If humans could reanimate one of our ancient ancestors, we could quickly learn much more about how people once went about their lives than any study of dusty bones and artifacts would reveal. Our forebear might even teach us a few old tricks that could be used to help the living.
That is in essence what researchers in Germany and Hungary were after when they re-created Harbinger3_DR, a long-extinct precursor of at least two modern human genes: they wanted to watch it operate inside living cells. Not just any DNA relic, Harbinger3_DR is an ancient transposon—a so-called jumping gene, able to cut itself out of an organism’s genome and reinsert itself in a different location. Modern scientists would love to master its secrets so they could more precisely control where genes introduced for gene therapy incorporate themselves into a patient’s DNA strand.
Only vestiges remain of the original Harbinger3_DR in human genomes, but versions of the transposon are alive and well in other organisms, including the zebra fish. Those have shown that the gene tends to home in on genome regions containing a particular sequence of DNA. “The reason we chose Harbinger3_DR was this unexpectedly specific insertion site,” says Zoltán Ivics of the Max Delbrück Center for Molecular Medicine in Berlin, who led the experiments. “We were hoping to use this [reincarnated] element for later studies, to understand how it selects this specific target site.”
With the zebra fish gene as a template, Ivics’s group synthesized a Harbinger3_DR with the necessary components to function in human cells. Whereas most genes encode a protein useful to the organism, transposons are self-serving parasites and encode only enough machinery to keep moving themselves around the genome. That equipment usually includes an enzyme, known as a transposase, that performs the cutting and pasting. The Harbinger3_DR sequence also encoded a mysterious molecule the researchers called Myb-like, for its resemblance to another protein.
The scientists delivered the construct into cultured human cells, which started manufacturing the transposons’ encoded proteins. Ivics and his colleagues observed that the Myb-like protein was essential to getting the transposase enzyme into the cell nucleus and to recruiting it to the transposon’s tips, where the enzyme first cuts the gene from a DNA strand and then pastes it in a new location. In follow-up experiments, Ivics wants to glean more detail about how the two proteins control the gene’s insertion site. “We’re hoping that we may discover aspects of the DNA interaction that can help us to specify or engineer certain domains to target a gene,” he explains.
Ivics and other researchers want to press transposons into service as safer delivery vehicles for therapeutic genes. Inactivated viruses are currently the only means of permanently inserting a new gene into a patient’s DNA, but the viruses integrate fairly randomly into the host genome. Viral insertion into critical genes has triggered lethal leukemias in several gene therapy recipients. Rarely, viruses can also regain their ability to reproduce, posing a risk of becoming infectious.
The keys to controlling transposons to deliver gene therapy will be learning to target them to specific areas of the genome, away from important genes, and disabling the element’s jumping ability once it has landed in the desired spot, according to Margy Lambert, a molecular biologist and biosafety specialist at the University of Wisconsin–Madison. If those kinks can be worked out, Lambert says, gene delivery by transposons would represent “a major advance, because they have the flexibility to maximize the advantages [of viral vectors] and minimize the disadvantages.”
Several researchers are already working on creating transposons lacking the capacity to make their own transposase. These versions could be delivered into cells with just enough of the enzyme to integrate themselves once and then stay put.
And Ivics, who in 1997 reanimated another ancient transposon that he dubbed Sleeping Beauty, showed last year that he could control its insertion site by directing it to specific target sequences. “Even if this technology is not mature enough yet for clinical use, the proof of concept has been done,” he says. Studying how the Harbinger3_DR transposon naturally targets specific sequences may also reveal some useful new techniques.
The cooperation between transposase and the Myb-like protein is “really unusual,” says Tian Xu, a geneticist at the Yale School of Medicine who works with a different transposon, called piggyBac, in mice and in human cells: “This very important study sheds new light on how transposons work.”
Ivics expects the better studied of his progeny, Sleeping Beauty, to be ready in about five years to make her debut in a gene therapy trial.
Note: This story was originally published with the title, "Ancient Gene, New Tricks".