Fossilized chromosomes in mammoth skin allow scientists to reconstruct genome, study says

(CN) — About 52,000 years ago, a wooly mammoth died near the Indigirka River in Siberia. Soon after its death, its body freeze-dried in the frigid wilderness, remaining preserved in the permafrost until it was discovered in 2018. This preserved the mammoth's skin down to the molecular level, leading scientists to a startling discovery: the fossilized, three-dimensional structure of the mammoth's chromosomes.

According to a research paper published Thursday in Cell, researchers used the fossil to uncover new information about mammoth genetics.

By studying the chromosome structure using a process called PaleoHi-C, researchers determined that mammoths have 28 chromosomes, just like modern elephants. However, there are several differences between mammoth chromosomes and those of its closest living relative, the Asian elephant. For example, the researchers noted differences in genes that handle hair growth, wound healing, and immune inflammatory response.

While the new analysis was limited in scope, the researchers believe they can use the fossilized chromosome to reconstruct the mammoth's entire DNA sequence.

"Fossil chromosomes are a game-changer, because knowing the shape of an organism’s chromosomes makes it possible to assemble the entire DNA sequence of extinct creatures," said Olga Dudchenko, senior investigator at the Center for Theoretical Biological Physics at Rice University, in a press release announcing the paper. "This enables the types of insights that would not have been possible before.”

Ever since the DNA of an extinct Quagga — a subspecies of Zebra — was retrieved from a museum specimen in 1984, scientists have speculated about using ancient DNA to map the genomes of long-extinct species. But DNA has a half-life of just 521 years. This means that by the time scientists retrieve ancient DNA, it's usually broken down into fragments of fewer than 100 base pairs. Since a creature's full DNA sequence can be billions of base pairs long, reconstructing a full genome from these small pairs is a nearly impossible task.

Fossilized chromosomes, however, contain hundreds of millions of adjacent base pairs — a degree of preservation that scientists previously thought to be impossible, because DNA tends to break down and diffuse over time.

“Einstein’s work makes a very simple prediction about chromosome fossils: under ordinary circumstances, they shouldn’t exist,” Dudchenko said in the press release. “And yet: here they are. It was a physics mystery!”

The researchers believe that a process called "glass transition," also known as "vitrification," preserved the chromosome. When certain materials fall below their "glass transition temperature," they get trapped in a "glassy" state, which appears solid even though it has no crystalline structure. This is the same process used to preserve tortilla chips, beef jerky, cereals, and instant coffee crystals.

“We confirmed this theory by doing experiments on old, freeze-dried beef jerky, which is much easier to find than woolly mammoth jerky,” Cynthia Pérez Estrada, co-first author of the study and a researcher at Rice University’s Center for Theoretical Biological Physics, said in the release. “We fired a shotgun at it. We ran over it with a car. We had a former starting pitcher for the Houston Astros throw a fastball at it. Each time, the jerky broke into tiny bits — shattering like a glass. But at the nano-scale, the chromosomes were intact, unchanged. That’s the reason these fossils can survive. That’s the reason that they were there, 52,000 years later, just waiting for us to find them.”

The researchers theorize that, given the right preservation conditions, DNA architecture could survive for up to 530 million years, though researchers are unsure how common such fossilized chromosomes will prove to be. However, they were able to prove that the long-term preservation of chromosome fossils is not unique to this single 52,000-year-old specimen. The scientists detected fossilized chromosomes using PaleoHi-C on a well-preserved juvenile female that died 39,000 years ago.

The researchers say they hope to use PaleoHi-C on a wide range of ancient materials to determine what conditions are required to preserve chromosome structures. The researchers already know that freeze-dried samples from cold environments can create the fossils, but there's a chance that samples hot-air dried in warmer environments might also fossilize the chromosomes. There's also a chance that artificial mummification processes could preserve these structures.

"Ancient Egyptian priests believed that mummification prepared a person or animal to be reanimated in a future life," the paper states. "They may have been closer to the mark than has been realized."

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