Recent molecular and computational advances in ancient DNA research have revealed that genome-scale epigenetic information can be retrieved from subfossil material. In fact, it appears that particular features of the chromatin, and its regulatory epigenetic marks at the time of death, are preserved within ancient DNA extracts. The characterization of this additional layer of information, which represents an interface between the genome and the environment and is not coded within modifications of the DNA sequence itself, opens new horizons for ancient DNA research. At the individual level, ancient epigenetic marks can provide novel molecular phenotypes of the age at death, diet restriction, and other stress conditions, including sociocultural changes. At the population level, they can complement classical inference based on genetic information to reveal the regulatory changes underlying divergence, speciation, and extinction. Exploiting such information will nonetheless be challenging, due to the nature of epigenetic data, which can vary across cell types, tissues, sex, and age, and be significantly influenced by genetic variation and environmental exposure.
KeywordsAncient DNA Cytosine deamination DNA methylation Epigenome Nucleosome protection
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