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Researchers Uncover Ancient Genetic Parasite From the “Dark Genome”

Double helix structure of DNA.
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Research published today in Nature sheds light on a small part of the so-called “dark genome” — the 98 per cent of the human genome whose biological function is largely not known.

In this case, an international multidisciplinary team reported the first high-resolution images and structural details of a genetic element known as LINE-1, which inserts itself into the human genome and is implicated in diseases such as cancer, autoimmune disorders and neurodegeneration, and even aging.

LINE-1 is described in the paper as an “ancient genetic parasite” with about 100 potentially active copies in each person. LINE-1 activity is often correlated with disease.

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Unlike DNA, which makes RNA and then proteins, retrotransposons like LINE-1 work backwards, making DNA from RNA and then inserting it into the genome. The enzyme needed for this process is called LINE-1 reverse transcriptase, or LINE-1 RT.

“Retrotransposons are often referred to as ‘jumping genes’ that insert themselves into our chromosomes with a copy-and-paste mechanism,” explains Matthias Götte, professor and chair of the Department of Medical Microbiology and Immunology at the University of Alberta and one of the eight co-corresponding authors.

“For this paper, we discovered the essential steps in this process, which could then lead us to ways to inhibit the enzyme and eventually treat those diseases.”

The team included researchers from institutions in the United States and Europe, as well as biotechnology partners. Götte’s lab was the only Canadian contributor to the research, which was led by investigators from Harvard Medical School and Boston-based biotechnology company ROME Therapeutics.

“Our integrated analyses reveal the inner workings of the molecular machine that has written nearly half of the human genome,” the researchers report. “Understanding LINE-1 structure and function is important both in evolution and, increasingly, in human disease.”

The Götte lab provided much of the biochemical data in the paper. “We expressed and purified LINE-1 RT in the lab and then did biochemical experiments to understand how it actually synthesizes new DNA from RNA and inserts it back into the genome,” he explains.

Götte is an expert on polymerases and RTs — or replication engines — of viruses such as HIV and HCV. He is now focused on those with high epidemic potential such as Ebola, Lassa and SARS-CoV-2.

“We identified similarities between the LINE-1 RT and the HIV-1 RT, but also differences, and that will allow us to develop drugs that are more specific to this particular LINE-1 enzyme,” says Götte.

“It was a large team effort with world-class structural biologists, and that’s why the science is absolutely fantastic,” he adds. “Effective treatments for important human diseases can only be developed with a very strong scientific foundation.”

Götte previously worked with a similar scientific team to publish research on the human endogenous retrovirus-K RT enzyme, which is also implicated in disease.

Götte credits his research associate Egor Tchesnokov for carrying out four years of experiments for this paper. “He’s extremely good at it, and I'm very grateful to have him in the lab.”

Reference: Baldwin ET, van Eeuwen T, Hoyos D, et al. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature. 2023. doi: 10.1038/s41586-023-06947-z

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