Freeze-drying transforms mammoth DNA into 3D ‘chrome glass’

The detailed study of the mammoth genome was made possible after an international team of scientists devised a way to apply a technique called Hi-C to the study of ancient DNA.SN: August 24, 2015).

“We’d known about Hi-C for a while, but we hadn’t figured out how to apply it to ancient DNA,” says Christina Wariner, a biomolecular archaeologist at Harvard University who was not involved in the study.

That’s because DNA breaks down over time: It’s hard to imagine tiny pieces of ancient DNA retaining the shape of chromosomes, Wariner says. And Hi-C, which is used to see the three-dimensional structure of meters of DNA packed into a cell’s nucleus, typically requires fresh, intact samples.SN: June 10, 2021).

Even Pérez Estrada’s colleagues, who work on 3D DNA structure at Baylor College of Medicine in Houston, didn’t think such a technique would work on degraded samples. Pérez Estrada thought so, and he tested Hi-C on a turkey bone left over from Thanksgiving dinner, tissue from a desiccated road-killed mouse he found on his way to work, and a piece of leather he’d removed from a bag.

“All of these experiments were interesting because they really showed that DNA structure is pretty resilient,” she says, “and in the case of mice, it remained intact despite cooking, despite the sun, despite the environment.”

But she wasn’t sure if the structures would hold up for thousands of years. So she teamed up with Marcela Sandoval-Velasco, then at the University of Copenhagen. Sandoval-Velasco had been studying ancient DNA for years and was interested in exploring 3D structures. She brought a “bag full of wonders,” Pérez Estrada says: museum specimens of ants, bees, coelacanths, fish, reptiles, birds, and animals, to Houston for examination. Pérez Estrada then traveled to Copenhagen, where the researchers examined an ancient polar bear skull and a mummified wolf.

The experiments often ended in failure: the Hi-C method they used on fresh samples didn’t work on the ancient ones, so they had to invent a new version, called PaleoHi-C. That’s research, says Sandoval-Velasco, now at the National Autonomous University of Mexico in Cuernavaca. “You go slowly. I repeat, there are failures, but you never give up.” Teamwork also helps, she says: the study brought together more than 50 scientists from different disciplines.

After years of partial success and failure, the team finally obtained the head skin of a woolly mammoth that died in Siberia about 52,000 years ago, and had been freeze-dried and preserved in permafrost.

The rapid drying trapped the ancient DNA in a dense, glass-like molecular state known as chromoglass, which the team of geneticists and theoretical physicists surmised could have prevented the DNA fragments from separating from each other.

In unconventional experiments using lab-made beef jerky, the team found that this glassy DNA remained stable at room temperature for at least a year and could survive a variety of blows, including being heated in a microwave, run over with a car, crushed by a fastball, and shot with a shotgun.

The mammoth’s glassy DNA held its chromosomes in place, allowing researchers to count the number of chromosomes in the animal for the first time. Mammoths have the same 28 pairs of chromosomes as elephants, Erez Lieberman Aiden, a geneticist at Baylor College of Medicine, said at a press conference on July 2. The basic structure of mammoth chromosomes is also the same as elephants.

Packed into the nucleus, the chromosomes resemble a skein of cat wool after a playdate: their tangled appearance belies a carefully coordinated internal structure.

Genes that are turned on are shuffled into one cellular compartment, like dancers taking over a dance floor, while genes that are turned off are relegated to a less prominent position in another. Examining the compartments, the researchers found 425 genes that were active in mammoths but not in elephants, and 395 genes that were active in elephants but not in mammoths.

These include: EGFRThe gene helps regulate skin and hair growth. In elephants, the gene was active, but not noticeable in mammoths. Turning it off in humans leads to longer, thicker eyelashes and excess hair growth, suggesting that keeping the gene away from the dance floor may have helped mammoths grow their long, shaggy coats.

The team looked at DNA from a second mammoth, killed by a sabre-toothed cat about 39,000 years ago and buried by human hunters, likely to preserve its meat. Although the hunters never returned to retrieve their prey, Aiden said, the researchers found that the mammoth also had chromophoric glass that preserved DNA loops, compartments and other 3-D structures. Freezing or rapid drying through high temperatures could produce similar DNA glass in other natural or artificial mummies, the team suggests.

“A lot of scientists will read this and start thinking, ‘Can this be applied?'” Wariner predicts. [PaleoHi-C] “Will it answer our own questions? Will it solve questions and problems that have been troubling us for a long time?”

There will be a learning curve, she said, in applying techniques that researchers studying ancient DNA didn’t even know were available. “This work opens a lot of new doors in the field, in directions we haven’t explored before,” she added. “I think it’s really exciting.”