'Junk DNA' is not actually junk, it's found to play a powerful role in the human body

For decades, scientists regarded large portions of our DNA as genetic junk – useless remnants of ancient viruses that invaded our ancestors’ genomes. These segments, known as transposable elements (TEs), were long dismissed as evolutionary fossils with no present-day function.

However, a new international study challenges the view that ancient viral DNA in our genome is useless. Researchers from Japan, China, Canada, and the US focused on a DNA family called MER11. These sequences influence when and where genes turn on, especially during early human development.

The bits of viral DNA are part of a larger group called transposable elements (TEs). Over millions of years, they copied themselves into different spots across our genome.

Today, they make up nearly half of human DNA. Once thought silent, TEs now appear to act as switches that help regulate nearby genes.

A young and active element

MER11 belongs to a class of TEs known as LTR retrotransposons. It likely entered primate genomes around 40 million years ago.

While older TEs have been more studied, younger ones like MER11 remained under-characterized due to their repetitive nature.

To understand MER11 better, researchers created a new classification system. They used evolutionary history and conservation in primates to sort sequences into four subgroups: MER11_G1 through MER11_G4. These range from oldest to youngest.

Uncovering hidden functions

This new method helped uncover regulatory signals hidden in junk DNA and missed by older annotation tools. Researchers matched these junk DNA MER11 subfamilies to epigenetic markers. These chemical tags influence gene activity by modifying DNA or its associated proteins.

They found that the youngest subfamily, MER11_G4, showed strong gene activation potential. Using lentiMPRA (lentiviral massively parallel reporter assay), they tested nearly 7000 MER11 sequences.

These experiments revealed that MER11_G4 sequences strongly boosted gene expression in human stem cells and neural cells.

Junk DNA in primates

The youngest MER11 subfamily stood out for having a unique set of transcription factor binding sites. These DNA motifs serve as landing pads for proteins that control gene activity. They are central to how cells interpret developmental or environmental signals.

The study also found that different primates – humans, chimps, and macaques – show slight variations in their MER11_G4 sequences. These differences may affect how genes are regulated across species.

“MER11_G4 binds to a distinct set of transcription factors,” explained Dr. Xun Chen from the Chinese Academy of Sciences. “This group gained different regulatory functions through sequence changes and contributes to speciation.”

A role in neurodevelopment

The paper added new details on how the junk DNA element MER11 may support specific stem cell states.

Junk DNA from MER11_G4 shows especially high activity in cells resembling early developmental stages. These include pluripotent stem cells and certain neural progenitors.

In neural contexts, MER11 elements were linked to genes involved in brain development. They showed strong regulatory activity in stem cells transitioning into neurons. These functions suggest that MER11 plays a role in setting up developmental gene networks.

Ancient viral DNA is not junk after all

The findings highlight a broader idea: viral DNA sequences that once invaded our genome can be adapted for important uses.

By tracking how these sequences evolve and testing their behavior, scientists are uncovering layers of genome regulation previously missed.

“Our genome was sequenced long ago, but the function of many of its parts remain unknown,” said study co-author Dr. Fumitaka Inoue from Kyoto University.

Transposable elements are thought to play important roles in genome evolution. Their full impact may only be revealed through deeper research.

Junk DNA has real power in evolution

This research significantly reshapes our understanding of what was once labeled as “junk DNA.” For many years, scientists believed these segments, especially those originating from ancient viral infections, served no purpose and remained as passive remnants within our genome.

However, this study on MER11 sequences reveals a very different story. Rather than being inactive bystanders, these viral sequences appear to play vital roles in gene regulation. They help determine when and where specific genes are expressed during critical periods of early development.

Junk DNA also influence the behavior of stem cells, guiding how they transition into specialized cell types. Even more striking is the possibility that such sequences contribute to the genetic differences that set species apart.

What was once dismissed as useless debris now emerges as an evolutionary toolkit – carefully honed over millions of years – to shape the biology of humans and other primates in subtle but essential ways.

The study is published in the journal Science Advances.

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