Figure: Retrons enable the rapid production and screening of millions of trackable DNA variations and their effects on bacteria simultaneously.

"Move over CRISPR, the retrons are coming!" Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Harvard Medical School (HMS) have created a new gene editing tool called Retron Library Recombineering (RLR) that enables millions of genetic experiments to be performed simultaneously.

CRISPR-Cas9 can find and cut specific pieces of DNA, but editing the DNA to create desired mutations requires tricking the cell into using a new piece of DNA to repair the break. This bait-and-switch is complicated to orchestrate, and can even be toxic to cells because Cas9 often cuts unintended, off-target sites as well. The RLR tool makes this task easier. RLR generates up to millions of mutations simultaneously, and "barcodes" mutant cells so that the entire pool can be screened at once, enabling massive amounts of data to be easily generated and analyzed.

Retrons have been known for decades, but their functions were unknown until June 2020 when a team finally figured out that retron ssDNA detects whether a virus has infected the cell, forming part of the bacterial immune system. Researchers are interested in retrons because they, like CRISPR, could be used for precise and flexible gene editing in bacteria, yeast, and even human cells. Another attraction of retrons is that their sequences serve as "barcodes" that identify which individuals within a pool of bacteria have received each retron sequence, enabling dramatically faster, pooled screens of precisely-created mutant strains.

"Being able to analyze pooled, barcoded mutant libraries with RLR enables millions of experiments to be performed simultaneously, allowing us to observe the effects of mutations across the genome, as well as how those mutations might interact with each other," said senior author George Church, who leads the Wyss Institute's Synthetic Biology Focus Area.

For more details about RLR, read the article in the Wyss Institute News.