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Highlights

•3D genome architecture is preserved in a 52,000-year-old woolly mammoth sample

•PaleoHi-C makes it possible to assemble the woolly mammoth’s genome

•Chromatin compartments also persist, enabling study of mammoth gene expression

•We propose that dehydration led to a glass transition arresting molecular movement

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.