Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Open Access Guideline
Open Access Guideline
Postgraduate Thesis Guideline
Postgraduate Thesis Guideline
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise
Download
Evolutionary Applications - 2024 - Çokoğlu - Investigating food production‐associated DNA methylation changes in.pdf
Date
2024-07-01
Author
Çokoğlu, Sevim Seda
Koptekin, Dilek
Fidan, Fatma Rabia
Somel, Mehmet
Metadata
Show full item record
This work is licensed under a
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License
.
Item Usage Stats
49
views
20
downloads
Cite This
The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×–58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.
Subject Keywords
ancient DNA
,
DNA methylation
,
epigenetics
,
genomics/proteomics
,
human evolution
,
Neolithic transition
URI
https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85197281641&origin=inward
https://hdl.handle.net/11511/110216
Journal
Evolutionary Applications
DOI
https://doi.org/10.1111/eva.13743
Collections
Department of Biology, Article
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
S. S. Çokoğlu, D. Koptekin, F. R. Fidan, and M. Somel, “Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise,”
Evolutionary Applications
, vol. 17, no. 7, pp. 0–0, 2024, Accessed: 00, 2024. [Online]. Available: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85197281641&origin=inward.