Abstract
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE – 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.
Highlights
Genomic methylation is variable under biotic and abiotic stresses in plants
A secondary control on an archaeological sample from a different stratum (Qasr Ibrim Islamic) showed complete demethylation at three sites and partial methylation at one, further supporting the Late Christian sample’s elevated genomic methylation in vivo. These data lead us to conclude that de-methylation of cytosines in ancient DNA exists as a diagenetic process
We conclude that the half-life value calculated for the loss of signal in the methylation assay is a result of both the DNA fragmentation process and the diagenetic de-methylation of cytosines over time, the rates of which are likely dependent on environmental conditions and tissue type
Summary
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with high activity around transposable elements. The site is of further interest due to the remarkable preservation of ancient RNA21 and DNA22,23, compared to the expectations of previous studies into thermal age of bone-originating DNA24–26. We believe this condition to be symptomatic of seed endosperm’s natural propensity for long-term stasis, and the arid climatic stability at the site[27]. We recently identified the presence of ancient RNA in barley from this site in the presence of an ancient RNA virus genome that likely was an agent of stress at the stratum where it occurred[21] This stratigraphic series of seeds are all thought to have been under the abiotic stress of low water availability, but locally adapted to these hostile environmental conditions[22]
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