COMPARISON OF METHYLATION PATTERNS IN ANCIENT HUNTER-GATHERERS AND FARMERS

Download

index.pdf

Date

2021-9

Author

Çokoğlu, Sevim Seda

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

444
views

190
downloads

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

URI

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

Collections

Graduate School of Natural and Applied Sciences, Thesis

Suggestions

OpenMETU
Core

Testing natural selection on polygenic trait-associated alleles in anatolia using neolithic and present-day human genomes Fer, Evrim; Somel, Mehmet; Department of Bioinformatics (2019) The Neolithic transition, which started approximately 10,000 year ago in west Eurasia and introduced sedentary life style and food production, led to major shifts in the human diet. Previous studies have reported strong selection signals on genes related to processing of plant-based diets (Buckley et al., 2017; Harris et al., 2019) or the consumption of dairy products (Schlebusch et al., 2013). With the advent of archeogenomics studies, genetic signatures of such adaptations have also been supported using D...
Optimisation of tissue culture, regeneration and Agrobacterium-mediated transformation paramaters in winter wheat cultivars (T.durum cv. Kiziltan-91 and T.aestivum cv. Bezostaja-01) Kavas, M.; Öktem, Hüseyin Avni; YÜCEL, MUSTAFA (2006-08-18) Wheat, like other cereal species, shows a common recalcitrance and strong genotypic variation in tissue culture and Agrobacteriummediated transformation. A variety of explant sources have been used for obtaining wheat plants from in vitro cultures and Agrobacterium- mediated transformation. These are: isolated microspores (Mejza et al., 1993), mature embryos (Özgen et al., 1998; Delporte et al., 2001), immature embryos (Ozias-Akins and Vasil, 1982; Vasil et al., 1990; Pellegrineschi et al., 2004), and immat...
Improvement of pea proteins’ properties by microwave glycation Ertuğrul, Ülkü; Öztop, Halil Mecit; Şümnü, Servet Gülüm; Department of Food Engineering (2020-9) The tendency to include plant proteins in the diet has increased significantly as consumers' preference for animal proteins decline. Sustainability goals, low manufacturing cost, and high nutritional value are also triggering this demand. For this reason, pea protein as a form of isolate and concentrate is often used in protein enriched diets due to its nutritive properties. Previously, improvement in its functional properties has been studied from many perspectives. Glycation, which is known as the i...
Architectural Discourse and Social Transformation During the Early Neolithic of Southeast Anatolia Atakuman, Çiğdem (2014-03-01) Within the Near Eastern research canon, the transition to more sedentary lifestyles during the Neolithic is often framed as an economic necessity, linked to plant and animal domestication, climatic change and population stress. In such a framework, an increasingly complex social structure, arising in response to the increasingly complex relations of agricultural production, is presumed. For example, some researchers would argue that feasting-based rituals became an arena of social control and an increasingl...
Interactive Effects of Lake Morphometry and Sticklebacks on the Trophic Position of Arctic charr (Salvelinus alpinus) across Lakes in Western Greenland Arranz, Ignasi; Davidson, Thomas Alexander; Benejam, Lluís; Brucet, Sandra; Sánchez-Hernández, Javier; Landkildehus, Frank; Lauridsen, Torben; Mazzeo, Nestor; Vidal, Nicolas; Özkan, Korhan; Gallego, Irene; Wischnewski, Juliane; Menezes, Rosemberg; Shurkhuu, Tserenpil; Jeppesen, Erik (2022-01-01) The structure and functioning of Arctic ecosystems have been drastically modified by global warming, with fish species potentially performing habitat shifts such as the northern expansion of generalist and warm-adapted species. The freshwater fish species Arctic charr (Salvelinus alpinus, hereafter charr) plays a key role in Arctic lake food webs, but sticklebacks (Gasterosteus aculeatus) may impact the trophic position (TP) of charr by affecting their habitat choice and food resources. In the present study...

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.