DNA sequencing technology is helping scientists find answers to questions that have plagued people for centuries. By mapping animal genomes, we get a better understanding of how the giraffe got its long neck and why the snakes are so long. Genome sequencing allows us to compare and contrast the DNA of different animals and figure out how they evolved and became what they became.
But sometimes we face a mystery. The genomes of some animals do not appear to include certain genes that appear in other similar species and must be present to keep the animals alive. These apparently missing genes have been called "dark DNA." Its existence can change our understanding of evolution.
For the first time, scientists led by Adam Hargreaves of Oxford University encountered this phenomenon while sequencing the genome of the sand rat (Psammomys obesus), a species of gerbil living in deserts. In particular, they wanted to study the genes of the gerbil associated with the production of insulin to understand why this animal is especially susceptible to type II diabetes.
When they searched for the Pdx1 gene, which controls insulin secretion, they found that insulin was missing, along with 87 other genes surrounding it. Some of these missing genes, including Pdx1, are vital and the animal cannot survive without them. Where are they?
The first clue was that in several tissues of the sand rat's body, scientists had found chemical products that could appear according to "instructions" from "missing" genes. This would only be possible if genes were present somewhere in the genome. And this would indicate that they were not missing, but simply disappeared.
The DNA sequences of these genes are very rich in guanine and cytosine, two of the four "base" molecules that make up DNA. We know that cytosine and guanine rich sequences pose problems for some DNA sequencing methods. And it becomes more likely that the genes we were looking for were in place, but difficult to find. For this reason, we called this hidden sequence "dark DNA" as a reference to dark matter, which makes up 25% of the universe, but which we cannot find.
Studying the sand rat genome, we found that in one part of it, in particular, there were many more mutations than in the genes of other rodents. All genes in this hotbed of mutations were with DNA rich in cytosine and guanine, and mutated to such an extent that they were difficult to detect using standard methods. An over-mutation often stops the gene from working, but somehow the sand rat's genes continue to play their roles despite the radical change in DNA sequence. This is a very difficult task for genes. It's like singing "Katyusha" using only vowels.
This kind of dark DNA has previously been found in birds. Scientists have found that 274 genes are "absent" in the currently sequenced avian genomes. Among them is the gene for leptin (a hormone that regulates energy balance), which scientists have not been able to find for many years. Once again, these genes have an extremely high content of cytosine and guanine and their products are found in the tissues of the bodies of birds, even if the genes themselves are not, as it were, in the genomic sequences.
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A ray of light in dark DNA
In most textbooks, there is a definition from which it follows that evolution proceeds in two stages: mutation is followed by natural selection. DNA mutation is a common and ongoing process that happens completely by accident. Natural selection determines which mutations should go through and which not, usually depending on what result they showed in the process of reproduction. In short, a mutation creates a variation in an organism's DNA, and natural selection decides whether to stay or drop it, and that's how evolution happens.
But pockets of high mutations in the genome mean that genes in certain locations have a higher chance of mutating than others. This means that such foci may be an underestimated mechanism that can also determine the course of evolution. This means that natural selection may not be the only driving force. Until now, dark DNA appears to have been present in two different and common types of animals. But it is still unclear how widespread it is. Could the genomes of all animals contain dark DNA, and if not, what makes gerbils and birds so unique? The most addictive puzzle will be to figure out what impact dark DNA has had on animal evolution. In the sand rat example, the focus of the mutation may have led to the adaptation of the animal to desert conditions. But on the other hand, the mutation may behappened so quickly that natural selection couldn't work fast enough to eliminate anything harmful in DNA. If so, harmful mutations could interfere with the sand rat's survival outside of its current desert environment. The discovery of such a strange phenomenon definitely raises questions about how the genome evolves and what we might be missing out on in existing genome sequencing projects. Perhaps we should turn around and take a closer look.and what we might have missed in existing genome sequencing projects. Perhaps we should turn around and take a closer look.and what we might have missed in existing genome sequencing projects. Perhaps we should turn around and take a closer look.
Ilya Khel
