“Junk” DNA Isn’t Useless, Scientists Discover—It Acts as a Genetic Switch
A groundbreaking new study reveals that so-called “junk” DNA, long dismissed as having no function, plays a crucial role in gene regulation, potentially rewriting our understanding of genome evolution.
For decades, scientists have been puzzled by the vast stretches of non-coding DNA within the human genome. These transposable elements (TEs), often referred to as “jumping genes” due to their ability to move around the genome, comprise nearly 50 percent of our DNA—a proportion even higher in other organisms. Now, an international team of researchers from Japan, China, Canada, and the US has demonstrated that a specific family of these TEs, called MER11, can act as powerful “genetic switches,” influencing gene expression without altering the underlying DNA sequence.
The research, published in the journal Science Advances, challenges the conventional classification of TEs and highlights the potential for a wealth of undiscovered genetic mechanisms. “Our genome was sequenced long ago, but the function of many of its parts remain unknown,” explained a study coauthor from Kyoto University.
The Legacy of Ancient Viruses
MER11 sequences are classified as long terminal repeat (LTR) retrotransposons, and their origins are surprisingly ancient. Researchers believe these sequences originated from an endogenous retrovirus (ERV) that infected a simian ancestor tens of millions of years ago. This virus essentially hijacked the DNA of its host cells, creating copies of its genetic material that persisted—though largely dormant—throughout evolution. Remarkably, at least eight percent of the human genome is derived from these ancient retroviruses.
This abundance of TEs, combined with inaccurate classification methods, has led to much of this genetic material being dismissed as “junk.” The authors argue that current methods for identifying and annotating TEs are flawed, causing potentially important sequences to be overlooked. This realization prompted them to develop and test their own classification system. “The proper classification and annotation of LTR instances is critical to understanding their evolution, co-option and potential impact on the host,” the authors wrote in the study.
A New Classification System Reveals Hidden Function
The team’s new system categorized MER11 sequences based on their evolutionary relationships and preservation across primate genomes. They then divided MER11 into four subfamilies—MER11_G1 through G4—based on their age. This allowed them to correlate the subfamilies with epigenetic marks, chemical modifications that influence protein function and, consequently, gene activity.
Crucially, epigenetic marks can modify cell behavior without physically altering the DNA itself, effectively silencing or activating genes. By linking MER11 subfamilies to these markers, the researchers aimed to uncover the extent of their impact on gene expression.
Testing approximately 7,000 MER11 sequences from humans and primates, the team discovered that the youngest subfamily, MER11_G4, exhibited a particularly strong ability to influence gene expression. This influence stems from unique DNA “motifs” within MER11_G4 that attract transcription factors—proteins that regulate which genes are switched on or off.
“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,” stated the lead author from the Chinese Academy of Sciences.
Implications for Evolutionary History
The findings have profound implications for our understanding of genome evolution. What was once considered “junk” DNA has gradually evolved to play a vital role in gene regulation, suggesting that a significant portion of our evolutionary history remains unexplored. “Transposable elements are thought to play important roles in genome evolution, and their significance is expected to become clearer as research continues to advance,” a study coauthor noted.
This discovery underscores the dynamic nature of the genome and the potential for previously overlooked sequences to hold the key to understanding complex biological processes. The research opens new avenues for investigating the intricate interplay between genes, epigenetic modifications, and the evolution of species.
