Deep in the gelatin matrix of the bacterium live small “cellular machines” called retrons that produce individual strands of DNA to detect certain viral infections. Now, for the first time, researchers have used these natural DNA scripts to modify genes in human cells. New study published y Nature Chemical Biologysuggests that this method may improve gene editing in different groups of animals.
Although the well-known CRISPR process Gene editing has made it much easier in recent years, and it “has its limitations,” said Seth Shipman, a senior author of the study and a bioengineer at the University of California, San Francisco. This process introduces an enzyme called Cas9 to cut DNA segments and provides the right DNA templates, developed by researchers, to include cells in the repair process. But this template DNA is created in the lab and must be inserted separately from the CRISPR components – and it doesn’t always penetrate the cell membrane.
Shipman and his colleagues instead used retrons to produce this DNA inside the cell itself, where the CRISPR process can easily use it. Retrons carry the enzyme reverse transcriptase, which builds DNA strands based on RNA. They also have “some strangely overlapping loops of RNA” that help them function, says Santiago Lopez, a UCSF graduate student and lead author of the study.
The researchers modified the retrons in the lab to produce the right template DNA. In addition, they lengthened the RNA loops, a change that turned out to allow each retro to produce more copies of DNA. Finally, they inserted retrons into the cells along with CRISPR components.
Using this process, retrons produced 10 to 100 times more template DNA in yeast cells than in human cells. Retrons have also achieved better editing accuracy in yeast than in human cells, possibly due to the different number of filaments or the way each cell type repairs DNA. “But, frankly, we’re not so worried now,” says Shipman, “because it’s just a kick in the door.” He says additional tweaks and optimizations are likely to bring very precise editing in human cells.
“If we can repurpose retrons to produce DNA as ‘donors’ in a patient’s cell, they can be used for gene therapy in diseases such as sickle cell anemia, which require the restoration of only small areas of abnormal genetic sequences,” says Molecular Biology University. Nebraska Channabasavaiah B. Gurumurthy, who was not involved in the study.
But the introduction of foreign DNA into human tissue cells can also “cause adverse immune responses that limit genetic modification,” said Jin-su Kim, director of the IBS Center for Genomic Engineering in South Korea, who was also not involved. Researchers using only CRISPR have developed processes to suppress such reactions, Kim adds, but still need to figure out how to place the retrons.