COMPARISON OF METHYLATION PATTERNS IN ANCIENT HUNTER-GATHERERS AND FARMERS

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2021-9

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Çokoğlu, Sevim Seda

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As the Neolithic transition dramatically changed human lifestyle and diet, one may expect epigenetic differences between pre-Neolithic Hunter-Gatherers (HGs) and Neolithic farmers (NFs) (Childe, 1940). In this study, we investigate methylation profile differences between the Pre-Neolithic and Neolithic individuals. It is today possible to infer methylation patterns of ancient DNA samples using programs such as epiPALEOMIX, which calculates a methylation score (MS) per CpG position from aDNA data (Hanghoj et al., 2016). This approach uses deamination patterns to assign a MS per CpG position in ancient DNA libraries treated by uracil-DNA glycosylase (UDG). Here we compiled published HG and NF genomes produced using UDG, either by shotgun sequencing or by 1240K SNP capture, from bone or tooth remains. After estimating MS values per genome, we applied statistical analyses to find methylation pattern differences between the subsistence types, HGs and NFs. We found 1147 genes showing significantly different MS values between prehistoric HGs and NFs. The subsistence type effect influenced more genes than sex or tissue. Intriguingly, we also observed a significant correlation between HG vs. NF methylation differences we identified in our ancient sample, and modern-day hunter-gatherer (MHG) vs. modern-day farmer (MF) genome-wide methylation differences identified in African populations. This result raises the possibility of the existence of universal methylation patterns that may have accompanied the Neolithic transition.

Subject Keywords

Neolithic, Paleolithic, Methylation profile, Methylation score, CpG positions, epiPALEOMIX, Shotgun sequencing, 1240K SNP capture

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https://hdl.handle.net/11511/93260

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Graduate School of Natural and Applied Sciences, Thesis

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Citation Formats

S. S. Çokoğlu, “COMPARISON OF METHYLATION PATTERNS IN ANCIENT HUNTER-GATHERERS AND FARMERS,” M.S. - Master of Science, Middle East Technical University, 2021.