Thanks to the latest technology, scientists are now increasingly able to decode the genetic makeup of long-extinct animals. Now a team has achieved a new breakthrough: for the first time, they have recovered and read the chromosomes of a woolly mammoth that died 52,000 years ago. This was possible because this animal was essentially freeze-dried in Siberia immediately after its death and left frozen in the permafrost. This “glazed” its DNA and even the large-scale arrangement of the DNA in its cells was preserved. This revealed, among other things, that the mammoths had 28 chromosomes – similar to today’s elephants. The researchers were even able to reconstruct the characteristic loops of the currently active DNA regions and thus gain information about the gene activity in the mammoth’s skin cells.
It has long been known that, under favorable conditions, the genetic material of a dead person or animal can be preserved for centuries or even millennia. This is especially the case when remains have been protected from decomposition in the Arctic permafrost or in tightly sealed, fine-grained material. Researchers can then extract DNA fragments from bones, teeth or skin remains, which are sequenced using special analysis equipment and computer programs and put together in the correct order. This makes it possible, for example, to determine evolutionary changes in the genetic material or mutations in species that are now extinct. What these short DNA fragments, usually only a few hundred base pairs long, cannot reveal, however, is the higher-level structure of the genome, for example how the DNA is divided into chromosomes and which sections were unpacked so that they could be read. This information can only be obtained if the chromosome structure of a fossil has also been preserved – and there is a method with which this structure can be read.
Vitrified genetic material
This is exactly what a team led by Marcela Sandoval-Velasco from the University of Copenhagen has now achieved for the first time. For five years, they genetically examined various fossils until they actually found a specimen with a preserved chromosome structure. It is a woolly mammoth that was frozen in the Siberian permafrost for around 52,000 years. Even fine tissues and structures such as skin and fur have been preserved from the fossil discovered in 2018. “We suspect that it was freeze-dried, so to speak, shortly after its death,” says co-author Olga Dudchenko from Baylor College of Medicine in Houston.
This mammoth therefore offered favorable conditions for the reconstruction of the chromosome structures. “The cell nucleus architecture in such a dehydrated sample can last for an incredibly long time,” explains Dudchenko. This is possible because the genetic material can “vitrify” under these conditions. The material solidifies and forms an amorphous but stable structure. “The chromatin glass is similar to the glass in our windows: it is solid, but not an ordered crystal,” explains senior author Erez Lieberman Aiden from Baylor College.
To decipher the structure of the ancient mammoth DNA, the team took a skin sample from the animal’s ear and then subjected the cells to a so-called Hi-C analysis. This shows which DNA sections are close to each other in the cell nucleus and therefore probably belong to the same chromosome. The analysis was successful and revealed the chromosome structure of an extinct animal for the first time: “What we found here is a sample in which the three-dimensional arrangement of these DNA fragments was frozen in place for tens of thousands of years,” says Sandoval-Velasco. “This preserved the structure of the chromosomes.” The researchers first tried to determine the exact number of mammoth chromosomes – with success: “We found that the woolly mammoths had 28 chromosomes, which makes perfect sense because modern elephants also have 28 chromosomes and they are the closest living relatives of the mammoths,” says co-author Juan Antonio Rodríguez from the University of Copenhagen.
Even indicators of gene activity were preserved
This is the first time that the team has succeeded in counting and reconstructing the chromosomes of an extinct animal. “Fossil chromosomes are a real game changer because they provide insights that were not previously possible,” says Dudchenko. For example, the analyses showed that the division of the genome into individual chromosomes has hardly changed in the last 52,000 years of proboscidean evolution: Compared to today’s elephants, there has been hardly any rearrangement of larger DNA sections, as the team found. Further analyses revealed that even the finest structures, such as chromatin loops measuring up to 50 nanometers, have been preserved in the mammoth chromosomes. “These DNA loops are important because they bring activating control sequences close to their target genes,” explains co-author Marc Marti-Renom from the National Center for Genome Analysis in Barcelona. These loops also reveal which genes were currently being actively read in the mammoth.
Using these and other structural features, the researchers were able to reconstruct the gene activity in the skin of the fossil woolly mammoth for the first time. “For the first time, we have mammoth tissue from which we now know which genes were switched on and which were not,” says Marti-Renom. “This is also the first time ever that we have been able to determine cell-specific gene activity in an old DNA sample.” According to the analyses, the pattern of active genes in the mammoth skin was most similar to that of today’s Asian elephants – with a few crucial differences: “It was shown that the activity pattern of key genes for the development of hair follicles looked completely different to that of elephants,” reports the researcher. This explains why the mammoths had thick fur, but today’s elephants are naked.
According to the team, this discovery and the methods it successfully used open up new possibilities for studying mammoths and other extinct animals. It could even potentially decipher the chromosome structure of Egyptian mummies and other well-preserved human remains. Once dehydrated, the vitrified genetic material remains stable even at room temperature, as Sandoval-Velasco and her colleagues found in additional tests with beef jerky. “Amazingly, the chromatin structure in one-year-old dehydrated beef withstood many perturbing effects such as being run over by a car, immersed in acid and even shotgun blasts,” they report.
Source: Marcela Sandoval-Velasco (University of Copenhagen) et al., Cell, doi: 10.1016/j.cell.2024.06.002