Ancient viral DNA may play a key role in early human development, new study suggests

The human genome is made up of 23 pairs of chromosomes, the biological blueprints that make humans … well, human. But it turns out that some of our DNA — about 8% — are the remnants of ancient viruses that embedded themselves into our genetic code over the course of human evolution.

These ancient viruses lie in sections of our DNA called transposable elements, or TEs, also known as “jumping genes” due to their ability to copy and paste themselves throughout the genome. TEs, which account for nearly half of our genetic material, were once waved off as “junk” DNA, sequences that appear to have no biological function. Now, a new study offers support for the hypothesis that these ancient viral remnants play a key role in the early stages of human development and may have been implicated in our evolution.

By sequencing TEs, an international team of researchers identified hidden patterns that could be crucial for gene regulation, the process of turning genes on and off. The findings were published July 18 in the journal Science Advances.

“Our genome was sequenced long ago, but the function of many of its parts remain unknown,” study coauthor Dr. Fumitaka Inoue, an associate professor in functional genomics at Kyoto University in Japan, said in a statement. “Transposable elements are thought to play important roles in genome evolution, and their significance is expected to become clearer as research continues to advance.”

There are many benefits to studying how TEs activate gene expression. It could help scientists understand the role that the sequences play in human evolution, reveal possible links between TEs and human diseases, or teach researchers how to target functional TEs in gene therapy, said lead researcher Dr. Xun Chen, a computational biologist and principal investigator at Shanghai Institute of Immunity and Infection of the Chinese Academy of Sciences.

With more research, “we hope to uncover how TEs, particularly ERVs (endogenous retroviruses, or ancient viral DNA), make us human,” Chen added in an email.

Embedded ancient viral DNA

When our primate ancestors were infected with viruses, sequences of viral genetic information would replicate and insert themselves in various locations in the host’s chromosomes.

“Ancient viruses are effective in invading our ancestral genomes, and their remnants become a big part of our genome. Our genome has developed numerous mechanisms to control these ancient viruses, and to eliminate their potential detrimental effects,” said Dr. Lin He, a molecular biologist and the Thomas and Stacey Siebel Distinguished Chair professor in stem cell research at the University of California, Berkeley, in an email.

For the most part, these ancient viruses are inactive and are not a cause of concern, but in recent years, research has shown that some of the transposable elements may play important roles in human diseases. A July 2024 study explored the possibility of silencing certain TEs to make cancer treatment more effective.

“Over the course of evolution, some viruses are degenerated or eliminated, some are largely repressed in expression in normal development and physiology, and some are domesticated to serve the human genome,” said He, who was not involved with the new study. “While perceived as solely harmful, some ancient viruses can become part of us, providing raw materials for genome innovation.”

But because of their repetitive nature, transposable elements are notoriously difficult to study and organize. While TE sequences are categorized into families and subfamilies based on their function and similarity, many have been poorly documented and classified, “which could significantly impact their evolutionary and functional analyses,” Chen said.

Ancient viral impact on human development and evolution

The new study focused on a group of TE sequences called MER11 found within primate genomes. By using a new classification system as well as testing the DNA’s gene activity, researchers identified four previously undiscovered subfamilies.

The most recently integrated sequence, named MER11_G4, was found to have a strong ability to activate gene expression in human stem cells and early-stage neural cells. The finding indicates that this TE subfamily plays a role in early human development and can “dramatically influence how genes respond to developmental signals or environmental cues,” according to a statement from Kyoto University.

The research also suggests that viral TEs had a part in shaping human evolution. By tracing the way the DNA has changed over time, the researchers found that the subfamily had evolved differently within the genomes of different animals, contributing to the biological evolution that resulted in humans, chimpanzees and macaques.

“To understand the evolution of our genome is one way to understand what makes humans unique,” said He. “It will empower us with tools to understand human biology, human genetic diseases, and human evolution.”

Exactly how these TEs were implicated in the evolutionary process is still unclear, Chen said. It is also possible that other TEs that have yet to be identified played distinct roles in the evolutionary process of primates, he added.

“The study offers new insights and potential leverage points for understanding the role of TEs in shaping the evolution of our genomes,” said Dr. Steve Hoffmann, a computational biologist at the Leibniz Institute on Aging in Jena, Germany, who was not involved with the study. The research also “underscores how much more there is to learn from a type of DNA once slandered as a molecular freeloader,” he added in an email.

Hoffmann was the lead researcher of a scientific paper that first documented the nearly complete genome map of the Greenland shark, the longest-living vertebrate in the world that can survive until about 400 years old. The shark’s genome was made up of more than 70% jumping genes, while the human genome is composed of less than 50%. While primate genomes are different from those of a shark, “the study provides further evidence for the potential impact of TEs on genome regulation” and “is a message with relevance for all genome researchers,” Hoffmann said.

By investigating how genomes have evolved, researchers can determine which DNA sequences have remained the same, which have been lost in time and which have emerged most recently.

“Taking these sequences into account is often critical to understanding, e.g., why humans develop diseases that certain animals don’t,” Hoffmann said. “Ultimately, a deeper understanding of genome regulation can aid in the discovery of novel therapies and interventions.”

Taylor Nicioli is a freelance journalist based in New York.

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