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) which died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding twenty-eight 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 use PaleoHi-C on a skin sample from a 52,000 woolly mammoth to assemble its genome using a reference assited 3D genome assembly method. We show how the method works by assembling a donkey genome, both de novo and using reference-assisted 3D genome assembly. We also assemble genomes of Asian and African elephants. We analyze and compare contact data for the woolly mammoth and the Asian and African elephants. We generate data for multiple Asian elephant tissues and show that the mammoth PaleoHi-C data contains cell-specific information. We map loops. We compare compartmentalization patterns to reveal genes whose transcription was potentially altered in mammoths vs. elephants. We use PaleoHi-C to infer 3D structures of woolly mammoth chromosomes. We perform a series of proof-of-principle experiments using beef to show that dehydration is beneficial for preservation of 3D genome architecture, even at elevated temperatures. The processed files also include reanalysis of GSM1551550-GSM1551578 (Rao, Huntley et al, 2014; Harris, Gu et al., 2023) and ENCFF531FEY (https://www.encodeproject.org/files/ENCFF531FEY).