ArticleCell2024
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.
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Article in Cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21citing papers in PubMed
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Who cites it
21 citing papers in PubMed.
- LAWS-HiC: A Locally Adaptive Weighting and Screening (LAWS) Approach to Improve Detection of Long-Range Chromatin Interactions from Hi-C Data.Methods and protocols · 2026Article
- Applying the Poincaré Disc Method to Analyze the Hierarchical Structure of TADs in Hi-C Data.Genes · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Kilobase-scale compartments enabled by CRUSH reveal regulatory programs across cell types, single-cells, and ancient mammoths.bioRxiv : the preprint server for biology · 2026Article
- Article
- Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost.Scientific reports · 2026Article
- Deciphering the 3D genome organization across species from Hi-C data.Nucleic acids research · 2026Article
- Understanding the physical processes behind DNA-DNA proximity ligation assays.Research square · 2025Article
- Closing the loops: chromatin loop dynamics after DNA damage.Nucleus (Austin, Tex.) · 2025Review
- The rise of historical epigenomics and temporal analysis of gene regulation.Genome biology · 2025Review
- X chromosome inactivation in mammals: general principles and species-specific considerations.EMBO reports · 2025Review
- Unveiling the Genome of the Diploid Wild Sugarcane RelativeInternational journal of molecular sciences · 2025Article
- Unveiling Multi-Scale Architectural Features in Single-Cell Hi-C Data Using scCAFE.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer.Genome biology and evolution · 2025Review
- Divergent 3D genome organization in livers of cave and surface morphs ofbioRxiv : the preprint server for biology · 2025Article
- Understanding the physical processes behind DNA-DNA proximity ligation assays.bioRxiv : the preprint server for biology · 2025Article
- Reframing Formalin: A Molecular Opportunity Enabling Historical Epigenomics and Retrospective Gene Expression Studies.Molecular ecology resources · 2025Review
- Energy landscape analysis of the development of the chromosome structure across the cell cycle.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sequencing RNA from old, dried specimens reveals past viromes and properties of long-surviving RNA.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
56 authors.
Marcela Sandoval-VelascoCenter for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark.
Olga DudchenkoThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA. Electronic address: olga.dudchenko@bcm.edu.
Juan Antonio RodríguezCenter for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain.
Cynthia Pérez EstradaThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Marianne DehasqueCentre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden.
Claudia FontsereCenter for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark.
Sarah S T MakCenter for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark.
Ruqayya KhanThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Vinícius G ContessotoCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Antonio B Oliveira JuniorCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
Achyuth KalluchiDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.
Bernardo J Zubillaga HerreraDepartment of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA.
Jiyun JeongThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Renata P RoyThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Departments of Biology and Physics, Texas Southern University, Houston, TX 77004, USA.
Ishawnia ChristopherThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
David WeiszThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Arina D OmerThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Sanjit S BatraThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Muhammad S ShamimThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Neva C DurandThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Brendan O'ConnellDepartment of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
Alfred L RocaDepartment of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Maksim V PlikusDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
Mariya A KusliyInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Svetlana A RomanenkoInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Natalya A LemskayaInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Natalya A SerdyukovaInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Svetlana A ModinaInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Polina L PerelmanInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Elena A KizilovaInstitute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia.
Sergei I BaiborodinInstitute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia.
Nikolai B RubtsovInstitute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia.
Gur MacholThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Krisha RathThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Ragini MahajanThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA.
Parwinder KaurUWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia.
Andreas GnirkeBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Isabel Garcia-TreviñoSan Antonio Zoo, San Antonio, TX 78212, USA.
Rob CokeSan Antonio Zoo, San Antonio, TX 78212, USA.
Joseph P FlanaganHouston Zoo, Houston, TX 77030, USA.
Kelcie PletchHouston Zoo, Houston, TX 77030, USA.
Aurora Ruiz-HerreraDepartament de Biologia Cel·lular, Fisiologia i Immunologia and Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
Valerii PlotnikovAcademy of Sciences of Sakha Republic, Yakutsk 677000, Russia.
Innokentiy S PavlovAcademy of Sciences of Sakha Republic, Yakutsk 677000, Russia.
Naryya I PavlovaInstitute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia.
Albert V ProtopopovAcademy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia.
Michele Di PierroDepartment of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA.
Alexander S GraphodatskyInstitute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia.
Eric S LanderBroad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
M Jordan RowleyDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.
Peter G WolynesCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA.
José N OnuchicCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Biosciences, Rice University, Houston, TX 77005, USA; Departments of Physics, Astronomy, & Chemistry, Rice University, Houston, TX 77005, USA.
Love DalénCentre for Palaeogenetics, SE-106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 10405 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden.
Marc A Marti-RenomCentre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain; Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain; ICREA, 08010 Barcelona, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain. Electronic address: martirenom@cnag.eu.
M Thomas P GilbertCenter for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway. Electronic address: tgilbert@sund.ku.dk.
Erez Lieberman AidenThe Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: erez@erez.com.
Funding
Center for Genome ImagingRM1HG011016 · NHGRI · HARVARD MEDICAL SCHOOL · PI WU, CHAO-TING · 2021 to 2025
$12.2MGENOME WIDE MAPPING OF LOOPS USING IN SITU HI-CUM1HG009375 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI LIEBERMAN-AIDEN, EREZ · 2017 to 2021
$4.7MTissue Size and Precision Control in Growing Hair FolliclesR01AR079150 · NIAMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Qing Nie, Maksim V Plikus · 2022 to 2026
$2.7MFine-Scale Genome Folding Relative to Transcription and LocationR35GM147467 · NIGMS · UNIVERSITY OF NEBRASKA MEDICAL CENTER · PI Michael Jordan Rowley · 2022 to 2026
$2.0MPAR-20-117R35GM146852 · NIGMS · NORTHEASTERN UNIVERSITY · PI Michele Di Pierro · 2022 to 2026
$2.0MNHGRI NIH HHS RM1 HG011016NHGRI NIH HHS UM1 HG009375NIAMS NIH HHS R01 AR079150NIGMS NIH HHS R35 GM146852NIGMS NIH HHS R35 GM147467
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.
Indexed as
GenomeMammothsSkinAnimalsChromatinDNA, AncientElephantsFemaleFossilsHumansMiceX ChromosomeChromatinDNA, Ancientancient DNAchromatin loopsfossilgenome architecturegenome assemblyglass transitionHi-Cvitrificationwoolly mammothX inactivation
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