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|||0000-0002-4635-6171, Dudchenko, Olga|||0000-0001-9163-9544, Rodríguez, Juan Antonio, Pérez Estrada, Cynthia, Dehasque, Marianne|||0000-0002-4640-8306, Fontsere, Claudia|||0000-0003-2233-6026, Mak, Sarah S.T., Khan, Ruqayya, Contessoto, Vinícius G., Oliveira Junior, Antonio B., Kalluchi, Achyuth, Zubillaga Herrera, Bernardo, Jeong, Jiyun, Roy, Renata P., Christopher, Ishawnia, Weisz, David, Omer, Arina D., Batra, Sanjit S., Shamim, Muhammad S., Durand, Neva C., O'Connell, Brendan, Roca, Alfred L., Plikus, Maksim V., Kusliy, Mariya A., Romanenko, Svetlana A., Lemskaya, Natalya A., Serdyukova, Natalya A., Modina, Svetlana A., Perelman, Polina L., Kizilova, Elena A., Baiborodin, Sergei I., Rubtsov, Nikolai B., Machol, Gur, Rath, Krisha, Mahajan, Ragini, Kaur, Parwinder|||0000-0003-0201-0766, Gnirke, Andreas, Garcia-Treviño, Isabel, Coke, Rob, Flanagan, Joseph P., Pletch, Kelcie, Ruiz Herrera Moreno, Aurora|||0000-0003-3868-6151, Plotnikov, Valerii, Pavlov, Innokentiy S., Pavlova, Naryya I., Protopopov, Albert V., Di Pierro, Michele, Graphodatsky, Alexander S., Lander, Eric S., Rowley, M. Jordan, Wolynes, Peter G., Onuchic, José N., Dalén, Love|||0000-0001-8270-7613, Marti-Renom, MarcA., Gilbert, M. Thomas P.|||0000-0002-5805-7195, Aiden, Erez L.
Tipo de recurso: artículo
Fecha de publicación:2024
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:300318
Acceso en línea:https://ddd.uab.cat/record/300318
https://dx.doi.org/urn:doi:10.1016/j.cell.2024.06.002
Access Level:acceso abierto
Descripción
Sumario: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.

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