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dc.creatorSmith, Rick W.A.
dc.creatorMonroe, Cara
dc.creatorBolnick, Deborah A.
dc.description.abstractWhile cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.en_US
dc.publisherPublic Library of Scienceen_US
dc.rightsCreative Commons Attribution 4.0 International
dc.subjectAncient DNAen_US
dc.subjectCytosine methylationen_US
dc.titleDetection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencingen_US
dc.description.citation2015. Smith RWA, Monroe C, Bolnick D. Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing. PLoS ONE 10 (5). DOI: 10.1371/journal.pone.0125344.

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  • Monroe, Cara
    This collection features scholarly work by Cara Monroe, a clinical faculty member in the anthropology department at Washington State University.

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Creative Commons Attribution 4.0 International
Except where otherwise noted, this item's license is described as Creative Commons Attribution 4.0 International