Gene transcripts from ancient wolf analyzed after 14,000 years in permafrost

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Gene transcripts from ancient wolf analyzed after 14,000 years in permafrost

The RNA - the ephemeral transcripts of genes - of the "Tumat puppy", a wolf from the Pleistocene, was isolated and its sequence analyzed in a new study by Oliver Smith of the University of Copenhagen and his colleagues published on July 30 in the open access journal PLOS Biology. The results establish the possibility of examining a range of RNA transcripts of ancient organisms, a possibility previously considered extremely unlikely due to the short life span of the RNA.

DNA, which encodes the "hard copy" of genes, is known to survive for thousands of years under favourable conditions. But RNA - the short-term working copy of a gene, which is transcribed from DNA in the cell and forms the instructions for protein production - is quickly broken down in living tissues by a series of recycling enzymes. This instability generally persists after death and, for this reason, researchers generally assumed that the probability of finding intact the RNA complement of an ancient cell - its transcriptome - was very low. But there were some exceptions, especially in plants, which led the authors to wonder if there were not ancient animal transcriptomes well enough preserved to be sequenced.

They isolated and analyzed RNA from liver tissue of a 14,300-year-old canine, possibly a wolf or a partially domesticated wolf-like creature, which had been preserved in Siberian permafrost until its discovery, as well as from tissue of two wolves from the 19th and 20th centuries for comparison purposes. Using various transcriptomic techniques and quality control measures, the team demonstrated that the RNA sequenced from the Pleistocene canine was truly representative of the animal's RNA, with many specific liver transcripts corresponding to more modern samples from wolves and dogs.

The transcriptome of the Siberian canine is the oldest RNA sequenced by far, surpassing the next transcriptome by at least 13,000 years. The authors note that unlike palaeogenomics, paleotranscriptomics is unlikely to become routine, because even under the best conditions, RNA is not as well preserved as DNA.

Nevertheless, there will probably be a large number of other naturally frozen specimens for which it is possible to decipher the transcriptome, opening up to researchers not only the genes of ancient organisms, but the flow of cellular activity encoded by the transcriptome.

"Ancient DNA researchers were previously reluctant to attempt to sequence ancient RNA because it is generally more unstable than DNA and more prone to enzymatic degradation," said Dr. Smith. "However, following our recent successes in sequencing old RNA from plant material, we have hypothesized that a well-preserved animal specimen frozen in permafrost may well retain sufficient material to sequence. To our great pleasure, we discovered that not only did we find RNA from various tissues, but in some cases the signal was so strong that we could distinguish between tissues in a way that made biological sense.

Knowing that RNA acts as an intermediary between DNA and proteins, both of which are more stable, it may be tempting to ask "so what? But we believe that the future of old RNA has great potential. For example, many of the most clinically relevant viruses that exist today have RNA genomes, and the stage of RNA is often crucial to understanding the complexities and complexities of gene regulation. This could have repercussions when discussing environmental stresses and the constraints that cause evolution."