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REVIEW: Progress and Prospects in Epigenetic Studies of Ancient DNA

Kristina V. Zhur1, Victor A. Trifonov2, and Egor B. Prokhortchouk1,a*

1Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia

2Institute for History of Material Culture, Russian Academy of Sciences, 191186 St.-Petersburg, Russia

* To whom correspondence should be addressed.

Received October 29, 2021; Revised November 17, 2021; Accepted November 17, 2021
Development of technologies for high-throughput whole-genome sequencing and improvement of sample preparation techniques made it possible to study ancient DNA (aDNA) from archaeological samples over a million year old. The studies of aDNA have shed light on the history of human migration, replacement of populations, interbreeding of Cro-Magnons with Neanderthals and Denisovans, evolution of human pathogens, etc. Equally important is the possibility to investigate epigenetic modifications of ancient genomes, which has allowed to obtain previously inaccessible information on gene expression, nucleosome positioning, and DNA methylation. Analysis of methylation status of certain genomic sites can predict an individual’s age at death and reconstruct some phenotypic features, as it was done for the Denisovan genome, and even to elucidate unfavorable environmental factors that had affected this archaic individual. In this review, we discuss current progress in epigenetic studies of aDNA, including methodological approaches and promising research directions in this field.
KEY WORDS: ancient DNA, paleoepigenetics, epigenetic clock, epigenome editing, obesity

DOI: 10.1134/S0006297921120051