It was 2012 when Love Dalén, a paleogeneticist at Stockholm University, first laid eyes upon a special specimen on a lab table in eastern Siberia.
"Our Russian collaborators said, 'Come here into this room,'" he recalls. "We walked in and there's this dead mammoth lying there. It doesn't look like it died yesterday, but you can't believe your eyes because it's so well preserved. It's a kind of holy hell moment when you see this."
The animal had been found thawing out of a permafrost cliff near the Siberian coastline — not quite the entire body of a juvenile mammoth that lived during the last Ice Age some 39,000 years ago.
It had remained buried and frozen for millennia. Now, in a paper published in the journal Cell, Dalén and his colleagues report that they managed to extract something remarkable from that ancient mammoth — RNA, the molecule that translates genes into proteins and which tends to degrade rapidly.
The results offer a glimpse into what was happening inside this ancient mammoth's cells when it died.
The molecules that maketh a mammoth
The Russians named the animal — which they believed to be a female based on visual inspection — Yuka.
"It does have deep scratch marks on its hindquarters," says Dalén. "It either was attacked by cave lions while it was alive, probably chasing it down, or maybe cave lions were scavenging on it after it had died."
Over the years, various researchers had studied and sequenced Yuka's DNA, "which is kind of a recipe for how to make a mammoth," explains Dalén. (That DNA contains genes, which carry instructions for building specific proteins.)
But he and his collaborators wondered about the mammoth's RNA — the flurry of little messenger molecules that translate that recipe into the building and operating of an actual mammoth.
"The RNA molecules instruct the cells how and when to make proteins," says Dalén.
Most every cell in an organism's body has the same DNA. And yet — depending on where they are and what they do in the body — those cells can look and behave differently from one another. "What makes these cells different is the RNA activity in them, which genes are turned on and off," he says. "That is what separates liver cells from muscle cells and so on."
"The whole set of RNAs contained in a cell at a given time point is very much dynamic [and] can also quickly change in response to many factors, like stress, daytime, feeding, sleep, contaminants, infections, etc," says Emilio Mármol Sánchez, a geneticist at the Center for Evolutionary Hologenomics at the University of Copenhagen.
Dalén, Sánchez, and their team figured that if they could get RNA out of that ancient mammoth, they'd have a snapshot of the genes that were in use around the moment when it died.
The only problem was that RNA doesn't usually hang around for very long. RNA tends to survive mere minutes or hours — generally not millennia.
"It felt like a very high-risk project," says Dalén. "It seemed like a completely crazy thing to try to do."
Still, there have been a smattering of studies that have turned up ancient RNA. "So we knew that there was a chance, if we had some really well-preserved samples, to get this to work," he says.
RNA reveal party
Dalén and his colleagues collected tissue samples from ten different mammoths, including Yuka, and painstakingly worked to extract RNA. The resulting fragments were all very short, either because they were small to begin with or because, despite being frozen, they had broken down with time.
Then came the challenging task of piecing those segments together, validating that they really were mammoth RNA. "The big bulk of the work is on the computational side to make sense of all these gigabytes of data," says Dalén.
On the other end of that analysis was something unmistakable, he says — woolly mammoth RNA.
Most of it was too fragmented to know what it was or where it came from, but three of the mammoths had sufficient material to analyze. That included Yuka, whose muscle had been sampled. The resulting RNA was related to slow-twitch muscle function and development. That was a reassuring confirmation but not surprising.
The team also found RNA that would have been produced in response to some kind of stress.
"That would be consistent with an animal being chased down by cave lions, but of course there could also be other explanations," says Dalén. "If you get stuck in mud, your muscles would be stressed out from trying to get out. So we can say that the muscles were stressed at the point of death, but we don't really know why."
In addition, some of Yuka's RNA came from a Y chromosome. A closer look at the animal's DNA confirmed it had one X and one Y chromosome.
"Genetically, Yuka was definitely a male," says Dalén. "In theory, Yuka could have developed as a female. But more likely those critical morphological parts were missing when they did the visual inspection, let's put it that way."
All told, Dalén says the results are a stunning proof of principle — that it's possible to know which genes were active in a now-extinct animal.
"You're actually seeing processes going on inside the cells right around the time it died," he says. "And these processes have then been frozen in time for 40,000 years."
Maanasa Raghavan, a paleogeneticist at the University of Chicago who didn't participate in the research, notes that the samples studied here were well-preserved and came from a fairly pristine environment. She's less certain whether the same techniques could be applied to specimens collected in temperate and tropical areas that are richly biodiverse but where preservation tends to be worse.
Still, Raghavan called the work "fabulous in terms of all sorts of technological barriers being shattered." She says future work with RNA in these and other mammoth specimens may offer insights into what drove the species to extinction.
María Ávila Arcos, an evolutionary genomicist at the National Autonomous University of Mexico who wasn't involved in the study, says the approach provides a new layer of insight into a species that vanished long ago.
"Having this information adds to our understanding how these creatures lived and how they adapted to their environment," she says.
She's excited by the results — and not just for mammoths. She says they point the way to the potential study of ancient RNA viruses.
"A lot of very important pathogens like Ebola, COVID, influenza — they have RNA genomes," says Ávila Arcos. "They mutate so rapidly. But if we want to understand their evolution or how these viruses have impacted populations in the past, we need to be able to recover the genetic material, which is RNA, from ancient samples."
In other words, Yuka's RNA has opened a window for us to consider its past, while allowing scientists to dream about all the discoveries that lie ahead.
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