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

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• dc.contributor.author Sandoval Velasco, Marcela
• dc.contributor.author Martí Renom, Marc A.
• dc.contributor.author Lieberman Aiden, Erez
• dc.date.accessioned 2024-09-23T06:32:38Z
• dc.date.available 2024-09-23T06:32:38Z
• dc.date.issued 2024
• dc.description.abstract Analyses 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.
• dc.description.sponsorship We thank Beth Shapiro and Richard Green (protocol development advice); Richard Mitchell, Peter Hotez, Aliaksandr Astrowski, Aviva Aiden, Sirui Zhou, Susannah Selber-Hnatiw, Guy Rouleau, Emil Karpinski, George Church, Saul Godinez, Zane Colaric, Shaiza Pasha, Galina Aglyamova, Jefferson Sinson, Anat Vivante, Sergei Kliver, Dimoklis Gkountaroulis, Camilo Chacón-Duque, Douglass Turner, Joel Cracraft, and Paul Sweet (discussions); Adam Fotos and Scistories (figures); Mahdi Sadr (videography); the Houston Zoo veterinary team, Dan Fisher, Hojun Song, Brandon Lyons, Ray Riley, and the Rosenthal Meat Science and Technology Center team at Texas A&M, Mary Thompson, and Stephen O’Brien (samples); Judah Aiden and Thomas Griggs (experiment assistance); and Ron Mathis (baseball pitching). E.L.A. acknowledges the McNair Medical Institute, NIH ENCODE (UM1HG009375), US-Israel Binational Science Foundation (2019276), and NSF-DBI-2021795. Center for Theoretical Biological Physics is supported by NSF-PHY-2019745, PHY-2210291 (to J.N.O.) and hardware donated by AMD. The Welch Foundation supported E.L.A. (Q-1866), J.N.O. (C-1792), and A.B.O.J. E.L.A. and M.A.M.-R. acknowledge NHGRI-RM1HG011016. M.A.M.-R. acknowledges Spanish Ministerio de Ciencia e Innovación (PID2020-115696RB-I00) and ERC-609989 under the 7th Framework Program FP7/2007-2013. M.T.P.G. and J.A.R. acknowledge ERC-681396, DNRF-143, and NNF-21OC0070726. M.J.R. acknowledges NIH-R35-GM147467. L.D. acknowledges Swedish Research Council (2017-04647 and 2021-00625) and ERC 101054984 PrimiGenomes. A.R.-H. acknowledges PID2020-112557GB-I00 and CGL2017-83802-P. M.D.P. and B.J.Z.H. acknowledge NIGMS/R35-GM146852. A.L.R. acknowledges USFWS-AFE2129-F22AP01215, UIUC College of ACES Seed Grant, and Fulbright Denmark. M.V.P. acknowledges NSF-DMS1763272, NIH-R01-AR079150, LEO Foundation (LF-AW-RAM-19-400008, LF-OC-20-000611), and Keck Foundation WMKF-5634988. Genome assembly was performed in association with the DNA Zoo Consortium (www.dnazoo.org), which acknowledges support from Illumina, IBM, and Pawsey Supercomputing Center.
• dc.format.mimetype application/pdf
• dc.identifier.citation Sandoval-Velasco M, Dudchenko O, Rodríguez JA, Pérez Estrada C, Dehasque M, Fontsere C, et al. Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. Cell. 2024 Jul 11;187(14):3541-62.e51. DOI: 10.1016/j.cell.2024.06.002
• dc.identifier.doi http://dx.doi.org/10.1016/j.cell.2024.06.002
• dc.identifier.issn 0092-8674
• dc.identifier.uri http://hdl.handle.net/10230/61194
• dc.language.iso eng
• dc.publisher Elsevier
• dc.relation.ispartof Cell. 2024 Jul 11;187(14):3541-62.e51
• dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/609989
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-115696RB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
• dc.relation.projectID info:eu-repo/grantAgreement/EC/HE/101054984
• dc.rights © 2024 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Hi-C
• dc.subject.keyword X inactivation
• dc.subject.keyword Ancient DNA
• dc.subject.keyword Chromatin loops
• dc.subject.keyword Fossil
• dc.subject.keyword Genome architecture
• dc.subject.keyword Genome assembly
• dc.subject.keyword Glass transition
• dc.subject.keyword Vitrification
• dc.subject.keyword Woolly mammoth
• dc.title Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion