Science 4 min read

Dark DNA: Exploring the Dark Side of Life

Iaremenko Sergii /

Iaremenko Sergii /

In astrophysics, cosmologists talk a lot about an exotic type of matter they refer to by “dark matter.”

They know dark matter is there and that it makes up most of the universe, though they can’t detect it with existing technology. So far, attempts at pinpointing dark matter particles have failed.

Likewise, in genetics, there’s a part of biological matter that remains shrouded in mystery. Geneticists have adopted the term “dark” used by astrophysicists to introduce “Dark DNA.”

Dark Side of the Genome: What is Dark DNA?

The concept of Dark DNA refers to a part of the genome that scientists poorly understand its role in life’s processes. Dark DNA is the biological counterpart of “dark matter.” We know dark DNA exists but can’t understand the biological function it serves.

Thanks to advanced DNA sequencing technologies, geneticists have been able to map out the genomes of many plants and animals. They could reveal some of the secrets of DNA’s role in evolutionary mechanisms.

For example, it’s a gene mutation that helped giraffes to get long necks and legs to adapt to their changing environment. “Hox” genes, involved in vertebrae development, allowed snakes to develop extra-long bodies.

Adaptation and natural selection that enable life to thrive on earth are based on genes. However, sometimes, geneticists can’t find the genes they know for sure should be there in the genome of certain animals.

While they can’t detect the gene itself, they somehow still able to see the expression of its associated protein. They’re dealing with “missing genes” or dark DNA.

Biological Dark Matter: Uncharted Biological Territory

Sometimes, scientists can’t find genes they know are critical to the survival of some animals. This was the case of biologist Adam Hargreaves as he describes it in an article published on The Conversation.

Hargreaves and his colleagues sequenced the genome of the sand rat, a desert-dweller species of gerbil native to North Africa and the Middle East.

Sand rats (Psammomys obesus) are known for their tendency to get type-2 diabetes. The team wanted to investigate genes related to insulin production, like Pdx1 (Pancreatic And Duodenal Homeobox 1).

To the researchers’ surprise, the Pdx1 gene was nowhere to be found in the sand rats’ genome, as were 87 other essential genes surrounding it.

However, the team did find chemical products that could only result from proteins Pdx1 and other missing genes usually code. This means the genes aren’t really missing but just hidden. It’s dark DNA.

Read More: Jumping Genes Could Help Crops Cope With Climate Stress

“The DNA sequences of these genes are very rich in G and C molecules, two of the four “base” molecules that make up DNA. We know GC-rich sequences cause problems for certain DNA-sequencing technologies. This makes it more likely that the genes we were looking for were hard to detect rather than missing. For this reason, we call the hidden sequence ‘dark DNA,’” writes Hargreaves.

Besides gerbils, this kind of dark DNA has also been found in birds. Previously, scientists found that 274 necessary genes were ‘hidden’ in all sequenced bird genomes. But they aren’t sure, yet dark DNA exists in all species since so far they have evidence only about gerbils and birds.

In order, mutation and natural selection are the two stages of evolution. Genes mutate randomly, all the time, then it is the natural selection that determines which mutations to keep and pass on, and which to dismiss. At least, that’s what the textbooks say.

But in the light of these developments, could dark DNA play an undefined role in biasing the evolution direction?

“The discovery of such a weird phenomenon certainly raises questions about how genomes evolve, and what could have been missed from existing genome sequencing projects.”

Details of the study are published in a paper in the journal PNAS.

Read More: New Study Uncovers Unique Genes Responsible for Human Evolution

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Zayan Guedim

Trilingual poet, investigative journalist, and novelist. Zed loves tackling the big existential questions and all-things quantum.

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