{Reference Type}: Journal Article
{Title}: Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.
{Author}: Sandoval-Velasco M;Dudchenko O;Rodríguez JA;Pérez Estrada C;Dehasque M;Fontsere C;Mak SST;Khan R;Contessoto VG;Oliveira Junior AB;Kalluchi A;Zubillaga Herrera BJ;Jeong J;Roy RP;Christopher I;Weisz D;Omer AD;Batra SS;Shamim MS;Durand NC;O'Connell B;Roca AL;Plikus MV;Kusliy MA;Romanenko SA;Lemskaya NA;Serdyukova NA;Modina SA;Perelman PL;Kizilova EA;Baiborodin SI;Rubtsov NB;Machol G;Rath K;Mahajan R;Kaur P;Gnirke A;Garcia-Treviño I;Coke R;Flanagan JP;Pletch K;Ruiz-Herrera A;Plotnikov V;Pavlov IS;Pavlova NI;Protopopov AV;Di Pierro M;Graphodatsky AS;Lander ES;Rowley MJ;Wolynes PG;Onuchic JN;Dalén L;Marti-Renom MA;Gilbert MTP;Aiden EL;
{Journal}: Cell
{Volume}: 187
{Issue}: 14
{Year}: 2024 Jul 11
{Factor}: 66.85
{DOI}: 10.1016/j.cell.2024.06.002
{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.