In recent years, northern parts of Siberia—a frigid region in north Asia—have been melting, leading many organisms once frozen in the perpetually frozen ground known as permafrost to thaw and become exposed. One of these newly revealed organisms was a one-year-old baby woolly mammoth carcass estimated to have been preserved in the permafrost for 52,000 years. 

This mammoth is one of the most well-preserved specimens ever discovered. Scientists have even been able to examine its chromosomes and chromatin, or condensed configurations of its DNA. Usually, DNA breaks down over time, leaving behind crumbs of what was once a fully intact three-dimensional structure of DNA. Yet, scientists found the fossilized chromatin within the carcass was packed so tightly that it resembled molecules within glass, earning it the name “chromoglass.” Chromoglass prevents DNA from moving and hinders the decomposition and crumbling of genetic material over time.

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Above: Photo of the 52,000-year-old baby mammoth carcass found in permafrost. Image courtesy of Reuters. 

The baby mammoth carcass itself is similar in chemical composition to beef jerky. This resemblance raised questions among scientists, leading them to preserve freeze-dried beef jerky for one year to conduct tests. These tests varied in intensity—from throwing baseballs to shooting a shotgun at the jerky samples. After all tests, the jerky still had its chromoglass intact.

Scientists have been able to examine the woolly mammoth’s genome from this preserved DNA using PaleoHi-C, an adaptation of the Hi-C technique discovered in 2009. Chromosomes exist within the nucleus of a cell and are made up of DNA strands packed together like a jumbled skein of yarn. Hi-C requires scientists to divide a DNA strand into smaller sections and then reconnect them using proteins that combine DNA fragments regardless of their original location within a genetic sequence. Scientists observed and marked paired DNA fragments to determine how many times fragments are attached. If two different fragments are attached and successfully stick together multiple times, the resulting loop shows the relation between the two fragments. In this way, scientists can determine the three-dimensional proximity of distant fragments stuck together.

Above: Diagram of the Hi-C method of recombining DNA. Image courtesy of Science News. 

Initially, researchers thought they could use Hi-C only on recent DNA samples. But through trial and error, a global team of over 50 scientists developed PaleoHi-C. The team used skin from the head of the mammoth’s carcass to determine that mammoths had 28 pairs of chromosomes, the same number of chromosomes as their modern-day relatives, elephants. In comparison to African and Asian elephant DNA, mammoths have high synteny, or a high number of genes that appear in the same sequence. 

Scientists were also able to determine which genes are active and inactive within mammoths and elephants through sequencing. Active and inactive genes are organized within subcellular sections within the nucleus. Researchers examined those compartments to determine that mammoths have 820 genes. Among those genes, 425 that are active in mammoths are inactive in elephants, while 395 that are active in elephants are inactive in mammoths. 

Above: Diagram demonstrating the scale and process of extracting woolly mammoth DNA. Image courtesy of Sandoval-Velasco et al., 2024.

The team also used the novel PaleoHi-C process on a 39,000-year-old sample and determined that the structure of chromosomes can remain intact for millennia and be preserved on a 50-nanometer scale. For woolly mammoths and other extinct species, PaleoHi-C represents a huge scientific breakthrough in paleontology that may lead to more insights in the field in the coming years.