By Jacob Comeaux, UC Santa Cruz science writing student
There’s a war raging within each of the 37.2 trillion cells in your body. Microscopic war is not a novel notion—our immune system fights off pernicious pathogens all the time. But scientists based at the UC Santa Cruz Genomics Institute have shown that our DNA, the genetic information that defines us, is engaged in ceaseless warfare with an astonishing adversary: itself.
The “war” is an evolutionary arms race spanning millions of years between elements of our DNA. Recently, evolutionary biologists David Greenberg and Frank Jacobs, led by principal investigator David Haussler, unveiled the imprints of this race in humans for the first time. The combatants are “jumping genes” called retrotransposons and the mediators that constantly struggle to suppress them.
“Changes within our DNA drive evolution,” says Greenberg, who is now a research scientist at Pacific Biosciences in San Francisco. “Everyone is curious about how we got here, and this arms race is a big part of the story.”
Retrotransposons are mobile sections of DNA that haphazardly bounce around our genome, the complete set of our genes. These aren’t rare; in fact, they make up more than 40% of our genetic material. Jumping genes are like viruses that infect animals and forcefully insert their genomes into the animals’ cells. They exist in our genome today as remnants of ancient viruses, but now they can only copy themselves and flit around within our genomes. Some of these jumping genes have lost their vigor, like dormant volcanoes, although they might become active again. Others continue to roam, deterred only by the mediators described by Greenberg, Jacobs, and their collaborators in Nature on September 28, 2014.
Active retrotransposons have three possible fates. Most of them copy-and-paste themselves into parts of DNA that have no effect on someone. Very rarely, a jumping gene lands in a region that actually helps its host—a new adaptation could possibly shield us from certain viruses. But retrotransposons can also disrupt important genes and cause diseases.
That’s where the regulatory genes come into play. Because most retrotransposons harm us rather than help us, we have evolved defensive genes to cripple the rogue genes from jumping. The master regulator of the genome is a protein called KAP1. KAP1 is so important to survival that most species have retained it over eons. It’s like an immune system—organisms that have it pass a healthy set of genes along to the next generation, and those that don’t die off, usually before they can reproduce. KAP1 stifles retrotransposons by smothering the mobile bits of DNA and preventing them from creating protein precursors. In other words, it nips unwanted genetic activity in the bud. But this regulator doesn’t work alone.
If retrotransposons are like fires threatening to damage our cells, KAP1 proteins are the firefighters that choke the fires with blankets and hoses. But something or someone must tell the firefighters where go to extinguish the fires. In human cells, proteins with the bizarre name of KRAB zinc-finger (KZNF) proteins serve this role. They are the vigilant watchdogs that locate the fires and alert the firefighters to suffocate the flames. No matter what kind of fire confronts the watchdogs and firefighters, they almost always find a way to douse it and prevent it from spreading. In our cells, evolution has kept up with the changing challenges of jumping genes. KZNF is one of the fastest-growing gene families in primates, making primates very good at responding to newly emerging retrotransposons.
Until the discovery by Greenberg and Jacobs, now an assistant professor at the University of Amsterdam, scientists did not know the collection of KZNF genes that fend off retrotransposons in primates and in us. Researchers had seen zinc-finger proteins in mice that tamp down jumping genes, but the new study is the first proof that the same thing happens in humans. The team showed that two KZNF genes found only in primates, ZNF91 and ZNF93, rapidly evolved to keep two distinct retrotransposon gene families in check soon after they first invaded the human genome.
The team started by homing in on zinc finger genes and determining which ones were the best at suppressing retrotransposons. Each of our cells contains 400 KZNF genes. Of these, 170 exist only in primates. Evolution models suggest that these 170 watchdog genes first appeared in great apes 18 to 25 million years ago. They’re still active today. The team reasoned that a zinc finger gene that keeps the genome from degrading should be an important component of human embryonic stem cells. So they focused on the 14 most utilized primate-specific KZNF genes and tested each of these to see which was best at crippling its microscopic rivals.
Haussler and the team took an elegant approach to discover the two most active zinc fingers, ZNF91 and ZNF93. First, they used a mouse embryonic stem cell line made by Japanese researchers, featuring a transplanted human chromosome, to observe the jumping genes unrestricted in a mouse cell. By removing the genes from a human system that also contains repressor genes, the team reasoned the retrotransposons would roar back to life. And indeed they did: retrotransposons went rampant in the cell now devoid of the watchdog zinc fingers. Further, when the scientists added primate zinc-finger regulators into the mouse cells containing the human chromosome, the newly active genes became dormant once again.
Greenberg modified a preexisting method to create this novel way of screening for specific zinc finger activity. “A lot of the time it’s like taking spaghetti and ice cream, mashing them together, and seeing if the combination works,” he says. “Most of the time it doesn’t, but we were lucky.” Greenberg’s data convinced the team that species-specific zinc fingers are tailored to cripple certain jumping genes. “When I saw the results, I knew we had slayed the dragon,” he says.
Next, the team re-created what the KZNFs used to look like—their sequences from millions of years ago, before the human lineage became distinct from the Great Apes. By looking back in time to construct what they thought to be the last common ancestral zinc fingers between humans, gorillas, orangutans, and macaques, they could trace how the suppressor genes changed through time.
“It was kind of like a time machine experiment, which I think everyone was excited about,” says Greenberg.
The team found that ZNF91 and ZNF93 each evolved new capabilities to restrict specific retrotransposons about 12 million years ago, right around the time humans started to diverge from other primates. Some of these new capabilities evolved in great apes and not in monkeys, meaning that these zinc fingers evolved quickly indeed. If they were slowly evolving, they would be observed in both closely related species. Our fire watchdogs were developing new tactics for locating fires at a faster rate than scientists had imagined.
ZNF91 proved to be the most specific and robust adversary against a jumping gene. It was the only zinc finger capable of halting more than 80 percent of a specific type of retrotransposon. Because the team tried many other zinc fingers against the bouncing gene and only this one worked, they concluded that species-specific zinc fingers are tailored to species-specific retrotransposons that have recently invaded the genome of the host. Our defensive genes are engineered to recognize certain rivals and to stay on duty to prevent them from spreading.
ZNF91 also silenced other cellular genes near the jumping gene. The closer the gene to the retrotransposon, the stronger the repression. If a fire breaks out in a crowded building, first responders might evacuate nearby buildings and monitor them even if the fire started elsewhere. Scientists believe that the complex manner in which our DNA responds to invading retrotransposons helps explain why our network of genes is so complicated, compared to those of other organisms.
The team’s other main target, ZNF93, provides more insight into the nature of the evolutionary arms race between retrotransposons and repressor genes. ZNF93 silences retrotransposons by recognizing a binding sequence on them and beckoning the KAP1 firefighters to hurry to the scene. The sequence on the mobile DNA that these zinc fingers recognize gives the retrotransposons extra fuel for their fires, increasing the rate at which they spread through the genome. But since zinc fingers sniff out the extra fuel source, most of the fires can’t spread at all.
However, the team’s “time machine” experiment revealed that an evasive retrotransposon subfamily ditched this recognition sequence about 12.5 million years ago. Without it, there was no way for the zinc fingers to find the fire to put it out. This demonstrates that the arms race keeps shifting. KZNF genes continue to expand and evolve to suppress retrotransposons, but mobile DNA fights back by adapting to evade zinc fingers. Scientists believe this cycle explains why the KZNF genes are one of the most rapidly expanding families of genes in our cells. We need our vigilant and adaptive zinc fingers to protect us from mobile and harmful DNA.
No one can predict how this microscopic evolutionary arms race will unfold in millennia to come. As long as our mediators keep fighting back, our cells will keep jumping genes in check and our minuscule, but mighty, firefighters will continue to douse the fires that threaten us.
Jacob Comeaux will graduate in December 2015 with a biology degree from UC Santa Cruz. He wrote this story for SCIC 160: Introduction to Science Writing.