An incredibly well-preserved woolly mammoth specimen that died 52,000 years ago in Siberia has now had its chromosome structure reassembled for the first time.
In 2018, a 52,000-year-old woolly mammoth was found preserved, complete with skin and muscle, in the Siberian permafrost. Scientists used a new technique, called Hi-C, to analyse the 3D structures of the mammoth genome for the first time.
The research team hopes Hi-C can be used to study other extinct species, although the right set of conditions is needed to preserve DNA in ancient samples.The 52,000-year-old specimen was so well preserved that hair follicles and the shape of the muscles were still intact, with one scientist likening the location of the find to dying "in the deep freezer". While older mammoth DNA has been previously sequenced, these were the first 3D structures, called chromosomes, assembled for any ancient DNA sample. Chromosomes — packages of tightly wound DNA — are where creatures like mammoths and humans store and duplicate genetic information within cells.by an international team of scientists, revealed the species had 28 chromosomes — the same number as both the Asian and African elephants.One of the researchers, biotechnologist Parwinder Kaur of University of Western Australia, said the mammoth DNA was an "incredible" discovery.The team, led by Erez Lieberman Aiden of Baylor College of Medicine in the US, wanted to know if DNA structures could survive after tens of thousands of years. They had been playing with a technique called Hi-C, which creates a 3D structure of a genome — including the chromosomes and the way DNA sits within them. To put it to the test on an ancient specimen, they needed to find a mammoth carcass in tip-top shape. It took the researchers five years to land on a suitable specimen — an immensely well-preserved portion of mammoth skin called YakInf, which was uncovered in 2018 near Belaya Gora in Siberia. They knew straight away that it was something special because the hair was still intact, which suggested the mammoth hadn't gone through periods of thawing and refreezing. "You could actually see individual hair follicles from this woolly mammoth, and that's quite remarkable," Professor Lieberman Aiden said at a press conference.The dehydrated skin sample has been described as glass-like or freeze-dried, which trapped the fragments of DNA in place. "What we think happened is that this sample freeze dried, forming a kind of beef jerky," Professor Lieberman Aiden said.Normally, after an animal or other creature dies, its DNA quickly breaks into smaller and smaller pieces as it and the body decays."And the more degraded the sample, the more missing data points are there." By the time the DNA becomes ancient — hundreds or thousands of years after death — researchers only have access to small sections of the DNA to piece back together, like an incomplete jigsaw puzzle. If researchers have access to lots of samples, this is easier, as it works like having multiple copies of the same jigsaw puzzle with different missing pieces. Teams also can sometimes use "reference genomes" from genetically similar species to check they are on the right track.Hi-C works in a similar way to this reference genome but in 3D, and detects which sections of fragmented DNA are likely to be neighbours and interact with each other. The team used Hi-C to create the 28-chromosome mammoth genome in detail, then referenced it against the genomes of modern Asian and African elephants.even older , woolly mammoth genomes have been constructed by combining information from multiple samples, or using reference genomes to fill in the gaps. But because of the freeze-dried nature of the samples, the team could analyse not only the genome itself, but also its shape and structure, which provides more information.genes were switched on and off within the skin cells, the first time researchers have done so. They discovered certain genes involved with cold adaptation and hair growth were turned on in a mammoth, but not in an elephant. Sally Wasef, a palaeogeneticist at Queensland University of Technology who was not involved in the research, was impressed with the techniques."I'd love to see how they're going to apply it to different samples."While experts agree this is an impressive discovery, finding specimens as old and well-preserved as the 52,000-year-old mammoth skin won't happen often."They're very lucky because the mammoth died in the 'deep freezer,'" University of Melbourne geneticist Andrew Pask said.This means there's no chance that Australia could harbour an animal as well preserved and as ancient as the mammoth, Professor Pask added."The DNA is smashed to pieces. We're just too warm." While cold, freezer-like environments are the best place to find other samples, the team behind the latest study suggest that hot, dry environments may also produce the glass-like DNA state suitable for Hi-C analysis.But Dr Wasef believes that ancient Egyptian DNA may be too degraded.Instead, she thinks the technique could be used on ancient hominids like Denisovans — whose fossils have also been found in cooler areas like Siberia — to see how they differed from our species,"It will tell you more about the environment where they lived, their interactions with the environment around them, and what led to their extinction."While uncovering a 52,000-year-old chromosome was exciting in itself, the researchers were also interested in how the technique could help bring ancient species back to life, known as de-extinction. Professor Lieberman Aiden is one of two senior authors on the paper who are advisors to biotechnology startup Colossal Biosciences, the company working on reviving the mammoth. Professor Pask and his team are working to recreate the Tasmanian tiger, which has been extinct for almost 90 years.Professor Pask heads the Thylacine Integrated Genetic Restoration Research lab, which is a partnership between the University of Melbourne and Colossal. For him, the mammoth chromosome finding is encouraging, but is not "a total game changer" for de-extinction.Even though we might be able to bring the thylacine back from extinction this science exhibition asks whether we should."We're trying to do it with some of the better preserved thylacine tissues, just to see if we could get some architecture," he said. "There are some specimens that were put into ethanol and then placed in a museum collection, and have been kept at good temperatures for their entire storage."" being the ultimate keystone species ... is an extraordinary responsibility," Professor Lieberman Aiden said. "I hope we act responsibly with all the powerful technologies at our disposal — de-extinction being one of them."Wild dog or dingo? Ancient DNA study suggests there's not much dog at allTrump says he could end the Russia-Ukraine war 'within a day'. It's enough to send shivers down Australia's spine Anti-violence campaigner says government must listen to 'voices from the bush' after Alice Springs curfewAbused since age 3, it took more than 50 departmental reports and 10 years to remove Sally from that homeAustralian couple found dead at luxury Philippines hotelDolphins overcome controversial penalty try to snap losing streakTrump says he could end the Russia-Ukraine war 'within a day'. It's enough to send shivers down Australia's spine Man charged over fatal hit-and-run in Sydney's west swapped cars and fled country after crash, court toldTrump says he could end the Russia-Ukraine war 'within a day'. It's enough to send shivers down Australia's spine Anti-violence campaigner says government must listen to 'voices from the bush' after Alice Springs curfewAbused since age 3, it took more than 50 departmental reports and 10 years to remove Sally from that home
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