Study finds viral junk DNA plays critical role in human development

Ancient viruses left a legacy in your DNA. And it turns out, that legacy may be helping shape who you are.

A recent international study has shown that certain bits of ancient viral DNA, long dismissed as genetic "junk," actually play powerful roles in turning genes on and off—especially during early human development. The work centers around a group of sequences called MER11, which belong to a larger class of DNA fragments known as transposable elements, or TEs. These sequences once came from viruses but now make up nearly half of your genome.

For years, scientists thought these repetitive sequences were nothing more than useless leftovers from ancient infections. But new evidence suggests otherwise. Researchers have now found that MER11, far from being silent, may act as important genetic switches, controlling how and when genes are activated.

The results, published in Science Advances, could reshape how we understand gene regulation and human evolution.

Transposable elements—also called “jumping genes”—were first discovered in the 1940s by cytogeneticist Barbara McClintock. She found that these DNA segments could move around the genome, copying and inserting themselves into new locations. That "copy-and-paste" ability allowed them to spread over millions of years.

Today, TEs account for about 45% of the human genome. Many are remnants of endogenous retroviruses (ERVs), which infected germline cells long ago and became permanently embedded in our DNA. Their long terminal repeats, or LTRs, once helped viruses reproduce. Now, in some cases, these same sequences help regulate human gene activity.

Because they are so repetitive and similar, studying TEs has been extremely difficult. Most genomic tools have trouble distinguishing between slightly different copies. That has made it hard to figure out what these sequences are actually doing.

To get past this roadblock, a team of scientists from Japan, China, Canada, and the United States created a new method for classifying these genetic elements. Rather than using standard annotation software, which often lumps similar sequences together, the researchers grouped MER11 sequences based on how they evolved and how well they were preserved in primates.

This new classification divided the MER11 family into four subgroups, called MER11_G1 through G4. These subfamilies range from oldest (G1) to youngest (G4). By breaking down the sequences this way, the team could finally see how different versions of MER11 behaved in human cells.

Then came the next big question: Do these sequences actually do anything? To find out, the researchers used a powerful tool known as lentiMPRA, short for lentiviral massively parallel reporter assay. This technique lets scientists test thousands of DNA snippets at once by inserting them into cells and watching what happens.

They tested nearly 7,000 MER11 sequences in human stem cells and early-stage neural cells. What they found was striking—especially in the youngest group, MER11_G4. These sequences had a strong ability to turn on nearby genes. They also contained distinct regulatory "motifs," short regions of DNA that act as landing pads for transcription factors, the proteins that control gene activity.

Further analysis showed that MER11_G4 sequences had evolved differently in humans, chimpanzees, and macaques. Some versions had picked up small mutations over time that increased their power to regulate genes in human stem cells. These changes, said lead researcher Dr. Xun Chen, suggest that MER11_G4 gained new regulatory functions over time and played a role in shaping species differences.

“This group binds to a distinct set of transcription factors, indicating that it contributes to speciation,” Chen explained.

The discovery helps support a larger idea: that DNA from ancient viruses has not only survived inside our cells but evolved into tools our bodies now use. In fact, at least 8% of the human genome comes from these old viral fragments. While most were silenced long ago by our cells—using tools like DNA methylation and RNA interference—a few stuck around with useful features.

Some of these useful sequences have been co-opted to serve specific roles in stem cells. For example, certain LTRs contain binding sites for pluripotency-related factors like POU5F1 and SOX2, which are crucial in early development. Others, like HERVH-LTR7 and LTR5_Hs, have been shown to act as gene enhancers, influencing how hundreds of genes behave.

What’s especially exciting is that these ancient elements aren’t static. They continue to evolve and diversify across primate lineages, creating new regulatory networks. This means the genetic switches inside your cells today might be quite different from those in another species—even one closely related.

The current standard for identifying TEs is a tool called RepeatMasker, which compares DNA to a library of known sequences. But this method often fails to catch important differences between nearly identical fragments. It also doesn’t work well when sequences have evolved or recombined.

To address that, the researchers used a phylogenetic strategy. By analyzing the genetic “family tree” of MER11 and related elements, they identified evolutionary links that earlier methods had missed. Their approach revealed 75 new LTR subfamilies across 53 primate-enriched lineages and reclassified over 3,800 sequences. That’s nearly one-third of the previously misidentified instances.

“This refined annotation makes it possible to better understand the evolution in primate genomes,” the authors write.

Their method didn’t just identify new patterns—it predicted how well each TE could act as a gene regulator. That’s a key step toward understanding how genomes are shaped, not just by natural selection, but by the viral remnants buried within them.

Understanding how TEs work could help solve one of biology’s biggest mysteries: how cells know which genes to turn on and when. This has implications for everything from development to disease.

“Transposable elements are thought to play important roles in genome evolution,” said Dr. Fumitaka Inoue from Kyoto University, one of the study’s co-authors. “Their significance is expected to become clearer as research continues to advance.”

This study proves that DNA once written off as junk is actually part of the sophisticated system that helps build and run your body. It’s a reminder that evolution doesn’t waste what it can reuse. Even viral scars in your DNA can be turned into something meaningful.

As the authors show, better classification and deeper understanding of these sequences will unlock new insights into how your genome really works—and how it got to be the way it is.

Note: The article above provided above by The Brighter Side of News.

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