For the first time, researchers have sequenced RNA from an extinct animal species — the Tasmanian tiger, or thylacine (Thylacinus cynocephalus).
Using muscle and skin samples from a 132-year-old museum specimen, scientists isolated millions of RNA sequences. This genetic material provides information about the animal’s genes and the proteins that were made in its cells and tissues. The findings, published in Genome Research1, offer hope that RNA locked up in the world’s museum collections could provide new insights into long-dead species.
Being able to look at RNA in particular “opens up a whole new potential source of information”, says Oliver Smith, a geneticist at the medical-diagnostics company Micropathology in Coventry, UK. “As opposed to looking at what a genome is, we can look at what the genome does.”
The Tasmanian tiger was a carnivorous marsupial that lived on the island of Tasmania in southeast Australia. The last known Tasmanian tiger died in captivity in 1936, but a handful of specimens have been preserved in museums.
Researchers studied thylacine remains that had been stored at the Stockholm Natural History Museum since 1891. They collected three muscle samples and three skin samples, each weighing about 80 milligrams.
Obtaining RNA from historical samples is challenging because unlike DNA — which is highly stable and has been extracted from extinct species that lived more than one million years ago — RNA rapidly breaks down into smaller fragments. “Outside of living cells, it’s believed to be degraded or destroyed in minutes,” says study co-author Marc Friedländer, a geneticist at Stockholm University.
The team developed a protocol specifically for extracting ancient RNA from tissue samples, adapting standard methods that are used on fresher samples. Nevertheless, “it was surprising that we found these authentic RNA sequences in this mummified Tasmanian tiger”, says Friedländer.
The researchers extracted and purified 81.9 million and 223.6 million RNA fragments from the thylacine’s muscle and skin, respectively. After removing duplicates and very short sequences, they identified 1.5 million RNA sequences from muscle tissue and 2.8 million from skin.
RNA provides information about how gene expression varies between tissues, says co-author Emilio Mármol-Sánchez, a computational biologist at Stockholm University.
In the muscle samples, the research team found sequences corresponding to 236 genes, including some that code for actin and titin — proteins that enable muscles to stretch and contract. In the skin samples, they found sequences corresponding to 270 genes, including the one that encodes the structural protein keratin.
The researchers also found a small number of RNA molecules from viruses that lived in or infected the Tasmanian tiger. Being able to trace and recover these molecules opens the door to studying ancient viruses, says Hannes Schroeder, an ancient-DNA researcher at the University of Copenhagen.
The study of ancient DNA is well established, but ancient RNA sequencing is still underdeveloped, says Smith. This study, he adds, “is giving a new life into a field which is under-represented and under-rated”. He hopes to see future studies routinely combine both DNA and RNA sequencing.