Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

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dc.citation.firstpage3541en_US
dc.citation.issueNumber14en_US
dc.citation.journalTitleCellen_US
dc.citation.lastpage3.562E-54en_US
dc.citation.volumeNumber187en_US
dc.contributor.authorSandoval-Velasco, Marcelaen_US
dc.contributor.authorDudchenko, Olgaen_US
dc.contributor.authorRodríguez, Juan Antonioen_US
dc.contributor.authorPérez Estrada, Cynthiaen_US
dc.contributor.authorDehasque, Marianneen_US
dc.contributor.authorFontsere, Claudiaen_US
dc.contributor.authorMak, Sarah S. T.en_US
dc.contributor.authorKhan, Ruqayyaen_US
dc.contributor.authorContessoto, Vinícius G.en_US
dc.contributor.authorOliveira Junior, Antonio B.en_US
dc.contributor.authorKalluchi, Achyuthen_US
dc.contributor.authorZubillaga Herrera, Bernardo J.en_US
dc.contributor.authorJeong, Jiyunen_US
dc.contributor.authorRoy, Renata P.en_US
dc.contributor.authorChristopher, Ishawniaen_US
dc.contributor.authorWeisz, Daviden_US
dc.contributor.authorOmer, Arina D.en_US
dc.contributor.authorBatra, Sanjit S.en_US
dc.contributor.authorShamim, Muhammad S.en_US
dc.contributor.authorDurand, Neva C.en_US
dc.contributor.authorO’Connell, Brendanen_US
dc.contributor.authorRoca, Alfred L.en_US
dc.contributor.authorPlikus, Maksim V.en_US
dc.contributor.authorKusliy, Mariya A.en_US
dc.contributor.authorRomanenko, Svetlana A.en_US
dc.contributor.authorLemskaya, Natalya A.en_US
dc.contributor.authorSerdyukova, Natalya A.en_US
dc.contributor.authorModina, Svetlana A.en_US
dc.contributor.authorPerelman, Polina L.en_US
dc.contributor.authorKizilova, Elena A.en_US
dc.contributor.authorBaiborodin, Sergei I.en_US
dc.contributor.authorRubtsov, Nikolai B.en_US
dc.contributor.authorMachol, Guren_US
dc.contributor.authorRath, Krishaen_US
dc.contributor.authorMahajan, Raginien_US
dc.contributor.authorKaur, Parwinderen_US
dc.contributor.authorGnirke, Andreasen_US
dc.contributor.authorGarcia-Treviño, Isabelen_US
dc.contributor.authorCoke, Roben_US
dc.contributor.authorFlanagan, Joseph P.en_US
dc.contributor.authorPletch, Kelcieen_US
dc.contributor.authorRuiz-Herrera, Auroraen_US
dc.contributor.authorPlotnikov, Valeriien_US
dc.contributor.authorPavlov, Innokentiy S.en_US
dc.contributor.authorPavlova, Naryya I.en_US
dc.contributor.authorProtopopov, Albert V.en_US
dc.contributor.authorDi Pierro, Micheleen_US
dc.contributor.authorGraphodatsky, Alexander S.en_US
dc.contributor.authorLander, Eric S.en_US
dc.contributor.authorRowley, M. Jordanen_US
dc.contributor.authorWolynes, Peter G.en_US
dc.contributor.authorOnuchic, José N.en_US
dc.contributor.authorDalén, Loveen_US
dc.contributor.authorMarti-Renom, Marc A.en_US
dc.contributor.authorGilbert, M. Thomas P.en_US
dc.contributor.authorAiden, Erez Liebermanen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2024-11-04T16:25:09Zen_US
dc.date.available2024-11-04T16:25:09Zen_US
dc.date.issued2024en_US
dc.description.abstractAnalyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth’s death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.en_US
dc.identifier.citationSandoval-Velasco, M., Dudchenko, O., Rodríguez, J. A., Estrada, C. P., Dehasque, M., Fontsere, C., Mak, S. S. T., Khan, R., Contessoto, V. G., Junior, A. B. O., Kalluchi, A., Herrera, B. J. Z., Jeong, J., Roy, R. P., Christopher, I., Weisz, D., Omer, A. D., Batra, S. S., Shamim, M. S., … Aiden, E. L. (2024). Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell, 187(14), 3541-3562.e51. https://doi.org/10.1016/j.cell.2024.06.002en_US
dc.identifier.digitalPIIS0092867424006421en_US
dc.identifier.doihttps://doi.org/10.1016/j.cell.2024.06.002en_US
dc.identifier.urihttps://hdl.handle.net/1911/117980en_US
dc.language.isoengen_US
dc.publisherElsevieren_US
dc.rightsExcept where otherwise noted, this work is licensed under a Creative Commons Attribution (CC BY) license. Permission to reuse, publish, or reproduce the work beyond the terms of the license or beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleThree-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sampleen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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