Dark DNA: the latest mystery in the world of Genetics

Hope we all know about dark matter. But if you do not, then do not worry. Dark matter is a type of matter that cannot be seen directly. But it is a fundamental part of our universe & plays a central role in our current understanding of the universe. Dark matter exists because of the effect it has on objects that we can observe directly.

Like dark matter in the cosmos, there is a biological dark matter that is dark DNA which is raising some fundamental questions about genetics and evolution. The Controversially dark DNA even be a driving force of evolution. So, let us discuss about it-

DNA sequencing technology is helping scientists in finding out the hidden information about animals for centuries. And by this technology we all started to believe that DNA has all the information of everything. Genome sequencing technology allows us to compare & contrast the DNA of different animals & their evolution. By mapping out animal genomes, we now have a better idea of how the Giraffe got its huge neck & why Snakes are so long. If we look about humans, we can also see the difference between us by our skin colours, eye colours, hair, nose, height etc.

So, what is Dark DNA?

Some animal genomes have missing part in their DNA, which is thought to be important for existence. This apparently missing part of DNA/genes have been dubbed “Dark DNA”. And Its existence could change the way we understand about evolution.

In a recent study, scientists looked at one case involving sand rats (Psammomys obsus), a species of gerbil that lives in deserts of North Africa & Middle East. Sand rat is a strange desert creature. It lives in burrows. Eats around 80% of its body mass in leaves each day & does not drink water but the odd thing about this gerbil is that some of its DNA appears to be missing. If we put it in a lab then something strange happens, when fed a normal diet the standard fair for lab rodents sand rats tend to become fleshy & develop type 2 diabetes. The mystery of why these gerbils are so susceptible to the disease has remain unsolved but when we looked for a gene called Pdx1 that codes for many roles including in the development of the pancreas & controls the secretion of Insulin, found missing.

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Fig: Pdx1 (Pancreatic & duodenal homebox 1)

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Pdx1 was not only missing gene. in fact, a big chunk of DNA containing 87 genes which are found on the same chromosome in other animals was nowhere to be seen. Many of these genes like Pdx1 are essential for survival. 

The DNA sequences of these genes are rich in G and C molecules which are two of four bases “AGCT” which makes up the DNA. We know that GC rich sequences are problematic for some DNA sequencing technologies. Which makes sense that these genes are not detectable rather than completely missing. Because of that, researchers called this region “missing part” of DNA as a “Dark DNA” with reference to Dark matter which covers about 25% of the universe which scientist have no clue about it.

Scientists were stunned when they found these creatures are living healthy without these genes. What we can found in their corresponding RNA transcripts which are the copies of stretches of genetic code that cells use as templates to make proteins. But where were the genes gone?

Most textbooks describe evolution is a twostep process. First, random genetic mutation which creates variation in an organism’s DNA. Then comes natural selection, which acts like a filter deciding which mutations are passed on. This usually depends on whether they confer some sort of advantage. Although not everything produced over the study of evolution is an adaptation. So, natural selection is the sole driving force pushing the direction in which organisms evolve. But a dark DNA to the picture & that’s not necessary the case if genes contained within these mutation hotpots have a greater chance of mutating than those elsewhere they will display more variation on which natural selection can act so the traits they confer will evolve faster. In other words, dark DNA could influence the direction of evolution giving a driving role to mutation. Indeed, the mutation rates in dark DNA may be so rapid that natural selection cannot act fast enough to remove deleterious variants in the usual way. Such genes might even become adaptive later. If a species faces a new environmental challenge for example, if sand rat sees nutritionally rich food then they will develop diabetes & die. That could mean they are constrained to living in deserts. So dark DNA could be both their liberator & their jailer.

  • Z M Tauhidul Islam Shijan

Undergrad, Department of Genetic Engineering & Biotechnology

Shahjalal University of Science & Technology, Sylhet.


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