دورية أكاديمية
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.
| العنوان: | Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample. |
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| المؤلفون: | Sandoval-Velasco M; Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark., Dudchenko O; The 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., Rodríguez JA; Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; Centre Nacional d'Anàlisi Genòmica, CNAG, 08028 Barcelona, Spain., Pérez Estrada C; The 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., Dehasque M; Centre 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., Fontsere C; Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark., Mak SST; Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark., Khan R; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Contessoto VG; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA., Oliveira Junior AB; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA., Kalluchi A; Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA., Zubillaga Herrera BJ; Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA., Jeong J; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Roy RP; The 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., Christopher I; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Weisz D; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Omer AD; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Batra SS; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Shamim MS; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Durand NC; The 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., O'Connell B; Department 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., Roca AL; Department of Animal Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA., Plikus MV; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA., Kusliy MA; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Romanenko SA; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Lemskaya NA; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Serdyukova NA; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Modina SA; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Perelman PL; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Kizilova EA; Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia., Baiborodin SI; Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia., Rubtsov NB; Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia., Machol G; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Rath K; The Center for Genome Architecture and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Mahajan R; The 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., Kaur P; UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia., Gnirke A; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Garcia-Treviño I; San Antonio Zoo, San Antonio, TX 78212, USA., Coke R; San Antonio Zoo, San Antonio, TX 78212, USA., Flanagan JP; Houston Zoo, Houston, TX 77030, USA., Pletch K; Houston Zoo, Houston, TX 77030, USA., Ruiz-Herrera A; Departament 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., Plotnikov V; Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia., Pavlov IS; Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia., Pavlova NI; Institute of Biological Problems of Cryolitezone SB RAS, Yakutsk 677000, Russia., Protopopov AV; Academy of Sciences of Sakha Republic, Yakutsk 677000, Russia; North-Eastern Federal University, Yakutsk 677027, Russia., Di Pierro M; Department of Physics, Northeastern University, Boston, MA 02115, USA; Center for Theoretical Biological Physics, Northeastern University, Boston, MA 02215, USA., Graphodatsky AS; Institute of Molecular and Cellular Biology SB RAS, Novosibirsk 630090, Russia., Lander ES; Broad 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., Rowley MJ; Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA., Wolynes PG; Center 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., Onuchic JN; Center 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., Dalén L; Centre 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., Marti-Renom MA; Centre 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., Gilbert MTP; Center for Evolutionary Hologenomics, University of Copenhagen, DK-1353 Copenhagen, Denmark; University Museum NTNU, 7012 Trondheim, Norway. Electronic address: tgilbert@sund.ku.dk., Aiden EL; The 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. |
| المصدر: | Cell [Cell] 2024 Jul 11; Vol. 187 (14), pp. 3541-3562.e51. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Cell Press Country of Publication: United States NLM ID: 0413066 Publication Model: Print Cited Medium: Internet ISSN: 1097-4172 (Electronic) Linking ISSN: 00928674 NLM ISO Abbreviation: Cell Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Cambridge, Ma : Cell Press Original Publication: Cambridge, MIT Press. |
| مواضيع طبية MeSH: | Mammoths*/genetics , Genome*/genetics , Skin*, Animals ; Female ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics |
| مستخلص: | 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. Competing Interests: Declaration of interests E.L.A., M.T.P.G., and L.D. are on the scientific advisory board of Colossal Biosciences and hold stock options. From 2021 to 2023, M.A.M.-R. received consulting honoraria from Acuity Spatial Genomics. E.L.A. and O.D. are inventors on US provisional patent applications 16/308,386 (E.L.A. and O.D., filed 12/7/2018), 16/247,502 (E.L.A. and O.D., 1/14/2019), and PCT/US2020/064704 (E.L.A., 12/11/2020) by the Baylor College of Medicine and the Broad Institute, relating to the assembly methods in this manuscript. (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.) |
| معلومات مُعتمدة: | R35 GM147467 United States GM NIGMS NIH HHS |
| فهرسة مساهمة: | Keywords: Hi-C; X inactivation; ancient DNA; chromatin loops; fossil; genome architecture; genome assembly; glass transition; vitrification; woolly mammoth |
| المشرفين على المادة: | 0 (Chromatin) 0 (DNA, Ancient) |
| تواريخ الأحداث: | Date Created: 20240712 Date Completed: 20240712 Latest Revision: 20240724 |
| رمز التحديث: | 20240725 |
| DOI: | 10.1016/j.cell.2024.06.002 |
| PMID: | 38996487 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1097-4172 |
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| DOI: | 10.1016/j.cell.2024.06.002 |