies have attempted to analyze methylation in ancient DNA. Indeed, it was only recently shown that methyl groups can be preserved in ancient DNA. However, it is unknown whether methylation patterns can be recovered from all (or most) ancient samples with preserved nuclear DNA. If they can, it may ultimately be possible to directly infer patterns of gene activity in ancient populations.

In this study, we assessed the preservation of cytosine methylation in ancient DNA from the remains of 25 prehistoric Native Americans from California, Illinois, Kentucky, and Mexico. These samples were previously shown to contain endogenous mitochondrial and nuclear DNA. We analyzed the cytosine methylation states of CpG-rich retrotransposons, which are epigenetically inactivated by cytosine methylation in humans. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite. Bisulfite products were pyrosequenced, and C-to-T conversions at potentially methylated CpG dinucleotides were quantified. We found that cytosine methylation is readily recoverable from human remains with preserved nuclear DNA from a variety of localities over the time depth tested (~6000 years). This study presents the first direct evidence of cytosine methylation in ancient human remains, suggesting that it may be possible to analyze patterns of gene activity in the distant past. This study also provides a diagnostic tool for assessing whether epigenetic marks can be recovered from ancient samples of interest.

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