Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing

摘要: While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed ancient DNA. Most existing of epigenetic marks DNA inferred patterns highly degraded samples using post-mortem damage to cytosines as a proxy for levels. However, this approach limits the inference compared with direct bisulfite sequencing, current gold standard analyzing at single nucleotide resolution. In study, we used sequencing assess from skeletal remains 30 Native Americans ranging age approximately 230 4500 years before present. Unmethylated were converted uracils by treatment sodium bisulfite, products CpG-rich retrotransposon pyrosequenced, and C-to-T ratios quantified CpG position. We found that is readily recoverable most samples, given adequate preservation endogenous nuclear addition, our results indicate precision estimates inversely correlated aDNA preservation, such low concentration show higher variability measures percent than high concentration. particular, study above 0.015 ng/μL generated consistent methylation. This presents evidence large collection human remains, indicates it possible analyze populations approaches.