Dark DNA: How Genes in DNA Could Be Missing

Have you heard of “dark matter” before? No doubt many of you have heard of it. Dark matter; It is the matter that we know to be in the universe, but that we have not yet detected, that make up more than a quarter of the universe. Like dark matter, dark regions are found in our genetic material. Biologist Adam Hargreaves deals with dark DNA in his study of sand rats (Psammomys obesus). Fat sand rats are animals that exhibit different behaviors. They live in dens or hollows, eat a lot of leaves, and do not drink water.

The weirdest thing about these animals is that some of their DNA are missing. In the study with these mice, they are trying to explain the dark DNA. After the dark DNA issue started to come to light, it became the focus and curiosity of many scientists. This topic has shown us again that there are many things that we do not know in the world of biology and that are waiting to be discovered. Along with dark DNA came many questions about genetics and evolution. E.g; Could it be dark DNA that supports evolution?

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Sand rats live in the desert, and when scientists took them into the lab, they observed a different set of phenomena. They encountered obesity and type 2 diabetes in sand rats that received a “normal” diet in vitro. This result emerged in the 1960s and has been used in many diabetes studies. However, why sand rats are so susceptible to this disease remained a mystery. It was determined that the gene causing this sensitivity was the Pdx1 gene. The Pdx1 gene encodes the Pdx1 protein but also has many functions. E.g; It takes part in the development of the pancreas and provides the active or passive change of the insulin gene.

This gene is a gene found in all vertebrate animals.

However, although sand rats have a normal pancreas and can secrete insulin; In their genetic studies, scientists could not detect this gene in sand rats, and this was considered meaningless. With the situation, Adam Hargreaves and 17 other researchers sequenced the sand vole genome. In this genome study, they encountered something even more surprising than previous studies. They found that not only Pdx1 was missing, but other genes as well.

They also found RNA transcripts (the genetic code that cells use to synthesize proteins), but the situation remained interesting because the genes were not there. After obtaining the RNA transcripts and carefully examining these transcripts, they got a big clue. genetic code; Contains A, T, G, and C bases. However, there was something that caused the sequences in these transcripts to be strange. What made these sequences interesting was that the G and C bases were more concentrated than the others.

The scientists involved in the study had never encountered such a situation before. But this result might have helped explain the situation. They used the cesium chloride ultracentrifugation technique, a technique of rapidly spinning DNA fragments in a concentrated salt solution, to cause the dense fragments, namely the G and C bases, to sink to the bottom. With these fragments separated, they tried sequencing them separately and it worked. What they found was a mutation site. Extensive mutations were seen in these regions of the DNA, with some changing their A or T bases to G or C. There were far more mutations in the Pdx1 gene in sand mice than had been seen before in that gene.

Mutations can often change the function of a gene.

In particular, changes in these dark DNA regions that are difficult to detect can shed light on evolutionary studies. The striking mutations seen in the genes prompted the scientists working on the subject to review their ideas and thoughts. How much more change could a gene tolerate and continue to function? In a wide variety of different places and studies, it turns out that dark DNA is actually very common. After the sand rats, they found many genes that were supposed to be present in birds as well, but whose presence they could not detect.

After that, genome studies need to be done much more efficiently and carefully, because there is no clear finding about dark DNA, and it also causes curiosities to increase, and scientists think that a much more comprehensive study is needed to solve it. They think that with new technologies and comprehensive techniques, they can handle this dark DNA issue with solid data. At the same time, with each genome study with different species, scientists will be even more vigilant against dark DNA.

Some of the main terms of evolution, which are also encountered in evolution;

Variation, mutation, adaptation, and natural selection accompany us in many of the results we have reached in dark DNA studies. If in genes containing mutation sites; If a mutation is more likely to occur elsewhere in the genome, variations in which natural selection is involved are more likely to occur in these species. Thus, they evolve faster. In short, dark DNA can influence the direction of its evolution. We mentioned that sand rats live in deserts if we take the risk again; sand rats actually adapted to an arid and harsh climate, and they did so with regions of rapid and intense mutation that took place.

So when they eat a normal, nutritious diet, they can develop diabetes and die. That is, sand rats were restricted to living in the desert. As a result, dark DNA remains an enigmatic issue. However, as we tried to explain above, many studies are being carried out and many conclusions and interpretations are reached. These studies show that we still have a lot to learn about how genomes evolve at the molecular level, and how this process leads to the awe-inspiring diversity of life on Earth.

Resources: 

1. https://www.newscientist.com/article/mg23731680-200-dark-dna-the-missing-matter-at-the-heart-of-nature/
2. https://www.nature.com/articles/d41586-018-00920-x