Study reveals the role of ancient viral DNA in early human development

 The human genome consists of 23 pairs of chromosomes, the biological blueprints that make us human. However, it turns out that a portion of our DNA—about 8%—is made up of ancient viral remnants that have integrated themselves into our genetic code over the course of human evolution.

These ancient viruses reside in parts of our DNA known as transposable genetic elements, also called "jumping genes," because of their ability to replicate and insert themselves into different locations within the genome.

Jumping genes make up roughly half of our genetic material and were previously considered "junk" DNA—sequences that appeared to have no biological function. But a new study supports the hypothesis that these ancient viral remnants played a crucial role in the early stages of human evolution and may have even contributed to our development.

By sequencing these jumping genes, an international team of researchers was able to identify subtle patterns that may be critical in gene regulation, the process by which genes are switched on or off. The study's findings were published last July in the journal Science Advances.

"The human genome has been sequenced for a long time, but the function of many of its parts remains unknown," explained Dr. Fumita Inoue, an associate professor of functional genomics at Kyoto University in Japan and one of the study's authors, in a statement. "Jumping genes are believed to play an important role in genome evolution, and their significance is expected to become clearer as research progresses."

"There are many benefits to studying how jumping genes activate gene expression," noted lead researcher Dr. Shun Chen, a computational biologist and principal investigator at the Shanghai Institute of Immunology and Infection, Chinese Academy of Sciences. "These studies could help scientists understand the role these sequences play in human evolution, uncover potential links between transposable elements and human diseases, or teach researchers how to target functional transposable elements in gene therapy."

“We hope that further research will reveal how jumping genes, especially endogenous retroviruses—that is, ancient viral DNA—make us human,” Chen added in an email.

Endogenous viral DNA

When our primate ancestors were infected with viruses, sequences of viral genetic information replicated and inserted themselves into various locations within the host’s chromosomes.

“Ancient viruses were very efficient at invading our ancestral genomes, and their remnants now make up a significant part of our genome,” Dr. Lin He, a molecular biologist and professor of stem cell research at the University of California, Berkeley, said in an email. “Our genome has evolved many mechanisms to control these ancient viruses and eliminate their potentially harmful effects.”

These ancient viruses are often inactive and not a cause for concern, but research in recent years has shown that some jumping genes may play important roles in human diseases. A study published in July 2024 explored the possibility of silencing some of these jumping genes to make cancer treatment more effective.

However, due to their repetitive nature, studying and regulating jumping genes is extremely challenging and notoriously complex. Although jumping gene sequences are classified into families and subfamilies based on their function and similarity, many, according to Chen, are inadequately documented and classified, "which can significantly impact their evolutionary and functional analyses."

The Impact of Ancient Viruses on Human Evolution and Development

The new study focused on a group of jumping gene sequences known as MER11, found within primate genomes. Using a new classification system and DNA gene activity testing, the researchers identified four previously unknown subfamilies.

The newly incorporated sequence, designated MER11_G4, was found to have a strong ability to activate gene expression in early human stem cells and nervous system cells. This finding suggests that this subfamily of jumping genes plays a role in early human evolution and can "significantly influence how genes respond to evolutionary signals or environmental factors," according to a statement from Kyoto University.

The research also points to the fact that jumping genes of viral origin played a role in shaping human evolution. By tracking how DNA has changed over time, the researchers found that this subfamily evolved differently within the genomes of different animals, contributing to the biological evolution that led to the emergence of humans, chimpanzees, and macaques.

"Understanding the evolution of our genome is one way to understand what makes humans unique," said researcher He. "It will give us tools to understand human biology, human genetic diseases, and human evolution."

However, Chen noted that the precise way these jumping genes participated in the evolutionary process remains unclear. He added that it is also possible that other, as yet undiscovered, jumping genes played different roles in the evolutionary trajectory of primates.

Dr. Steve Hoffmann, a computational biologist at the Leibniz Institute for the Study of Ageing in Jena, Germany, who was not involved in the study, said: “This study provides new insights and potential starting points for understanding the role of jumping genes in shaping the evolution of our genome.”

He added in an email that the research “also underscores how much can be learned about a type of DNA that was previously considered a mere molecular parasite.”