Messages Across Millennia: Recovering Ancient RNA from the Woolly Mammoth

Deep within the frozen ground of Siberian permafrost, traces of life have endured far longer than once imagined. Among the molecular remnants preserved in ancient remains, DNA has long served as the primary window through which scientists investigate the genetics of extinct organisms from the Cenozoic era. RNA, however, tells a different story. This molecule is far more fragile and typically breaks down rapidly after death, making it widely regarded as an unlikely survivor across geological time. Yet an investigation involving ten Late Pleistocene woolly mammoths (Mammuthus primigenius) has opened an unexpected new chapter in the study of ancient biomolecules. Researchers succeeded in extracting RNA from frozen mammoth tissues preserved in permafrost, primarily from muscle and skin. Most remarkably, one individual—known as Yuka, a juvenile mammoth that lived roughly 39,000 years ago—yielded RNA fragments detailed enough to reconstruct patterns of gene expression within its cells. This discovery represents the oldest known record of ancient RNA carrying biologically meaningful information.

Locations where the 10 woolly mammoth specimens were discovered in eastern Siberia; the Arctic Ocean is shown at the center of the map（Image source：Mármol-Sánchez E et al. (2025)， CC BY 4.0 ）

In living organisms, genetic information stored in DNA is transcribed into RNA molecules. Some of these RNA molecules are then translated into proteins, the functional components that carry out cellular processes. RNA therefore occupies a dynamic position within the molecular machinery of life. Beyond serving as an intermediate between DNA and protein, RNA regulates gene activity, participates in RNA splicing within the nucleus, and performs numerous additional roles in cellular metabolism. Because RNA molecules are chemically reactive and easily degraded by enzymes, it has long been assumed that they cannot persist for extended periods after an organism's death. The present research challenges that assumption. By carefully extracting and sequencing RNA preserved within mammoth soft tissues, scientists demonstrated that under extremely cold and stable conditions—such as those found in permafrost—RNA fragments can survive tens of thousands of years.

When researchers isolate DNA or RNA from ancient remains, contamination is always a concern. Modern microbial cells, environmental DNA, or even human cells shed during handling can become mixed with the original molecules from the ancient organism. To ensure authenticity, the mammoth RNA sequences were carefully analyzed for molecular signatures characteristic of ancient nucleic acids. Patterns of nucleotide mismatches, accumulated chemical damage, and comparisons with modern genomes were used to evaluate whether the sequences truly originated from the mammoths themselves. The RNA fragments recovered from Yuka and two additional mammoth specimens displayed typical signs of age-related molecular decay, including cytosine deamination and base loss. The distribution of mismatches closely matched patterns known from ancient DNA studies, reinforcing the conclusion that these RNA molecules were genuinely ancient rather than modern contaminants.

Genetic data derived from the chromosomes also revealed something unexpected about Yuka. Prior to molecular analysis, the individual had been interpreted as female based on external anatomical features. However, sequencing results showed clear evidence of an XY chromosome complement, demonstrating that Yuka was actually a male juvenile mammoth. This genetic determination highlights the ability of molecular data to clarify biological details that may be ambiguous when relying solely on physical morphology.

The RNA recovered from Yuka's muscle tissue also revealed striking patterns of gene expression. Messenger RNAs and small regulatory RNAs known as microRNAs showed expression profiles highly characteristic of muscle cells. Several genes associated with slow-twitch muscle fibers—including MYH7, TNNT1, TNNC1, and TPM2—were particularly abundant. Slow-twitch muscle fibers are specialized for endurance and sustained activity, suggesting that the sampled tissue may have been dominated by this fiber type. These gene expression signatures resemble patterns seen in the muscles of modern large mammals, implying that mammoth muscle physiology shared many functional similarities with that of living species.

Beyond protein-coding genes, regulatory microRNAs were also well preserved in the ancient tissue. Two muscle-specific microRNAs, Mir-1 and Mir-133, were especially abundant. These molecules are widely recognized in modern mammals as key regulators of muscle development and gene expression. Their presence in Yuka's tissues provides further confirmation that the recovered RNA reflects authentic cellular activity from the mammoth's muscle cells shortly before death.

Interestingly, several additional microRNAs—including Mir-124-3p, Mir-184-5p, and Mir-9-5p—were also detected in Yuka's muscle samples. In modern humans these microRNAs are more commonly associated with processes such as cell proliferation and phagocytosis, and they are rarely abundant in muscle tissue. Their presence in mammoth muscle raises intriguing questions about whether these molecules performed different regulatory roles in ancient proboscideans or reflect biological processes not yet fully understood.

The study also sheds light on how RNA degrades over long periods of time. As samples grow older, RNA fragments become progressively shorter and more fragmented. In fact, the degradation observed in ancient RNA appears even more severe than that typically seen in ancient DNA. Longer RNA fragments were most often derived from exons, the coding segments of genes that remain in mature RNA transcripts after splicing. Shorter fragments were more frequently associated with introns or other genomic regions, and some may originate from environmental contamination introduced after the organism's death.

Another intriguing outcome of the analysis involves the discovery of potential new regulatory elements. By examining RNA expression patterns, researchers identified candidate microRNA gene loci within the mammoth genome that had not been previously recognized in modern mammalian genomes. These findings suggest that ancient RNA data may help reveal regulatory sequences overlooked in modern genomic studies, providing insight into how gene regulation operated in extinct species.

Despite its promise, the field of ancient RNA research still faces significant challenges. Successful recovery of RNA has so far been limited mostly to specimens preserved in extreme environments, such as permafrost or very dry conditions. RNA molecules degrade rapidly under typical environmental conditions, meaning that only exceptionally preserved remains are likely to retain detectable transcripts. Furthermore, extracting usable RNA from ancient tissues involves numerous technical difficulties. Chemical damage, fragmentation of molecules, loss of reactive ends needed for sequencing, and biases introduced during amplification can all complicate analysis. Compared with ancient DNA, reconstructing ancient RNA datasets remains considerably more difficult.

Even with these limitations, the implications of this research are profound. For the first time, scientists can observe traces of cellular activity from an extinct animal that lived tens of thousands of years ago. Rather than inferring biology solely from DNA sequences, ancient RNA allows researchers to glimpse which genes were actively expressed in particular tissues. From muscle fiber composition and metabolic activity to regulatory networks controlling gene expression, molecular echoes of ancient cellular processes can now be examined directly.

Research overview: RNA and DNA samples obtained from 10 woolly mammoths were analyzed to examine gene expression hotspots, sequence damage patterns, exon read abundance, sex identification, and tissue-specific gene expression profiles（Image source：Mármol-Sánchez E et al. (2025)， CC BY 4.0 ）

As analytical techniques improve, ancient RNA may become an increasingly powerful complement to ancient DNA and paleoproteomics. Together, these molecular approaches promise a far more complete reconstruction of extinct organisms. Instead of merely recovering their genomes, researchers may eventually reconstruct aspects of their cellular physiology and biological functions. In doing so, ancient RNA provides an extraordinary new perspective on the biology of long-vanished species, allowing fragments of their living molecular systems to emerge once again from the deep past.

Author: Shui-Ye You

Reference:

Mármol-Sánchez E et al. (2025). Ancient RNA expression profiles from the extinct woolly mammoth. Cell.

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