Epigenomic Modifications in Modern and Ancient Genomes

Abstract

Epigenetic changes have been identified as a major driver of fundamental metabolic pathways. More specifically, the importance of epigenetic regulatory mechanisms for biological processes like speciation and embryogenesis has been well documented and revealed the direct link between epigenetic modifications and various diseases. In this review, we focus on epigenetic changes in animals with special attention on human DNA methylation utilizing ancient and modern genomes. Acknowledging the latest developments in ancient DNA research, we further discuss paleoepigenomic approaches as the only means to infer epigenetic changes in the past. Investigating genome-wide methylation patterns of ancient humans may ultimately yield in a more comprehensive understanding of how our ancestors have adapted to the changing environment, and modified their lifestyles accordingly. We discuss the difficulties of working with ancient DNA in particular utilizing paleoepigenomic approaches, and assess new paleoepigenomic data, which might be helpful in future studies.

Reconstructing DNA methylation maps of ancient populations

“…Thus, in all cohorts, except Baqah_BA the number of CpG positions whose coverage allows for reliable reconstruction of aDNA methylation is larger than in these popular commercial arrays. A recent study claims that even shotgun coverage as low as 10x might suffice to reconstruct DNA methylation, using windows of up to 50 consecutive CpG positions ( 38 ). Using this estimate, we get that 75% of Caribbean_CER windows are amendable to reconstruction, and 1% of Baqah_BA ( Supplementary Table S2 ).…”

Human brains preserve in diverse environments for at least 12 000 years

“…Isolation of ancient chromatin (a complex of DNA and proteins forming chromosomes) from preserved nervous tissues might enable investigation of epigenetic patterns of aDNA methylation [ 98 ]. These heritable changes in gene expression are phylogenetically informative molecular targets that elucidate evolutionary trajectories [ 99 ] and ecological adaptations [ 100 ] at the population level, as well as permitting the study of phenotype (e.g. age at death [ 101 ] and morphological characters [ 102 ]) of ancient individuals.…”

Temporal collections to study invasion biology

“…These analyses could be coupled with direct reconstruction of gene expression profiles from natural history specimens (e.g., Marmol‐Sanchez et al., 2023), which is now possible, thanks to the development of protocols for extracting RNA from preserved specimens (e.g., Speer et al., 2022). DNA methylation patterns have already been investigated in ancient and historical specimens (e.g., Gokhman et al., 2014; Gokhman et al., 2016; Hahn et al., 2020; Niiranen et al., 2022; Orlando et al., 2015; Pedersen et al., 2014; Rubi et al., 2020; Smith et al., 2014), indicating that this approach holds promise for unravelling the role of heritable epigenetic modifications in facilitating rapid adaptation to environmental shifts. However, the effects of sample age, preservation method, contamination and the sensitivity of epigenetic marks to the environment mean their feasibility will be dependent on the specimen type and preservation method (Hahn et al., 2020; Raxworthy & Smith, 2021).…”