“Dark matter” genome driving new species evolution?

Genetic “dark matter” may drive the emergence of new species. The findings suggest a way to rescue “doomed” animal hybrids.

Writer: Sara Maria Majernikova
Editor: Ismat Ghuman
Artist: Zach Ng

According to Jagannathan et al. (2018), these lengthy, repeating segments of the genome, known as satellite DNA, may eventually prohibit mismatched animals from mating by scrambling the chromosomes in their hybrid offspring. If animals from distinct populations are unable to mate, they will diverge over time, resulting in speciation. 

Only 1% of the 3 billion nucleotides in the human genome are ‘coding’ – used to build the proteins that define features like eye colour and height. Other regions of DNA may, among other things, inform the body how many copies of a protein to create or switch genes on or off in various organs. Despite this, over 10% of the human genome is made up of long, repetitive lengths of satellite DNA that scientists didn’t believe accomplished anything for many years, according to research co-author Madhav Jagannathan, an assistant professor at the ETH Zurich Institute of Biochemistry in Switzerland. Satellite DNA repeats were quite prevalent in species and extensively seen in eukaryotes or life-forms with cell nuclei, however, they were mostly discarded as junk DNA according to Jagannathan

However, in a 2018 research, Jagannathan, then at the Massachusetts Institute of Technology (MIT), and his former postdoctoral supervisor, biologist Yukiko Yamashita, also at MIT, revealed that part of this DNA fulfilled an important function: it organises DNA inside the nucleus of a cell. This research discovered that specific proteins capture DNA molecules and arrange them in tightly packed bundles of chromosomes known as chromocenters. They discovered that satellite DNA instructs these grabby proteins on how to bundle and order chromosomes. 

Jagannathan and Yamashita discovered another job for satellite DNA in the latest research, which was published on July 24 in the journal Molecular Biology and Evolution. The researchers were looking at fertility in the fruit fly Drosophila melanogaster. The flies’ chromosomes distributed outside the nucleus after the researchers removed a gene that codes for a protein called prod, which attaches to satellite DNA to generate chromocenters. The flies perished because they lacked the capacity to appropriately assemble their chromosomes. 

Jagannathan found this noteworthy since the missing protein is unique to Drosophila melanogaster. This means that the proteins that attach to these fast-developing satellite DNA sequences must likewise be rapidly evolving. To put this theory to the test, Jagannathan crossed Drosophila melanogaster females with males of a different species, Drosophila simulants. The hybrids, as predicted, did not survive long. When the researchers examined the flies’ cells, they saw malformed nuclei with DNA spread throughout, much as they had seen when the prod protein was eliminated in prior tests. 

So how does this imply that satellite DNA might be the driving force for speciation? The researchers believe that if satellite DNA changes swiftly and two organisms create different satellite-DNA-binding proteins, they would not be able to produce healthy offspring. This incompatibility might occur fast because chromocenter binding proteins and satellite DNA segments evolve differently in various populations or species. To put this theory to the test, they altered satellite DNA-binding genes, causing incompatibility in both parents. They developed healthy hybrids after rewriting the flies’ DNA to be compatible. 

Such satellite DNA conflicts, according to Jagannathan, might play a significant role in the emergence of new species. He expects that more research will be able to verify their concept of hybrid incompatibility with other species. This discovery might eventually lead to a method for scientists to save “doomed” hybrids, or hybrids that do not live long after birth. This might open the path for hybridization to be used to save severely endangered animals like the Northern White Rhino, which has just two females left. 

Finally, the new study validated Jagannathan’s suspicion that satellite DNA had a role as the evolution could not be so wasteful. The finding of such a strange event undoubtedly raises issues about how genomes change and what current genome sequencing programmes may have overlooked. Perhaps, going back and looking again?

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