Epigenetics of Ancient DNA

Abstract

Initially, the study of DNA isolated from ancient specimens had been based on the analysis of the primary nucleotide sequence. This approach has allowed researchers to study the evolutionary changes that occur in different populations and determine the influence of the environment on genetic selection. However, the improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression. It was discovered recently that the methylation status of the regulatory elements of the HOXD cluster and MEIS1 gene changed during human evolution. Epigenetic changes in these genes played a key role in the evolution of the limbs of modern humans. Recent works have demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes. In the nearest future, if a preserved fossils brain is found, it will be possible to identify the evolutionary changes in the higher nervous system associated with epigenetic differences.

Keywords: DNA methylation; ancient DNA; epigenetics.

Fig. 1

Scheme of cytosine methylation detection in ancient DNA via substitution rates of C-T relative to the original chain during deamination. Taq polymerase is not sensitive to the presence of uracil, and Pfu polymerase cannot continue the chain synthesis in the presence of uracil. Deamination of methylated cytosines (mC) does not affect the ratio of C-T substitutions detected using Taq- and Pfu-polymerases. Deamination of unmethylated cytosines creates “impassable” uracil for Pfu polymerase. Thus, all the readings starting from T (in the context of genomic CG) in NGS libraries prepared using Pfu polymerase definitely indicate the methylation status of cytosine in ancient DNA.

Fig. 2

Graph of the spectral density (power spectral estimation). Analysis of the region around genes transcription starts (+/- 1000 bp), correction with respect to the distribution of background readings in the analysis of the DNA of modern elephants was performed. We used the genome sequencing data of a baby mammoth found in 2009 in the downstream of the Khroma River (Prokhorchuk E.B. et al., unpublished data). The age of the finding exceeds 50,000 years.