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Reviving the Lost: Scientists Recover RNA From an Extinct Species for the First Time

Tasmanian tiger specimen used in the study and preserved in desiccation at room temperature in the Swedish National History Museum in Stockholm.” Credit: Emilio Mármol Sánchez (photograph) and Panagiotis Kalogeropoulos (editing).

A recent study successfully isolated and sequenced century-old RNARibonucleic acid (RNA) is a polymeric molecule similar to DNA that is essential in various biological roles in coding, decoding, regulation and expression of genes. Both are nucleic acids, but unlike DNA, RNA is single-stranded. An RNA strand has a backbone made of alternating sugar (ribose) and phosphate groups. Attached to each sugar is one of four bases—adenine (A), uracil (U), cytosine (C), or guanine (G). Different types of RNA exist in the cell: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>RNA molecules from a Tasmanian tiger specimen preserved at room temperature in a museum collection. This achievement marked the first-ever reconstruction of skin and skeletal muscle transcriptomes from an extinct speciesA species is a group of living organisms that share a set of common characteristics and are able to breed and produce fertile offspring. The concept of a species is important in biology as it is used to classify and organize the diversity of life. There are different ways to define a species, but the most widely accepted one is the biological species concept, which defines a species as a group of organisms that can interbreed and produce viable offspring in nature. This definition is widely used in evolutionary biology and ecology to identify and classify living organisms.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>species. The research team highlights that these discoveries hold significance for global initiatives aimed at reviving extinct species, such as the Tasmanian tiger and the woolly mammoth, and for research on pandemic RNA viruses.

Marc R. Friedländer

Marc R. Friedländer. Credit: Niklas Norberg Wirtén/SciLifeLab

The Tasmanian tiger, also known as the thylacine, was a remarkable apex carnivorous marsupial that was once distributed all across the Australian continent and the island of Tasmania. This extraordinary species found its final demise after European colonization, when it was declared as an agricultural pest, and a bounty of £1 per each full-grown animal killed was set by 1888. The last known living Tasmanian tiger died in captivity in 1936 at the Beaumaris Zoo in Hobart, Tasmania.

Recent efforts in de-extinction have focused on the Tasmanian tiger, as its natural habitat in Tasmania is still mostly preserved, and its reintroduction could help recover past ecosystem equilibriums lost after its final disappearance. However, reconstructing a functional living Tasmanian tiger not only requires a comprehensive knowledge of its genome (DNADNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>DNA) but also of tissue-specific gene expression dynamics and how gene regulation worked, which are only attainable by studying its transcriptome (RNA).

“Resurrecting the Tasmanian tiger or the woolly mammoth is not a trivial task, and will require a deep knowledge of both the genome and transcriptome regulation of such renowned species, something that only now is starting to be revealed,” says Emilio Mármol, the lead author of a study recently published in the Genome Research journal by researchers at SciLifeLab in collaboration with the Centre for Palaeogenetics*, a joint venture between the Swedish Museum of Natural History and Stockholm University.

RNA molecules recovered from the Tasmanian tiger

The researchers behind this study have sequenced, for the first time, the transcriptome of the skin and skeletal muscle tissues from a 130-year-old desiccated Tasmanian tiger specimen preserved at room temperature in the Swedish Museum of Natural History in Stockholm. This led to the identification of tissue-specific gene expression signatures that resemble those from living extant marsupial and placental mammals.

The recovered transcriptomes were of such good quality that it was possible to identify muscle- and skin-specific protein-coding RNAs, and led to the annotation of missing ribosomal RNA and microRNA genes, the latter following MirGeneDB recommendations.

Love Dalén

Love Dalén. Credit: Sören Andersson

“This is the first time that we have had a glimpse into the existence of thylacine-specific regulatory genes, such as microRNAs, that got extinct more than one century ago,” says Marc R. Friedländer, Associate Professor at the Department of Molecular Biosciences, The Wenner-Gren Institute at Stockholm University and SciLifeLab.

This pioneering study opens up new exciting opportunities and implications for exploring the vast collections of specimens and tissues stored at museums across the globe, where RNA molecules might await to be uncovered and sequenced.

“In the future, we may be able to recover RNA not only from extinct animals but also RNA virusA virus is a tiny infectious agent that is not considered a living organism. It consists of genetic material, either DNA or RNA, that is surrounded by a protein coat called a capsid. Some viruses also have an outer envelope made up of lipids that surrounds the capsid. Viruses can infect a wide range of organisms, including humans, animals, plants, and even bacteria. They rely on host cells to replicate and multiply, hijacking the cell's machinery to make copies of themselves. This process can cause damage to the host cell and lead to various diseases, ranging from mild to severe. Common viral infections include the flu, colds, HIV, and COVID-19. Vaccines and antiviral medications can help prevent and treat viral infections.” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>virus genomes such as SARS-CoV2 and their evolutionary precursors from the skins of bats and other host organisms held in museum collections”, says Love Dalén, Professor of evolutionary genomics at Stockholm University and the Centre for Palaeogenetics.

The authors of the study say they are excited for future holistic research developments integrating both genomics and transcriptomics towards a new era in palaeogenetics beyond DNA.

Reference: “Historical RNA expression profiles from the extinct Tasmanian tiger” by Emilio Marmol-Sanchez, Bastian Fromm, Nikolay Oskolkov, Zoe Pochon, Panagiotis Kalogeropoulos, Eli Eriksson, Inna Biryukova, Vaishnovi Sekar, Erik Ersmark, Bjorn Andersson, Love Dalen and Marc Friedlander, 18 July 2023, Genome Research.
DOI: 10.1101/gr.277663.123

Source: SciTechDaily