Certain scientific findings may be considered colossal or even epic in scale; however, few compare to a “mammoth” new study describing the three-dimensional genome architecture of preserved cells from a 52,000-year-old animal skin sample thanks to a primeval-sounding yet cutting-edge technique known as PaleoHi-C! Epigenetics research goes pre-historic!
A veritable “stampede” of researchers led by Olga Dudchenko, Marc A. Marti-Renom, M. Thomas P. Gilbert, and Erez Lieberman Aiden aimed to advance the study of ancient DNA from small-scale to large-scale differences. They developed an in situ Hi-C-based technique (PaleoHi-C) to capture chromosomal conformation data to explore whether ancient DNA could survive the assay. Therefore, they tested a permafrost-preserved female woolly mammoth skin sample (or jerky!) to determine the level of chromosomal 3D morphology preservation, reveal how this data would inform the study of ancient animal biology, and discover how this info could have endured the inexorable passing of time.
Sandoval-Velasco, Dudchenko, Rodríguez, Estrada, and colleagues tell us of their mammoth architectural discovery using PaleoHi-C:
- Mammoth cells display architectural features visible in modern Hi-C maps, such as chromosome territories, Barr bodies, active and inactive chromatin compartments, domains, and loops
- Persistence of these structures suggests the potential survival of the underlying protein machinery, such as the CTCF and cohesin protein complexes
- Chromosomal morphological features remain intact on scales as short as 50 nm, forming non-mineralized fossils or subfossils that persist over extraordinarily long periods of time
- They generated a woolly mammoth genome assembly with the help of a novel algorithm for reference-assisted 3D genome assembly, including karyotype reconstruction, yielding 28 chromosome-length scaffolds
- A comparison of contact patterns to those in elephant skin identified genes with an altered transcriptional state in woolly mammoths, including critical regulators of hair growth such as Edaradd and Egfr
- The woolly mammoth inactive X chromosome exhibits a tetradic architecture distinct from the bipartite inactive X chromosome architecture in humans/mice
- Active and inactive genome compartments in mammoth skin closely resemble Asian elephant skin
- Analysis of how the 3D architecture of ancient cells endured reveals that ancient chromatin behaves in a manner consistent with a “glass transition” (or vitrification) – where cooling and dehydration arrest molecular diffusion
- Spontaneous freeze-drying of woolly mammoth tissue shortly after death in the cold Siberian climate may induce chromatin glass (“chromoglass” for short) formation to preserve chromosomal morphology
Saber tooth-tiger? Giant sloth? A dodo? This mammoth study may now support the generation of de novo genome assemblies for more ancient, extinct species. To end, the authors noted an “unconventional” means of confirming that trapping chromosomes inside freeze-dried woolly mammoth “jerky” aided the preservation of chromosomal morphology.
“We confirmed this theory by doing experiments on old, freeze-dried beef jerky, which is much easier to find than woolly mammoth jerky,” explained co-first author Dr. Cynthia Pérez Estrada “We fired a shotgun at it. We ran over it with a car. We had a former starting pitcher for the Houston Astros throw a fastball at it. Each time, the jerky broke into tiny bits – shattering like a glass. But at the nano-scale, the chromosomes were intact, unchanged. That’s the reason these fossils can survive. That’s the reason that they were there, 52,000 years later, just waiting for us to find them.”
For more on how PaleoHi-C helped to make a “mammoth” genome architecture discovery, see Cell, July 2024.