Fossils of ancient chromosomes found for the first time in 52,000-year-old woolly mammoth skin

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A piece of woolly mammoth skin excavated from the Siberian permafrost has been found to contain fossil chromosomes in a first-of-its-kind discovery, according to a new study.

Researchers unearthed the 52,000-year-old remains in 2018 near the village of Belaya Gora in northeastern Siberia, where freezing temperatures helped preserve the structure of the chromosomes — tiny threadlike structures that carry genetic material, or DNA — in fine detail.

While ancient DNA samples have been found many times before, they are typically highly fragmented and contain only hundreds of letters of genetic code. The fossil chromosomes contain millions, offering a far more complete picture of an animal’s genetic code.

“Fossil chromosomes have never been found before,” said Erez Lieberman Aiden, a professor of molecular and human genetics at the Baylor College of Medicine and co-corresponding author of the study published Thursday in the journal Cell.

In prior findings, the fragments were also lacking an organized structure, Lieberman Aiden added. “Here, the fragments are clearly arranged in 3D — essentially as they were in the original chromosomes in the living mammoth.”

The chromosomes, which the researchers point out are “non-mineralized fossils, or subfossils,” are in a state of preservation good enough to assemble the genome, or the sum of all the genetic material, of an extinct species, according to Olga Dudchenko, an assistant professor of molecular and human genetics at Baylor College of Medicine and co-first author of the study.

“We strongly believe that this is not going to apply to just the mammoth or this particular mammoth,” said Dudchenko, who is also a senior investigator at the Center for Theoretical Biological Physics at Rice University, “but is basically opening up a new field that has tremendous potential.”

DNA diffusion

DNA within different cell types is laid out in distinct and specific 3D structures that give insight into the particular properties or traits of that cell type, said Kevin Campbell, a professor of environmental and evolutionary physiology at the University of Manitoba in Canada, who was not involved in the study.

Upon death, body cells quickly degrade, and this 3D structure is lost within a few days or less, he added. In Arctic animals such as the woolly mammoth, the degradation is slower due to freezing temperatures, but the DNA still becomes damaged, and over long periods it is expected to lose the structure and the attributes that make up the species’ biology.

“However, this study is the first to demonstrate that this is not necessarily always the case,” Campbell said in an email.

“DNA is a very, very long molecule, and once it sits there after an animal dies, it starts to degrade and gets chopped into shorter pieces,” Dudchenko said.

“What you normally expect is that all of these pieces will start shifting in respect to each other and just kind of float away, losing any organization that was there,” Dudchenko said. “But clearly, in this particular sample, that didn’t happen.”

This loss of structure is called diffusion, and how to prevent it is well-known to food scientists — and not dissimilar from the making of beef jerky, she added.

“Arresting diffusion is key to preserving foods, so if you want to have something that is shelf stable for a long time, you basically need a combination of dehydration and cooling,” she said. “Any shelf stable food that’s not canned is probably in a state of arrest of diffusion.”

When the mammoth the skin sample came from died, conditions might have been just right to kick-start this process naturally. “(The carcass) could have spontaneously undergone the same procedure that right now we use commercially all the time,” Dudchenko said, “removing substantial amounts of water, arresting diffusion inside and locking those pieces of chromosomes in place, allowing us to read them off 52,000 years after the fact.”

But even though it was well preserved, the DNA was not completely intact. “Each chromosome, originally one DNA molecule, has fragmented into millions of DNA molecules,” Aiden said in an email. “But the molecules have otherwise not moved terribly much, even at the nanometer scale, which is why we call it a fossil chromosome.”

If this sample were a book, Lieberman Aiden said, the binding would be gone, leaving a large number of unbound pages, or DNA fragments. Diffusion is like the wind blowing the pages away, making it impossible to put them back in order. But in this sample, the pages never got blown away; they remained in a neat pile, just as they were before the binding was lost.

Shooting beef jerky

The researchers confirmed this theory of preservation by running some experiments on beef jerky to see how badly they could mistreat the meat snack before the chromosomes inside it lost their structure.

“We decided to test how far this beautiful molecule can resist stress and harm by having one of the pitchers from the Houston Astros throw a fastball at it and firing a shotgun at it,” said Dr. Cynthia Pérez Estrada, co-first author of the study and a researcher at the Center for Genome Architecture at Baylor and at Rice’s Center for Theoretical Biological Physics.

“The beef jerky was breaking more and more, but the DNA structure was still there, telling us that DNA is extremely resistant and even more so in this type of glass-like state (like in the sample), where the molecules are basically frozen and behaving like a crystal,” Pérez Estrada added.

With the newly discovered genetic information found in the skin samples, the researchers were able to determine for the first time that the woolly mammoth had 28 pairs of chromosomes, just like modern elephants.

But the structure allowed them to go one step further and see which individual genes were active in the animal. “Everybody wants to know what exactly made it woolly,” Dudchenko said, “and we have some ideas thanks to the way that these chromosomes were preserved.”

Mammoth dreams

The researchers were able to compare individual genes from the mammoth sample with the equivalent ones in modern elephants, noting differences in the activity of genes that regulate hair follicles. But the DNA from elephants was also needed to assemble the mammoth genome.

“Our dream and hope was to assemble the mammoth genome completely, but right now, this is not quite where we are — we still used some information from its closest relatives to help, because the amount of data that we were able to get from the mammoth was lower than what you typically need,” Dudchenko said. “But the fundamentals tell us that, as we continue working towards this, we will be able to do it (without the help of elephant DNA).”

Could fossil chromosomes make the dream of resurrecting the woolly mammoth a reality? “The fundamental biology that we learn from this is going to be useful, there is no question about it,” Dudchenko said. “Are we closer? One step closer, but there’s still quite a few steps ahead and all sorts of other considerations that are beyond fundamental science.”

The researchers also hope that the same methodology used on the mammoth sample can be applied to samples from other species.

“We’re hoping to find chromosome structures in museum specimens,” said Marcela Sandoval-Velasco, a guest researcher at the Center for Evolutionary Hologenomics of the University of Copenhagen in Denmark and co-first author of the study. “Not only permafrost specimens, because that narrows it a lot, but also samples from museum collections. There’s an enormous potential there,” she added, citing the woolly rhino, extinct lions and the passenger pigeon as some of the extinct species that scientists might find out more about this way.

That potential opens the door to further discoveries, according to Pérez Estrada.

“It will take an immense effort to find suitable samples, so there will be a lot of work ahead — but I wouldn’t be surprised if we then discovered something new and completely different from what we have right now,” she said. “That is also a really exciting open question: What else and what other physical attributes (of DNA) can be preserved?”

Exciting findings

Researchers who were not involved with the study expressed enthusiasm about the findings.

This study is the first to reconstruct the structure, or architecture, of a genome from an extinct species that lived during the last ice age, said Peter Heintzman, a paleogeneticist at Stockholm University in Sweden. “This structural information provides insights into functions of the woolly mammoth genome that were invisible using previous genomic methods,” Heintzman said in an email. “This advance therefore helps to unlock a new and exciting frontier in paleogenomics, the study of ancient genomes, and will likely provide further insight into how extinct species evolved, lived, and died out.”

Because of how substantially degraded and fragmented DNA from ancient samples usually is, it was surprising to see the high-quality, chromosome-level reconstruction of the mammoth genome reported by this study, said Dmitry Filatov, a professor of biology at the University of Oxford in the United Kingdom.

“It is even more surprising that the researchers managed to infer which genes were active and which were switched off in the mammoth sample and compare this with gene expression in elephants,” Filatov said in an email. “This will certainly stimulate further paleo-genomic research in other species.”

Hendrik Poinar, director of the Ancient DNA Centre at McMaster University in Ontario, called the paper “super exciting.” Normally with fossil remains researchers can’t do anything remotely close to assembling a genome, Poinar said.

“I don’t know how many tissue samples will have this level of preservation,” he added in an email, “but I do think the method will make us think about novel ways to get DNA out of tissues in ways other than what we are used to.”

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