Unwinding the Mystery of ‘Dark DNA’

Priasha Dutta, Amity University Kolkata

WHERE IT ALL BEGAN

We have probably heard of “dark matter”, which is believed to make up more than a quarter of the universe. Although its presence is confirmed, scientists have not been able to detect it yet. Recently, elusive genetic matter has been detected in the genome. This biological counterpart of dark matter is called “dark DNA”; which has raised some serious questions about genetics and evolution. The first creature who revealed the indefinable nature of the genome is the fat sand rat (Psammomys obesus), where some of its DNA appeared to be missing.

The fat sand rat is a desert species native to North Africa and the Middle East. It lives in burrows, eats almost 80% of its body mass in leaves every day, and does not drink water. However, when the creatures were put in the lab and fed the standard diet for laboratory rodents, they become obese and developed type-2 diabetes. This discovery was made in the 1960s, causing sand rats to be the focus of study for scientists and biologists who were interested in understanding diabetes induced by nutrition in humans.

THE DISCOVERY OF THE “MUTATION HOTSPOT”

The Pdx1 protein coded by its respective gene has many roles, including switching on and off the insulin gene and the development of the pancreas. The Pdx1 gene is found in all vertebrates but not in sand rats, yet they have a normal pancreas and can secrete insulin. After sequencing the entire sand rat genome, a total of nearly 90 essential genes, found on the same chromosome in other animals, was missing. However, their corresponding RNA transcripts (the copies of stretches of genetic code that cells use as templates to form proteins) were present.

The RNA transcripts were G-C rich sequences, and the standard sequencing technology is not quite able to pick up DNA segments with high levels of G and C, which was a probable reason for the missing genes. Caesium chloride ultracentrifugation was the next alternative. Thus, having separated the G-C rich fragments in that method, they were sequenced and a region of DNA with a massive number of mutations (many of them changing from A or T to G or C bases) was found. This is termed as a “mutation hotspot”. For example, sand rat Pdx1 contains more mutations than any other version of the gene in the animal kingdom. This results in a Pdx1 protein that, in just one key region that binds to DNA, has at least 15 amino acids differing from the normal version.

Mutations usually compromise the function of a gene, and the genes in dark DNA are so essential for survival that they have hardly changed over the course of evolution. Yet somehow the sand rat’s Pdx1 gene functions normally despite the dramatic mutation levels. This mysterious discovery made researchers rethink how many mutations a gene can tolerate and still work. The divergence of Pdx1 might explain why sand rats develop diabetes if their Pdx1 protein turns out to be not as beneficial as its counterpart in other animals. It also explains why Pdx1 initially seemed to be absent.

THE PREVALENCE OF DARK DNA IN THE ANIMAL KINGDOM

Twelve other species of gerbils (a small rodent) showed the absence of Pdx1, implying that they can possess this enigmatic dark DNA as well. Several bird genomes sequenced so far lacked more than 270 genes present in most vertebrate genomes, including important genes like the one coding for leptin, a hormone that controls hunger. Scientists now estimate that around 15% of all bird genes have been overlooked in previous studies. This implies that dark DNA could be quite widespread and current ideas about how genomes evolve have to be redefined. By comparing thousands of whole genomes that have been sequenced in the past, biologists are trying to find out which genes have been lost in certain families and which new ones have arrived. This helps them see what makes groups of organisms differ from one another and how adaptation happens at the molecular level.

If this biological dark matter is common, then the genes that scientists thought to be missing might be present, only in an elusive form. Maybe gerbils and birds are extreme cases and dark DNA is lesser widespread in other organisms. Both groups of animals show an oddly large variation in their chromosome number. This implies that during their evolution their chromosomes may have undergone breakage. Chromosomes break and recombine during the production of sex cells, causing genetic diversity. A process called GC-biased gene conversion occurs (meaning more G and C mutations than A and T ones). G and C bases can accumulate in regions, forming dark DNA. This can be a very valid reason for the prevalence of dark DNA in species with chromosomes that are prone to breakage.

THE INFLUENCE OF THIS ENIGMA ON EVOLUTION

Evolution is defined as a two-step process – the random genetic mutations creating variation in an organism’s DNA and then the phenomenon of natural selection. Natural selection is mainly responsible for pushing the direction in which organisms evolve. But if we consider the effects of the hidden part of the genome, then the genes present within the mutation hotspots are prone to mutation than the others. Thus, they will display more variation on which natural selection can act, so the exhibiting traits will evolve faster. Hence, dark DNA could influence the direction of evolution. Mutation rates in dark DNA can be so quick that natural selection cannot act rapidly enough to omit deleterious variants in the normal way. Such genes may become adaptive later if a species faces a sudden environmental challenge.

In sand rats, a massive rate of mutation in many dark DNA genes could have had a considerable effect on the species’ evolutionary course. Nonetheless, some selection must also act on the genes, else mutation would get uncontrolled and extreme, creating a region of nonsense genes, eventually leading to the loss of the species.

The sand rat’s dark DNA may have led to some adaptations that would not have occurred under normal circumstances. These have allowed it to survive without the Pdx1 protein, on very nutritionally poor food, and barely any water in a harsh desert environment with few predators. But since nutritionally rich food in a laboratory environment leads them to develop diabetes and die; we can assume that their unique genome has programmed them to live in deserts only.

CONCLUSION

The discovery of these dark mysteries in biology is so new that scientists are still trying to work out how common it is and the implications it has on the species that contain it. Moreover, scientists are already going beyond this double-stranded nucleic acid and studying the concepts of dark codons and dark variants of RNA as well as amino acids. With rapidly improving technology, newer and more accurate genome sequencing methods are being developed for further research. We may learn about the mechanisms of genomic evolution at the molecular level, whether it is actually a silent driving force of evolution and even discover new findings in genomes we thought were already decoded. Nevertheless, it is hoped that in the near future we can unlock the secrets held within the twists and turns of the dark DNA.

Also read: Use of Oncolytic viruses in metastatic cancer treatment!

References:

• Pracana, R., Hargreaves, A., Mulley, J., & Holland, P. (2020). Runaway GC Evolution in Gerbil Genomes. Molecular Biology And Evolution, 37(8), 2197-2210. https://doi.org/10.1093/molbev/msaa072
• Hargreaves, A. (2018). The hunt for dark DNA. New Scientist, 237(3168), 29-31. https://doi.org/10.1016/s0262-4079(18)30440-8
• Image permission (reusing the file): Tino Strauss published it under the CC-BY-SA-2.5.; License : This file is licensed under the Creative Commons Attribution-Share Alike 2.5 Generic license.

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