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

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 architectur...

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Detalles Bibliográficos
Autores: Sandoval Velasco, Marcela, Marti-Renom, Marc A., Lieberman Aiden, Erez
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Universitat Pompeu Fabra
Repositorio:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/61194
Acceso en línea:http://hdl.handle.net/10230/61194
http://dx.doi.org/10.1016/j.cell.2024.06.002
Access Level:acceso abierto
Palabra clave:Hi-C
X inactivation
Ancient DNA
Chromatin loops
Fossil
Genome architecture
Genome assembly
Glass transition
Vitrification
Woolly mammoth
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oai_identifier_str oai:repositori.upf.edu:10230/61194
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
title Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
spellingShingle Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
Sandoval Velasco, Marcela
Hi-C
X inactivation
Ancient DNA
Chromatin loops
Fossil
Genome architecture
Genome assembly
Glass transition
Vitrification
Woolly mammoth
title_short Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
title_full Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
title_fullStr Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
title_full_unstemmed Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
title_sort Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample
dc.creator.none.fl_str_mv Sandoval Velasco, Marcela
Marti-Renom, Marc A.
Lieberman Aiden, Erez
author Sandoval Velasco, Marcela
author_facet Sandoval Velasco, Marcela
Marti-Renom, Marc A.
Lieberman Aiden, Erez
author_role author
author2 Marti-Renom, Marc A.
Lieberman Aiden, Erez
author2_role author
author
dc.subject.none.fl_str_mv Hi-C
X inactivation
Ancient DNA
Chromatin loops
Fossil
Genome architecture
Genome assembly
Glass transition
Vitrification
Woolly mammoth
topic Hi-C
X inactivation
Ancient DNA
Chromatin loops
Fossil
Genome architecture
Genome assembly
Glass transition
Vitrification
Woolly mammoth
description 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.
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
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status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/61194
http://dx.doi.org/10.1016/j.cell.2024.06.002
url http://hdl.handle.net/10230/61194
http://dx.doi.org/10.1016/j.cell.2024.06.002
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Cell. 2024 Jul 11;187(14):3541-62.e51
info:eu-repo/grantAgreement/EC/FP7/609989
info:eu-repo/grantAgreement/ES/2PE/PID2020-115696RB-I00
info:eu-repo/grantAgreement/EC/H2020/681396
info:eu-repo/grantAgreement/EC/HE/101054984
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
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eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
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spelling Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sampleSandoval Velasco, MarcelaMarti-Renom, Marc A.Lieberman Aiden, ErezHi-CX inactivationAncient DNAChromatin loopsFossilGenome architectureGenome assemblyGlass transitionVitrificationWoolly mammothAnalyses 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.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.Elsevier202420242024info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/61194http://dx.doi.org/10.1016/j.cell.2024.06.002reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésCell. 2024 Jul 11;187(14):3541-62.e51info:eu-repo/grantAgreement/EC/FP7/609989info:eu-repo/grantAgreement/ES/2PE/PID2020-115696RB-I00info:eu-repo/grantAgreement/EC/H2020/681396info:eu-repo/grantAgreement/EC/HE/101054984© 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/).http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/611942026-06-12T07:21:37Z
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