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What can a 14 000-year-old puppy tell us about the impact of domestication and environmental stress on DNA?

There is evidence, especially in plants, that epigenetic changes, created in individual organisms because of environmental stresses, can be passed down through the generations and become fixed. Would harsh environments surrounding early dogs, combined with selective breeding, show traces of this epigenetically-mediated evolution? One project set out to answer the question.

Fundamental Research

DNA methylation patterns, (which determine whether a gene is ‘switched on’ or ‘switched off’) are the epigenetic modification most seen as a result of environmental stress. While this is clearly seen in plants, there is a growing body of evidence suggesting this is also the case in animals. To find out if this is the case, and to analyse the relationship between stress-induced modification and the DNA methylation patterns that could have been caused during early domestication, EpiCDomestic considered bone fragments. A collection of such remains from different environments (Siberia, Greenland and Denmark) spanning a large time-scale, from the Upper Palaeolithic (around 30 000 years before now) to the second millennium CE, gave the EpiCDomestic project the chance to identify molecular variation where domestication has taken different regional trajectories. “We have to work with what we’ve got,” says principal investigator Dr Oliver Smith, who conducted the research with the support of the Marie Skłodowska-Curie programme. “In the majority of cases, that was bone. We were looking for something to do primarily with skeletal morphology, but this kind of work always throws up unexpected results – so we are looking at all genes with known functions.” One of the challenges they faced was the fact that patterns of epigenetic modification vary among individuals, different tissues within an individual, and even different cells. This makes it difficult to build up a coherent picture. To keep things as simple as possible, the team decided to begin by using the same tissue type between samples. “The vast majority of archaeological tissues are bone, so we thought we could look for genes associated with morphological development relevant to breeding purposes, at least to begin with. An exception to this was a frozen, 14 000-year-old puppy, whelped from a domesticated dog from Tumat, a village in Siberia.” The remains were so well preserved that it gave Dr Smith the chance to come at the question from another angle. “Since this was such an opportunity, we looked to see if the epigenome of different tissues could match their respective transcriptomes – that is to say, if the ‘switched on or off’ state of the genes would match the expressed level of those genes we saw in the RNA (transcriptome), for each of those tissues.” It’s early days, but the researchers’ initial analysis leads them to believe that, even after all this time, it is still possible to tease out these complementary signals. “These are very preliminary analyses and we are in uncharted waters, so we can’t make any grand claims yet!” Dr Smith adds. This work is innovative and possible now due to our improved understanding of ancient DNA, in particular how it becomes damaged and degraded. Researchers only recently realised that they could use the damage patterns as a guide to DNA methylation. Some have done so before, on humans (Neanderthals and Denisovans), and Dr Smith previously worked on barley. “But the work was done more as a proof-of-principle than with a specific evolutionary question in mind,” he explains. Now research in the field is gathering momentum, meaning analysis of such damage patterns could shine a light on other interesting aspects of DNA methylation. Dr Smith is particularly interested in the ancient RNA aspect: “14 000-year-old RNA from animal tissue, which is preserved enough to show biologically meaningful tissue-specific profiles, is a methodological milestone. When we consider the huge numbers of RNA viruses, for example HIV, rabies and measles, we have a potentially new and exciting source of biomolecular information about the past.”

Keywords

EpiCDomestic, epigenetic, stress-induced modification, DNA methylation patterns, biomolecular information, Upper Palaeolithic, ancient RNA

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