Your DNA Is Full of Ancient Viruses – And They’re Running the Show

For years, scientists thought certain parts of our DNA were useless—leftovers from ancient viruses that served no purpose. But a new international study has flipped that idea on its head.

Researchers have discovered that these so-called “junk” DNA sequences, inherited from viruses millions of years ago, actually help control how our genes behave—especially during the earliest stages of human development. Some of these viral fragments seem to act like on-off switches for genes and may even help explain what makes humans different from other species. It turns out, the ghosts of ancient viruses are still shaping our lives today.

Hidden Powers of Ancient Viral DNA

Some stretches of our DNA are made up of repeated sequences known as transposable elements (TEs), which originally came from ancient viruses. Over millions of years, these viral fragments multiplied in our genetic material using a copy-and-paste process. Today, they account for nearly half of the entire human genome. Scientists used to believe these sequences were useless, but new research suggests that some TEs act like “genetic switches,” turning nearby genes on or off depending on the type of cell.

Studying these elements has been a challenge because they tend to look almost identical and repeat many times throughout the genome. Younger families of TEs, like one called MER11, have been especially hard to analyze and are poorly labeled in current genetic databases. This has made it difficult for researchers to understand what they actually do.

To address this, scientists created a new method to sort and classify TEs. Rather than relying on the usual annotation tools, they grouped MER11 sequences by how closely they were related over time and how consistently they appeared in primates. With this approach, they reclassified MER11A, B, and C into four clearly defined subfamilies called MER11_G1 through G4, ordered from the oldest to the newest.

Epigenetic Insights Reveal Functional Roles

With this updated classification, the team uncovered patterns that had been missed before. They looked at how these newly defined MER11 groups matched up with epigenetic markers—chemical tags on DNA and its associated proteins that help regulate gene activity. The results showed that their new classification better reflected the actual biological roles these elements play compared to earlier methods.

To test whether MER11 sequences could directly influence gene activity, the researchers used a technique called lentiMPRA (short for lentiviral massively parallel reporter assay). This method allows scientists to examine thousands of DNA sequences at once by inserting them into cells and measuring how strongly each one boosts gene expression. Using lentiMPRA, the team tested nearly 7,000 MER11 sequences from humans and other primates, observing how they affected gene behavior in both human stem cells and early neural cells.

The Power and Uniqueness of MER11_G4

The results showed that MER11_G4 (the youngest subfamily) exhibited a strong ability to activate gene expression. It also had a distinct set of regulatory “motifs,” which are short stretches of DNA that serve as docking sites for transcription factors, the proteins that control when genes are turned on. These motifs can dramatically influence how genes respond to developmental signals or environmental cues.

Further analysis revealed that the MER11_G4 sequences in humans, chimpanzees, and macaques had each accumulated slightly different changes over time. In humans and chimpanzees, some sequences gained mutations that could increase their regulatory potential during in human stem cells.

Young MER11_G4 binds to a distinct set of transcription factors, indicating that this group gained different regulatory functions through sequence changes and contributes to speciation, lead researcher Dr. Xun Chen explains.

Rethinking “Junk” DNA in Evolution

The study offers a model for understanding how “junk” DNA can evolve into regulatory elements with important biological roles. By tracing the evolution of these sequences and directly testing their function, the researchers have demonstrated how ancient viral DNA has been co-opted into shaping gene activity in primates.

“Our genome was sequenced long ago, but the functions of many of its parts remain unknown,” co-responding author Dr. Inoue notes. Transposable elements are thought to play important roles in genome evolution, and their significance is expected to become clearer as research continues to advance.

Reference: “A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage” by Xun Chen, Zicong Zhang, Yizhi Yan, Clement Goubert, Guillaume Bourque and Fumitaka Inoue, 18 July 2025, Science Advances.
DOI: 10.1126/sciadv.ads9164

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