Scientists have sequenced RNA from a nearly 40,000-year-old woolly mammoth leg, the oldest ancient RNA ever recovered. These fragile molecules could reveal which genes were active in the animal’s final hours and what was happening inside the animal’s muscles when it died.
The specimen studied was a mammoth, nicknamed Yuka, found well-preserved in Siberian permafrost. Unlike DNA, which records an organism’s genetic blueprint, RNA reveals which genes were active at a particular moment. While previous studies have documented the traces of ancient DNA from carcasses like Yuka, fragments of ancient RNA remained elusive. The reason is that RNA is far more fragile than DNA, and it usually degrades within a few days if not preserved.
In an email to New Atlas, one of the co-authors of the study, Love Dalén, explained how the research team approached the hunt for elusive ancient RNA.
“We suspected the main reason RNA degrades is due to RNAse enzymes in the cells, and figured that if we could sample mammoths that had frozen quickly after death, it had a chance of working," he wrote.
To extend the ancient RNA record in extinct paleofauna, a team led by Dalén and Emilio Mármol Sánchez collected soft tissues from muscle and skin samples of 10 woolly mammoths, dating from 10,000 to 50,000 years old. They then used a sterilized lab to prevent any modern contamination and extracted RNA by using protocols tailored for highly degraded nucleotide fragments. From the same samples, they pulled DNA for comparison to confirm the authenticity of the RNA signals through cross-checking.
“RNA sequences matched a tissue profile for muscle," Dalén told New Atlas. "That made it highly unlikely that we were seeing contamination from e.g. modern humans, microbes, or plants in the surrounding sediments.”
The results identified over 340 protein-coding messenger RNAs, over 900 non-coding RNAs, with roughly 60 microRNAs. The gene expression in the muscle tissue suggested a predominance of slow-twitch muscle fibers indicating the mammoth's muscles were built for stamina, ideal for long, steady travel across the cold, expansive steppes.
The detected RNA molecules included the signs of cellular distress, i.e., the code for proteins involved in metabolic regulation in times of stress. This finding correlated with previous suggestions that cave lions may have attacked or scavenged on Yuka.
The RNA analysis also helped resolve a longstanding mystery about Yuka’s sex. Prior studies reported Yuka as a female, based on DNA and external examination. Surprisingly, Yuka's RNA and DNA bore Y-chromosome markers, confirming it was a male.
“Honestly, [we were] relieved, as this was the only mammoth for which our sex identity record did not match the previously registered one, and of course, this was our best sample in terms of RNA data," the co-author of the study, Emilio Mármol Sánchez, told New Atlas.
Moving forward, Dalén says the future study of RNA in ancient animals will open up exciting new frontiers for understanding how these animals lived.
“We will be able to identify which genes that were important in creating the phenotype of extinct animals,” he told us. “For example, it would be really interesting to study RNA expression patterns in mammoth hair follicles to examine which genes were active during hair growth. That would help us narrow down which genes were responsible for the wooliness of woolly mammoths.”
The study was published in the journal Cell.
Source: Stockholm University
