Penn biologists show evidence of a two-way genomic arms race involving repetitive DNA

Biological arms races are common in nature. Cheetahs, for example, have developed an elegant body shape that lends itself to fast running, allowing them to feast on equally fast gazelles, the fastest of which can escape predation. At the molecular level, immune cells produce proteins to conquer pathogens, which can in turn develop mutations to evade detection.

Although less known, other games of one-upmanship unfold within the genome. In a new study, biologists at the University of Pennsylvania show, for the first time, evidence of a bilateral genomic arms race involving repeating stretches of DNA called satellites. “Opposing” the rapidly evolving satellites in the arms race are similar rapidly evolving proteins that bind to these satellites.

Although satellite DNA does not encode genes, it can contribute to essential biological functions, such as the formation of molecular machines that process and maintain chromosomes. When satellite repeats are not properly regulated, alterations in these crucial processes can result. Such disturbances are hallmarks of cancer and infertility.

Using two closely related species of fruit flies, the researchers probed this arms race by deliberately introducing a mismatch between species, pitting, for example, one species’ satellite DNA against the satellite-binding protein of the other. other species. Serious alterations in fertility have resulted, highlighting the delicate balance of evolution, even at the level of a single genome.

“We typically think of our genome as a cohesive community of elements that make or regulate proteins to build a fertile, viable individual,” says Mia Levine, assistant professor of biology at Penn’s School of Arts & Sciences and lead author of the work. . , Posted in Current biology. “It evokes the idea of ​​a collaboration between our genomic elements, and that is largely true.

But some of these elements, we think, actually harm us. This disturbing idea suggests that there must be some mechanism to control them.”

Mia Levine, assistant professor of biology, Penn’s School of Arts & Sciences

The researchers’ findings, which are likely to be relevant in humans as well, suggest that when satellite DNA occasionally escapes the management of satellite-binding proteins, significant fitness costs can arise, including impacts on the molecular pathways necessary for fertility and perhaps even those relevant in the development of cancer.

“These findings indicate that there is antagonistic evolution between these elements that may impact these apparently conserved and essential molecular pathways,” says Cara Brand, a post-doctoral fellow in Levine’s lab and first author of the work. “This means that, during evolution, constant innovation is needed to maintain the status quo.”

Evolutionary paradox

It has long been known that the genome is not made up of genes alone. Between the genes that give rise to proteins, one can find long stretches of what Levine calls “gibberish.”

“If genes are words and you had to read the history of our genome, those other parts are inconsistent,” she says. “For a long time it was ignored as genomic junk.”

Satellite DNA is part of this so-called “garbage”. In Drosophila melanogaster, the fruit fly species often used as a scientific model organism, satellite repeats make up about half of the genome. Because they evolve so quickly with no apparent functional consequence, however, scientists believed the satellite repeats were unlikely to do anything useful in the body.

But more recent work has revised this “junk DNA” theory, revealing that “gibberish,” including satellite repeats, plays a variety of roles, many of which relate to maintaining genome integrity and structure in the core.

“So it presents a paradox,” Levine says. “If these regions of the genome that are highly repetitive actually perform important tasks or, if not managed properly, can be harmful, that suggests we need to control them.”

In 2001, a group of scientists put forward a theory suggesting that coevolution was taking place, with satellites evolving rapidly and satellite-binding proteins evolving to keep pace. Over the next two decades, scientists have offered their support for the theory. Through genetic manipulation, these studies introduced a satellite binding protein from one species into the genome of a closely related species and observed what happens as a result of incompatibility.

“Often these gene swaps cause dysfunction,” Brand says, “particularly disrupting a process that is typically mediated by regions of the genome that are enriched for repetitive DNA.”

New tools to prove the case

This research supported the theory of coevolution. But until researchers can experimentally manipulate both the satellite-binding protein and satellite DNA, it would be impossible to prove that the disturbance they observed is due to an interaction between the two elements.

In the current work, Levine and Brand have found a way to do just that. Another species of fruit fly, Drosophila simulanshas no satellite repeat that spans 11 million nucleotide base pairs found in its close relative, D. melanogaster. This satellite was known to occupy the same cellular location as a protein called Maternal Haploid (MH). The researchers also had access to a mutant strain of D. melanogaster which do not have the 11 million base pair repeat.

“It turns out that the fly can live and reproduce very well without this repetition,” says Levine. “So it gave us a unique opportunity to manipulate both sides of the arms race.”

To first investigate the satellite-binding protein side, the researchers used the CRISPR/Cas9 gene-editing system to delete the original HD gene from D. melanogaster and add the D. simulans version of the gene. Compared to the control females, the female flies with the D. simulans The HD gene had drastically reduced fertility, producing far fewer eggs.

Flies that completely lacked MH, however, were unable to produce offspring; the embryos were not viable.

“It was interesting because it showed that these satellite-binding proteins are essential, even though they evolve rapidly,” says Brand. “Gene swapping showed us that we could rescue the ability to make embryos. But another function, related to the production of ovaries and eggs, was impaired.”

By looking closely at the ovaries, Brand and Levine discovered that the apparent cause of reduced egg formation and ovarian atrophy was DNA damage. Such damage often triggers a checkpoint protein to halt developmental pathways. When the researchers repeated the experiments on a fly with a broken checkpoint protein, egg production levels were restored to a higher level.

Levine and Brand were then ready to test the other side of the coevolutionary arms race, to find evidence that the problems with the swapped HD protein were due to incompatibility with the 11 million base pair satellite, or if they were acting on a different genetic element. Here they relied on D. melanogaster strain that was missing the repeat and found that the gene swap no longer had any effect on these flies. DNA damage levels, egg production and ovary size were all normal.

Examining the closest relative of the HD protein in humans, a protein called Spartan, has given scientists a clue as to the mechanism behind these findings. In humans, Spartan is believed to digest proteins that can get stuck on DNA, posing an obstacle to the various processes and packaging that DNA must undergo. “After everything we had discovered so far,” Levine says, “we thought maybe this bad version of the protein was chewing on something it shouldn’t.”

One of the proteins Spartan often targets is topoisomerase II, or Top2, an enzyme that can help resolve tangles in tightly coiled and tangled DNA. To see if the negative effects of the HD gene mismatch were due to inappropriate Top2 degradation, they overexpressed Top2 and found that fertility was restored. The reduction in Top2, on the other hand, exacerbated the reduction in fertility.

“This repair process that MH is involved in happens in yeast, in flies, in humans, through the tree of life,” says Brand. “Yet we are seeing rapid or adaptive evolution of these implicated proteins. This suggests that this seemingly conserved and essential pathway requires evolutionary innovation.” In other words, coevolution must happen quickly, just to maintain this essential pathway.

Implications beyond flies

In future work, Brand and Levine will look to see if segments of the genome beyond satellites are involved, and will look in other organisms, including mammals, to dig deeper into the molecular players in these evolutionary arms races.

“There’s no reason to believe that these arms races only happen in flies,” says Levine. “The same kinds of proteins and satellites in primates are also rapidly evolving and that tells us that what we’re studying is broadly relevant.”

The focal genes implicated in this study have important roles in human health. Spartan mutations have been linked to cancer, and inefficient regulation of satellite DNA could shed light on infertility and miscarriage.

“The number of miscarriages is remarkably high, and satellite DNA is certainly an unprobed source of aneuploidy and genome instability,” says Levine.


University of Pennsylvania

Journal reference:

Brand, CL, et al. (2022) Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homologue poisons germline genome integrity. current biology.

Martin E. Berry