Ancient DNA can shed light on the past in myriad ways — for instance, genes and mutations may reveal important adaptations or physiological changes. But gene-regulating molecules latched onto the DNA, known as epigenetic marks, may also reveal important clues. Epigenetic marks get added or removed from DNA in response to environmental influences such as famine and disease, hence offering insights into an organism’s life. Now researchers say they can study ancient DNA epigenetic marks in large swaths of archaeological populations, potentially revealing details about the effects that ancient environments had on ancient societies.
One widely studied kind of epigenetic mark is cytosine methylation. This kind of chemical modification has been widely studied in living species, but prior studies had detected cytosine methylation only in a few isolated ancient remains, such as a 4,000-year-old Paleo-Eskimo from Greenland.
Scientists had generally thought that the current gold standard for analyzing cytosine methylation in modern DNA at the scale of single nucleotides, a technique known as bisulfite sequencing, was mostly useless when applied to ancient DNA. The technique degrades normal DNA, and ancient DNA has already been degraded by time; this, they thought, would make for fruitless searches, explains researcher Rick Smith, an anthropological geneticist at the University of Texas at Austin.
But Smith and his colleagues discovered that bisulfite sequencing can indeed be a powerful way to analyze cytosine methylation in ancient DNA. In their investigation of 30 ancient humans from five archaeological sites in North America, ranging in age from 230 to more than 4,500 years old, the researchers successfully detected cytosine methylation in 29 of the samples. Smith and his colleagues Cara Monroe and Deborah Bolnick detailed their findings online May 27 in the journal PLOS ONE.
“I find it extremely exciting to think that DNA methylation — a signature of how available genes were to be expressed thousands of years ago — can still be detected in all of these ancient bones from so many different sites throughout the U.S.,” says genetic anthropologist Amy Non at Vanderbilt University in Nashville, Tenn., who did not take part in this study. “No one before has been able to detect DNA methylation from so many ancient humans using direct bisulfite sequencing methods.”
One previous study that used bisulfite sequencing on six samples from a single 26,000-year-old bison specimen could only detect cytosine methylation in one of the samples. “Our findings demonstrate a dramatically higher success rate,” says Smith, noting that previously-studied samples were much older, and thus perhaps more degraded.
The amount of cytosine methylation seen in the 30 samples that Smith and his colleagues analyzed varied greatly (largely due to the quality of DNA preservation in the samples), and they detected no significant pattern of methylation based on age or location.
Future research could focus on DNA methylation in gene regions of known function, Non says. Preservation of DNA methylation across numerous samples should allow researchers to “ask questions about the effects that violence, malnutrition, stress, social status, or other environmental exposures may have had on the genes of ancient human populations,” she says. “However, we must be careful not to get too carried away.” Non suggests that it’s too soon to say that these ancient DNA methylation differences indicate much about ancient levels of gene expression, which is a product of a much more complicated set of processes than just DNA methylation alone. Instead of reconstructing gene expression per se, Smith says his group plans to use cytosine methylation as a biomarker of past experiences.
Non now plans to collaborate with Smith and his colleagues on a project investigating ancient DNA methylation in Peruvian mummies, and in historic African slave burials from a plantation site in Nashville. If the samples show sufficient preservation of DNA methylation, they may be able to glean the effects of ancient violence, diet and other factors on methylation levels throughout the genome. “We hope to understand how experiences of social stress can become biologically embedded to affect an entire population at the genetic level,” she says.