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Ancient RNA: Does Next Generation Sequencing Offer a New Window into the Past?

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The wonders of ancient DNA (‘aDNA’) have become so commonplace that they almost cease to amaze. At this point, we’ve sequenced the genomes of Neanderthals, woolly mammoths, and Pleistocene Cave Bears, and each week it seems there are new and exciting aDNA stories in the news.

But what about ancient RNA?

As we have come to appreciate the importance of gene expression in health, disease, and evolution, interest in analyzing RNA has increased. You don’t hear much about ancient RNA though. Until recently, most researchers believed that the instability of this molecule prevented it from surviving intact for very long, at least under typical conditions. For this reason, it has not received much attention from the scientists who study ancient biomolecules.

Sequencing aRNA from ancient maize kernels

All of that changed this year, when scientists successfully sequenced aRNA from 700-year-old kernels of maize. This advance was described by Sarah Fordyce and Maria C. Ávila-Arcos of the Natural History Museum of Denmark and their coworkers in a journal article in PLoS ONE entitled “Deep Sequencing of RNA from Ancient Maize Kernels.” Using RNAseq, they were able to recover both RNA and DNA sequences from these kernels.

Thirsty and stressed

Incredibly, the average read length of the maize RNA fragments was longer than that of the DNA fragments. Most (~80%) of the RNA reads were of ribosomal origin, but multiple reads mapping to other genes were detected too. Interestingly, RNA for genes linked to water deficiency and stress appeared to be especially prominent among the transcripts.

An explanation for this sturdy RNA

How is it possible that these ancient RNA molecules survived for so long inside the kernels? The authors explain that seeds require diverse RNA transcripts to germinate. Because their very lives depend on the stability of RNA, seeds have likely evolved built-in mechanisms to protect these fragile molecules over long periods of time. In one study, researchers even demonstrated that a 2,000-year-old date seed excavated from an archaeological site near the Dead Sea could germinate and grow, indicating that it’s RNA must have remained in reasonable condition after thousands of years. Thus, the authors’ decision to target aRNA in ancient maize kernels in this study was a good bet.

What does the future hold for aRNA?

What does the ability to perform RNAseq on ancient samples add to the scientist’s toolkit? In addition to characterizing the genetic blueprint of ancient organisms, using aDNA, we could potentially learn more about how genetic plans were actually carried out, using aRNA. Gene expression influences all sorts of important features of seeds, including desiccation tolerance, dormancy, and germination.

A single timepoint?

Tom Gilbert, Professor of Palaeogenomics at the University of Copenhagen and the senior author of the article, observes, “There is always the challenge that RNA reflects only a timepoint in an organism’s life, so one has to be very careful. But conceptually, if you say had seeds from a single site, through time, you could look at if anything was differentially expressed through time, and then try and work out what this means about the environment or plant itself.” The authors acknowledge that careful studies of aRNA are needed to assess the potential of ancient gene expression studies.

Opening up the past

Will we see a flurry of new aRNA studies in the future? And will this technique be limited to seeds or will it succeed in other types of samples? It remains to be seen, but this appears to be an important first step in expanding the range of biomolecules we can study in ancient samples. The ability to analyze aRNA using next gen sequencing could open entire new vistas on the past.

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