{"id":97420,"date":"2024-07-12T17:03:25","date_gmt":"2024-07-12T15:03:25","guid":{"rendered":"https:\/\/www.pcb.ub.edu\/fossils-of-ancient-chromosomes-discovered-in-the-remains-of-a-52000-year-old-mammoth\/"},"modified":"2024-07-18T10:19:39","modified_gmt":"2024-07-18T08:19:39","slug":"fossils-of-ancient-chromosomes-discovered-in-the-remains-of-a-52000-year-old-mammoth","status":"publish","type":"post","link":"https:\/\/www.pcb.ub.edu\/en\/fossils-of-ancient-chromosomes-discovered-in-the-remains-of-a-52000-year-old-mammoth\/","title":{"rendered":"Fossils of ancient chromosomes discovered in the remains of a 52,000-year-old mammoth"},"content":{"rendered":"

A team led by scientists from Baylor College of Medicine, University of Copenhagen, and Centre Nacional d\u2019An\u00e0lisi Gen\u00f2mica (CNAG<\/a>), based in the Barcelona Science Park, and Centre for Genomic Regulation (CRG) report discovering fossils of ancient chromosomes in the remains of a woolly mammoth that died 52,000 years ago. Fossil chromosomes are much larger than previously-known types of ancient DNA. This scientific milestone is featured on the cover of Cell.<\/strong><\/p>\n

The discovery involves the participation of\u00a0Dr. Marc A. Mart\u00ed-Renom<\/strong>, ICREA research professor and group leader at Centre Nacional d’An\u00e0lisi Gen\u00f2mica (CNAG) and Centre for Genomic Regulation (CRG), and Dr. Juan Antonio Rodr\u00edguez<\/strong>, researcher at CNAG in Barcelona and the University of Copenhagen.<\/p>\n

\u201cWe\u2019ve known that tiny fragments of ancient DNA can survive for long periods of time,\u201d said Dr. Marcela Sandoval-Velasco<\/strong> of the\u00a0Center for Evolutionary Hologenomics at the University of Copenhagen and co-first author of the new study. \u201cBut what we found\u00a0here is a sample where the three-dimensional arrangement of these DNA fragments was frozen in place for tens of millennia,\u00a0thereby preserving the structure of the whole chromosome.\u201d<\/p>\n

Fossil chromosomes are a powerful new tool for studying the history of life on Earth. That\u2019s because typical ancient DNA\u00a0fragments are rarely longer than 100 base pairs, or 100 letters of the genetic code \u2013 far smaller than the full DNA sequence of\u00a0an organism, which is often billions of letters long. By contrast, fossil chromosomes can span hundreds of millions of genetic\u00a0letters.<\/p>\n

\u201cBy comparing ancient DNA molecules to the DNA sequences of modern species, it\u2019s possible to find cases where single letters\u00a0of the genetic code have changed,\u201d said co-first and co-corresponding author Dr. Olga Dudchenko<\/strong>, assistant professor of\u00a0molecular and human genetics at The Center for Genome Architecture at Baylor College of Medicine and Senior Investigator at\u00a0the Center for Theoretical Biological Physics at Rice University. \u201cFossil chromosomes are a game-changer, because knowing the\u00a0shape of an organism\u2019s chromosomes makes it possible to assemble the entire DNA sequence of extinct creatures. This enables the types of insights that would not have been possible before.\u201d<\/p>\n

Since the fossil chromosomes came from a mammoth, one of the first things the team did was to determine the number of\u00a0chromosomes that the woolly mammoth possessed.<\/p>\n

\u201cWe found that they have 28 pairs of chromosomes, which makes a lot of\u00a0sense, because that\u2019s what modern elephants have, and they are the woolly mammoth\u2019s closest living relative.\u201d said\u00a0Dr. Juan\u00a0Antonio Rodr\u00edguez<\/strong>, co-first author of the study and a researcher at the University of Copenhagen and at Centre Nacional d\u2019An\u00e0lisi Gen\u00f2mica in Barcelona, Spain.\u00a0\u201cIt was extremely exciting to be able to count the chromosomes of an extinct creature for the first time. It\u2019s usually not possible to have this much fun simply counting from one to twenty-eight.\u201d<\/p>\n

The fossils of ancient chromosomes provide information about which genes were active<\/strong><\/h3>\n

By examining the fossil chromosomes, which derived from the mammoth\u2019s skin, it was possible to see which genes were active. This is because of a phenomenon called chromosome compartmentalization \u2013 the fact that active and inactive DNA tends to segregate into two spatial neighborhoods inside the cell nucleus. For most genes, the activity state matches what researchers saw in modern elephant skin. But not always.<\/p>\n

\u201cThe obvious question for us was: why is it a \u2018woolly mammoth\u2019? Why isn\u2019t it a \u2018shockingly bald mammoth\u2019?\u201d said Dr. Thomas Gilber<\/strong>t, director of the Center for Hologenomics and co-corresponding author of the paper. \u201cThe fact that the compartmentalization was still preserved in these fossils was critical, because it made it possible to look, for the very first time, at which genes were active in a woolly mammoth. And it turns out that there are key genes that regulate hair follicle development whose activity pattern is totally different from in elephants.\u201d<\/p>\n

The researchers saw more than just compartmentalization in the shape of these ancient chromosomes. In fact, the\u00a0chromosomes shared many structural features with modern chromosomes. The most spectacular of these features was also the tiniest: chromatin loops, structures as small as 50nm which the Baylor team had mapped in humans, for the first time, only 10\u00a0years ago.<\/p>\n

\u201cThe survival of loops in these ancient chromosomes is perhaps the most impressive part,\u201d said Dr.\u00a0Marc A. Marti-Renom<\/strong>, co-corresponding author on the study and Group Leader at Centre Nacional d\u2019An\u00e0lisi Gen\u00f2mica,\u00a0as well as the\u00a0Centre for Genomic Regulation, both in Barcelona, Spain. \u201cDNA loops, which are only 50 nanometers in size, are important\u00a0because they bring activating DNA sequences close to their gene targets. So, these fossils don\u2019t just show us which genes were\u00a0active \u2013 they show us why.\u201d<\/p>\n

Siberian permafrost, key to preserving chromosome structure<\/strong><\/h3>\n

Yet the researchers were left with a puzzle: how could the DNA fragments of ancient chromosomes possibly survive for 52,000\u00a0years with their three-dimensional structure intact? After all, in 1905 \u2013 his \u2018annus mirabilis\u2019, or \u2018miracle year\u2019 \u2013 Albert Einstein\u00a0published a classic paper calculating how quickly small particles, like bits of DNA, tend to move through a substance.<\/p>\n

\u201cEinstein\u2019s work makes a very simple prediction about chromosome fossils: under ordinary circumstances, they shouldn\u2019t exist,\u201d said Dr. Dudchenko<\/strong>. \u201cAnd yet: here they are. It was a physics mystery!\u201d.<\/p>\n

To explain this apparent contradiction, the researchers realized that the chromosome fossils were in a very special state, closely resembling the state of molecules in glass.<\/p>\n

\u201cChromoglass is a lot like the glass in your window: it\u2019s rigid, but it\u2019s not an ordered\u00a0crystal,\u201d said Dr. Erez Lieberman Aiden<\/strong>, co-corresponding author of the study, director of The Center for Genome Architecture, and professor at the Baylor College of Medicine. \u201cIf you zoom in on the individual particles, a piece of glass \u2013 or a piece of chromoglass \u2013 is basically a bumper-to-bumper nanoscale traffic jam in a world with no lane markers. Individual particles, or individual fragments of ancient DNA, just can\u2019t move very far in that situation. Even if you wait for thousands and thousands of years.\u201d<\/p>\n

The idea that the mammoth remains, unearthed in 2018 in Siberian permafrost, were preserved in a glass-like state is not so\u00a0farfetched. Without realizing it, many civilizations developed ways to induce a \u201cglass transition\u201d in their food as a way to\u00a0preserve it, usually by a combination of cooling and dehydration. This resulted in foods, like tortilla chips and beef jerky \u2013 that\u00a0are more brittle than the original food, but that last much longer. And it is why the glass transition has become a key concept for\u00a0modern food scientists. Essentially, the researchers discovered that the chromosome fossils had been trapped inside a piece of\u00a0freeze-dried woolly mammoth jerky.<\/p>\n

\u201cWe confirmed this theory by doing experiments on old, freeze-dried beef jerky, which is much easier to find than woolly\u00a0mammoth jerky,\u201d explained Dr. Cynthia P\u00e9rez Estrada<\/strong>, co-first author of the study and a researcher at The Center for Genome Architecture and at Rice University\u2019s Center for Theoretical Biological Physics. \u201cWe fired a shotgun at it. We ran over it with a car. We had a former starting pitcher for the Houston Astros throw a fastball at it. Each time, the jerky broke into tiny bits \u2013 shattering like a glass. But at the nanoscale, the chromosomes were intact, unchanged. That\u2019s the reason these fossils can survive. That\u2019s the reason that they were there, fifty-two thousand years later, just waiting for us to find them.\u201d<\/p>\n

\u00bb Reference article:<\/strong>\u00a0 Sandoval-Velasco, Marcela, et al. \u2018Three-Dimensional Genome Architecture Persists in a 52,000-Year-Old Woolly Mammoth Skin Sample\u2019. Cell, vol. 187, no. 14, July 2024, pp. 3541-3562.e51. DOI: https:\/\/doi.org\/10.1016\/j.cell.2024.06.002<\/a><\/p>\n

\u00bb Link to the news: <\/strong>web del CNAG website [+]<\/a><\/p>\n

\"\"

Cover artwork by artist Binia De Cahsan for Cell.<\/p><\/div>\n","protected":false},"excerpt":{"rendered":"

A team led by scientists from Baylor College of Medicine, University of Copenhagen, and Centre Nacional d\u2019An\u00e0lisi Gen\u00f2mica (CNAG), based in the Barcelona Science Park, and Centre for Genomic Regulation…<\/p>\n","protected":false},"author":14,"featured_media":97406,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"categories":[36],"tags":[],"class_list":["post-97420","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science"],"acf":[],"yoast_head":"\nFossils of ancient chromosomes discovered in the remains of a 52,000-year-old mammoth - Parc Cient\u00edfic de Barcelona<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.pcb.ub.edu\/en\/fossils-of-ancient-chromosomes-discovered-in-the-remains-of-a-52000-year-old-mammoth\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Fossils of ancient chromosomes discovered in the remains of a 52,000-year-old mammoth - 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