A new study published in the journal Science Advances has found that ancient viral DNA, long dismissed as “genetic junk,” plays a powerful role in regulating gene expression in humans. Researchers from Japan, China, Canada, and the US have identified a family of sequences called MER11, which have evolved to influence how genes turn on and off, particularly during early human development.
Transposable elements (TEs), repetitive DNA sequences that originated from ancient viruses, now make up nearly half of the human genome. While once thought to serve no useful function, recent research has shown that some TEs act like “genetic switches,” controlling the activity of nearby genes in specific cell types.
To overcome the challenge of studying highly repetitive and identical sequence TEs, researchers developed a new method for classifying them based on evolutionary relationships and conservation in primate genomes. This approach revealed previously hidden patterns of gene regulatory potential, including four distinct subfamilies of MER11 sequences: MER11_G1 through G4.
The team applied a technique called lentiMPRA to test the effects of nearly 7,000 MER11 sequences on human stem cells and early-stage neural cells. The results showed that the youngest subfamily, MER11_G4, exhibited strong ability to activate gene expression and had distinct regulatory motifs.
Further analysis revealed that MER11_G4 sequences in humans, chimpanzees, and macaques had accumulated different changes over time, including mutations that increased their regulatory potential in human stem cells. This suggests that ancient viral DNA has been co-opted into shaping gene activity in primates.
The study provides a model for understanding how “junk” DNA can evolve into regulatory elements with important biological roles. It highlights the importance of studying transposable elements and advances our knowledge of genome evolution.
Source: https://phys.org/news/2025-07-reveals-hidden-regulatory-roles-junk.html