Groundbreaking research has mapped the genome and 3D chromosomal architecture of a 52,000-year-old woolly mammoth, revealing details of its genetic activity and opening new perspectives for extinction research. An international team of researchers has assembled the genome and 3D chromosome structures of a 52,000-year-old woolly mammoth, the first time such a feat has been achieved for any ancient DNA sample.

Fossilised chromosomes, which are about a million times longer than most ancient DNA fragments, shed light on how the mammoth genome was organised in living cells and which genes were active in the skin tissue from which the DNA was extracted. This unprecedented level of structural detail was preserved because the mammoth sublimated shortly after death, meaning its DNA was preserved in a glassy state. The results are presented today (July 11) in the journal Cell. Cell.

Advances in genomic architecture

“This is a new type of fossil, and it’s at a scale that exceeds the scale of individual ancient DNA fragments; a million times more sequence,” says corresponding author Erez Lieberman Aiden, director of the Center for Genome Architecture at Baylor College of Medicine. “This is also the first time that a karyotype of any kind has been determined for an ancient sample.”

Knowing the three-dimensional architecture of the genome provides a lot of additional information beyond its sequence, but most ancient DNA samples consist of very small, mixed-up pieces of DNA. As Aiden developed his work mapping the 3D structure of the human genome, he thought that if he could find the right ancient DNA sample (with the 3D organization of the piece intact), the same strategies could be used to assemble ancient genomes.

Unprecedented DNA preservation

The researchers studied dozens of samples over five years before landing on the unusually well-preserved woolly mammoth, unearthed in northeastern Siberia in 2018. “We believe it spontaneously lyophilized shortly after death,” says corresponding author Olga Dudchenko, Ph.D., of the Center for Genome Architecture at Baylor College of Medicine. “The nuclear architecture in a dehydrated sample can survive for incredibly long periods of time.”

To reconstruct the mammoth’s genomic architecture, the researchers extracted DNA from a skin sample taken from behind the mammoth’s ear, using a technique called Hi-C, which allowed them to identify which regions of the DNA might be in close spatial proximity and interact with each other in their natural state in the nucleus.

Insights into the genetics of the woolly mammoth

“Imagine having a puzzle with three billion pieces, but no final picture of the puzzle to work with,” says Mark A. Marty-Renom, ICREA Research Professor and Structural Genomics correspondent at the National d’Anàlisi Genòmica (CNAG) and the Center for Genomic Regulation (CRG) in Barcelona. “Hi-C allows you to take a close-up picture before you start putting the pieces of the puzzle together.”

They then combined the physical information from the Hi-C analysis with DNA sequencing to identify regions of DNA that interact and create a neat map of the mammoth genome using the genomes of modern elephants as a template. The analysis showed that woolly mammoths had 28 chromosomes, the same number as modern Asian and African elephants. Remarkably, fossilized mammoth chromosomes also retain incredible physical integrity and detail, including nanoscale loops that bring transcription factors into contact with the genes they control.

By examining the compartmentalization of genes in the nucleus, the researchers were able to identify active and inactive genes (proxies for epigenetics or transcriptomics) in mammoth skin cells. The mammoth skin cells had different gene activation patterns compared to the skin cells of its closest relative, the Asian elephant, including genes potentially associated with wooliness and cold tolerance.

Effects of Termination Actions

“For the first time, we have woolly mammoth tissue where we know roughly which genes are turned on and which are turned off,” Marti-Renom says. “This is an extraordinary new type of data and the first measurement of cell-specific gene activity of genes in any ancient DNA sample.”

Although the method used in this study relied on unusually well-preserved fossils, the researchers are optimistic that the method could also be used to examine other ancient DNA samples, from mammoths to Egyptian mummies, as well as more recently preserved museum specimens.

Next steps for mammoths will include investigating the epigenetic patterns of other tissues. “These results have clear implications for modern efforts to stop the extinction of the woolly mammoth,” says corresponding author M. Thomas Gilbert, a paleogenomist at the University of Copenhagen and the Norwegian University of Science and Technology.