Extraction and sequencing of ancient DNA has revolutionized scientists’ understanding of numerous extinct species, but DNA can only tell us so much. RNA, however, can tell us which genes were actually “turned on,†offering unprecedented insight into the final moments of a deceased animal’s life. The recent recovery of surprisingly ancient mammoth RNA does exactly that.
The long-held belief that RNA is too fragile to survive even a few hours after death has discouraged experts from seeking it out in preserved mammoths and other ancient species, but new research upends this assumption. In the study, published Friday in the journal Cell, researchers successfully isolated and sequenced RNA molecules from Ice Age woolly mammoths for the first time ever.
These RNA sequences are the oldest ever recovered, extracted from mammoth tissues preserved in Siberian permafrost for nearly 40,000 years. This shows that RNA can remain viable in deceased tissues for far longer than previously believed. What’s more, the analysis revealed previously inaccessible details about woolly mammoth biology and what was happening in the moments before the animals died.
“With DNA alone, you might at most be able to try predicting if a gene was active or inactive, based on how tight or loose the DNA is packaged,†study lead author Emilio Mármol, a postdoc at the University of Copenhagen’s Globe Institute, told Gizmodo in an email. “But with RNA you can access the direct evidence of this expression in the form of RNA transcripts present in the cell.â€
Mármol and his colleagues extracted RNA sequences from the muscles and skin of 10 permafrozen woolly mammoth specimens found across Northeastern Siberia. Analysis of one specimen, a juvenile mammoth named Yuka, revealed RNA molecules that code for proteins that play key roles in muscle contraction and metabolic regulation under stress.
“We found some protein-coding and microRNA indicative of cell stress that could be due to the cell dying (i.e., we actually recovered the last glimpses of gene expression right before the cell died) or else as a prior sign of stress in the muscle,†Mármol explained.
“This might be a reflection of Yuka escaping from predators, probably cave lions, given the signs present in its body, but it is actually not possible to accurately discern if the stress markers are due to escaping from predators or to the cells dying based on our data,†he clarified.
The researchers also found muscle-specific microRNAs that are essential for muscle metabolism, providing direct evidence of gene regulation happening in real time in an ancient animal. What’s more, microRNA analysis helped confirm that the findings really came from ancient mammoths.
Most sequences of one particularly important microRNA (Mir-1) contained a rare mutation that is usually only found in elephants and their close relatives, though it can appear in a few other animals such as redworms and lampreys, according to Mármol.
“However, since we did not find any evidence of additional contamination from these species other than the mammoth, we do believe that these Mir-1 sequences harboring such [a] rare mutation [are] shotgun proof of them being real ancient RNA molecules,†he said.
The findings open up a whole new world of ancient genomic research. “We hope our work elicits renewed interest in exploring RNA in other old remains, not necessarily from the Ice Age or from extinct species, but also from medieval or historical remains of both extinct and extant organisms,†Mármol said.
Future studies could investigate combined DNA, RNA, and protein analysis to provide a more complete picture of the biology of ancient species, he explained. This could be useful not just for understanding complex organisms but also simple life forms like RNA viruses.
“Many past pandemics for which we do not still know the origin might have been caused by RNA viruses,†Mármol said. Gaining a more robust understanding of past RNA viruses would not only elucidate their evolution, but also help us predict and combat future pandemics, he added.