The genetic makeup of extinct animals can reveal a lot about their lifestyle and fate – this also applies to the iconic mammoths of the Ice Age. Now, for the first time, researchers have succeeded in obtaining not only the DNA of woolly mammoths, but also their RNA – the molecules that reveal which genes in a cell are currently active and have been copied. The RNA comes, among other things, from the mummified remains of a 39,000-year-old mammoth cub named “Yuka,” which was preserved in the permafrost of Siberia. This is the oldest RNA ever isolated from a dead animal, the team reports. The identified sequences revealed, among other things, that this mammoth cub was, contrary to what was thought, a male. They also provide evidence of muscle activity and cellular stress shortly before his death. In addition, the 39,000-year-old RNA demonstrates that messenger and microRNA, which were previously considered to be less durable, can survive longer under suitable conditions than previously assumed.
In the permanently frozen ground of permafrost, but also under other conditions that are favorable for preservation, tissue, bones and genetic material can be preserved over long periods of time. The DNA from such finds gives scientists the chance to gain unique insights into life, evolution and physiology of past living environments. Thanks to such analyzes of ancient DNA, researchers have gained valuable insights into human development and have also reconstructed the genomes of extinct species, including a woolly mammoth from the Ice Age that lived over a million years ago. However, there has been an important gap so far: DNA can reveal which genes an organism carries, but not whether these genes were active and how they were regulated. However, information about this can be provided by RNA – the genetic molecules that, for example, act as messenger RNA and bring the genetic instructions for proteins from the cell nucleus, or microRNA – short pieces of RNA that play an important role in the regulation of gene activity.
RNA search for permafrost mammoths
“Using RNA, we get direct information about which genes are activated, giving us an insight into, for example, the last moments of life of an Ice Age mammoth,” explains lead author Emilio Mármol from Stockholm University. “Such information cannot be obtained from DNA alone.” Until now, however, RNA was considered too fragile to be preserved for long because it is broken down very quickly by enzymes. Mármol and his team have now investigated whether this also applies to mammoth relics frozen in the permafrost. For their study, they took samples from ten woolly mammoths from the last Ice Age that were discovered in northern Siberia.
“We have already pushed the boundaries of DNA extraction well into the past over a million years. Now we wanted to find out whether we can also push RNA sequencing further into the past than previous studies,” says senior author Love Dalén from the Center for Paleogenetics in Stockholm. The team used multiple RNA sequencing methods and compared the obtained RNA with that of the Asian elephant to ensure that the reconstructed molecules also came from the mammoth.
The paleogeneticists were actually successful: they were able to isolate RNA residues from the samples of three of the ten mammoths. One of the animals, a mammoth cub nicknamed “Yuka” that was mummified in the permafrost for 39,000 years, had a particularly large number of RNA sequences preserved. “To our knowledge, these are the oldest surviving transcription signatures ever documented,” state Mármol and his colleagues. “This mammoth RNA is more than twice as old as RNA fragments previously reconstructed from a late Pleistocene canid.” This proves that RNA can survive far longer under suitable conditions than previously assumed. In total, the team managed to identify more than 300 messenger RNAs of protein-coding genes from the tissues of the mammoth cub. There were also around 60 different microRNAs that the paleogeneticists extracted from “Yuka” muscle cells. These short RNA sections do not carry genetic instructions for proteins, but rather regulate the cells’ protein production through their influence on messenger RNA. To do this, they attach themselves to certain sections of the messenger RNA and thus influence whether and to what extent their protein code is implemented.
“Yuka” was not a female and was under stress
Closer examination of the DNA and RNA sequences isolated from the mammoth cub revealed something surprising. Until now, paleontologists considered “Yuka” to be a female due to certain characteristics of her genital region and muscle structure. But comparative RNA analyzes showed that this animal had only half as much X chromosome DNA as is typical for a female. “This suggests the presence of only one X chromosome and therefore a male XY genotype,” report the researchers. In other words: Contrary to previous assumptions, Yuka was a young male mammoth. Analyzes of the RNA provided some insight into how the cub was doing at the time of its death. Many of the reconstructed RNA molecules came from active genes that play important roles in muscle cell development and muscle contraction. The team was also able to identify messenger RNA, which is typical for regulating metabolism under stress. “We found signs of cell stress, which is not surprising,” reports Mármol. “Previous research has already suggested that Yuka was attacked by cave lions shortly before his death.”
The paleogeneticists also gained new insights from the microRNAs extracted from the mammoth cub. “RNAs that do not code for proteins, such as microRNAs, were among our most exciting discoveries,” explains co-author Marc Friedländer from Stockholm University. “The muscle-specific microRNAs that we found in mammoth tissues are direct evidence of real-time gene regulation in prehistoric times. This is the first time something like this has been achieved,” he says. Comparisons of mammoth RNA with that of modern elephants also provided initial evidence of mammoth-specific peculiarities: “We found rare mutations in certain microRNAs that clearly prove their mammoth origin,” reports co-author Bastian Fromm from the Arctic University of Norway in Tromsø. “We were even able to discover new genes based on RNA evidence alone – something that has never been attempted before on remains this old.”
Taken together, these results demonstrate that RNA molecules can provide entirely new insights into the biology of long-extinct species. “This means that we can not only study which genes are turned on in different extinct animals,” says Dalén. “It may even be possible to sequence RNA viruses such as influenza and coronaviruses that are preserved in Ice Age remains.” He and his team now plan to combine prehistoric RNA with DNA, proteins and other preserved biomolecules in further studies. “Such studies could fundamentally change our understanding of extinct megafauna and other species by revealing the many hidden layers of biology that have remained frozen in time until today,” says Mármol.
Source: Emilio Mármol (Stockholm University), Cell, doi: 10.1016/j.cell.2025.10.025