Dark DNA

By Aaruni Arora

85% of the matter in the universe is made of dark matter that is yet to be detected. This remains a big, thrilling mystery that physicists all over the world are trying to solve. Excitingly, there is similar research ongoing in the realm of genetics. Gene mapping is useful for comparing DNA of different species in order to understand their functions and analyse evolution. Scientists have recently found some genetic matter that was not observable using former technologies. We still do not know why it is present, but just like dark matter has greatly influenced the universe’s structure and growth, this so-called dark DNA is believed to consist of highly mutated hotspots that are causing rapid evolution.

This dark DNA has been brought to light a couple of times, including when scientists were studying the gene sequence of sand rat (Psammomys obesus) to comprehend why these gerbils are especially prone to type 2 diabetes. During this, the researchers found that although, the gene Pdx1 that codes for insulin and around 90 similar genes were missing, their RNA transcripts and chemical products were somehow still present in the cells (Hargreaves, 2021).

Similar results were observed for birds, who apparently had 274 missing genes (as of 2018) that are essential for survival, including the gene for leptin (energy balance regulating hormone), but the chemical products of the same were present in the birds’ tissues (Hargreaves, 2018).

This means that these genes are not missing; they are hidden. These hidden sequences are rich in guanine and cytosine nucleobases (as seen from the RNA transcripts), which cause difficulty for DNA-sequencing technology to run accurately and implement precise gene mapping. This is why these genes were harder to detect in the first place, and hence got their name ‘dark DNA’ based on ‘dark matter’.

Thus, to avoid that blind spot and study this mysterious DNA, scientists used methods like caesium chloride ultracentrifugation. This examination of the P. obesus genome showed that some parts had greater mutation in the DNA than found in any other rodent species’ genomes. These guanine and cytosine rich stretches of DNA are dubbed as ‘hotspots’ and they have an extremely high rate of base mutations. The interesting bit here is that excessive mutation hinders and compromises the gene function; yet miraculously the gerbils’ genes seem to be functioning enough to allow for their existence. These findings have compelled the science community to reevaluate their work on gene mutation and its effect on function.

Moreover, this also suggests that dark DNA is widespread. The genomes interpreted in the past might be lacking some crucial data. This new database could help biologists compare various species to understand evolution and adaptation at a molecular level. This is important because these newfound hotspots are susceptible to further mutation that could significantly impact the direction of evolution, meaning that Darwin’s and Wallace’s theory of natural selection would not be the only driving force. The rate of these mutations might be too rapid for natural selection to take effect, and this makes these genes adaptable to let the organism survive in their surroundings.

Nonetheless, some scientists argue that if dark DNA is this widespread, then why did not we discover it before? One reason could be that those bird and gerbil species are severe cases that have a larger amount of dark DNA as compared to other organisms. This presents the question ‘what makes birds and sand rats unique?’ and could lead us to answering how the dark DNA came to be.

This discovery could also potentially mean that humans have dark DNA, as well. However, we cannot say that we certainly know what our entire human genome is there for. Moreover, some of this DNA that does not encode for proteins is identical across a range of species like humans, mice, and chicken. Even though we have been evolving separately for millennia, the fact that we share the sequences means that they are vital for our survival. Geneticists say this because removing parts of the gene sequences showed that these genes aid in brain development by fine-tuning the expression of protein-coding genes. Thus, this mutated DNA could help explain and cure neurological diseases like Alzheimer’s (Ebbert & Jansen-West, 2018).

In conclusion, dark DNA is a comparatively new and exciting field that has a lot of potential to help us learn more about ourselves, our environment, and our past. It might answer a few burning questions about evolution and possibly help find a cure to certain neurological diseases.


Huguet, J., 2018. ‘Dark DNA’ Is the Latest Mystery in the World of Genetics… But What Is It?. [online] Seeker. Available at: <https://www.youtube.com/watch?v=AJLxyp5PDeU.>

Hargreaves, A., 2021. Introducing ‘dark DNA’ – the phenomenon that could change how we think about evolution. [online] Available at: <https://theconversation.com/introducing-dark-dna-the-phenomenon-that-could-change-how-we-think-about-evolution-82867.>

Hargreaves, A., 2021. Dark DNA: The missing matter at the heart of nature, New Scientist,  Available at: <https://institutions.newscientist.com/article/mg23731680-200-dark-dna-the-missing-matter-at-the-heart-of-nature/.>

Nature.com. 2021. ‘Dark matter’ DNA influences brain development. [online] Available at: <https://www.nature.com/articles/d41586-018-00920-x.>

Ebbert, M., Jensen, T. and Jansen-West, K., 2018. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight. [online] Genome Biology 20. Available at: <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1707-2#rightslink.>

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