A New Gene Editing Tool Could Rival CRISPR, and Makes Millions of Edits at Once

With CRISPR’s rise as a gene editing marvel, it’s easy to forget its lowly origins: it was first discovered as a quirk of the bacterial immune system.

It seems that bacteria have more to offer. This month, a team led by the famed synthetic biologist Dr. George Church at Harvard University hijacked another strange piece of bacteria biology. The result is a powerful tool that can, in theory, simultaneously edit millions of DNA sequences, with a “bar code” to keep track of changes. All without breaking a single delicate DNA strand.

For now, these biological tools, called “Retron Library Recombineering ,” have only been tested in bacterial cells. But as CRISPR’s journey to gene therapy shows, even the weirdest discoveries from lowly creatures may catapult our wildest gene therapy or synthetic biology dreams into reality.
“This work helps establish a road map toward using RLR in other genetic systems, which opens up many exciting possibilities for future genetic research,” said Church.

You might already be familiar with how it works. There are two components: a type of RNA, and a protein. The “bloodhound” guide RNA tethers the Cas “scissor” protein to a particular gene. In the classic version, Cas chops up the gene to turn it off.

The new tool is called RLR, and the first “R” stands for retrons. These are widespread but utterly mysterious creatures whose “natural biology…is largely unknown,” the team wrote, though similar to CRISPR, they may be involved in the bacterial immune system.

First discovered in 1984, retrons are floating ribbons of DNA in some bacteria cells that can be converted into a specific type of DNA—a single chain of DNA bases dubbed ssDNAs . But that’s fantastic news for gene editing, because our cells’ double-stranded  DNA sequences become impressionable single chains when they divide. Perfect timing for a retron bait-and-switch.

Normally, our DNA exists in double helices that are tightly wrapped into 23 bundles, called chromosomes. Each chromosome bundle comes in two copies, and when a cell divides, the copies separate to duplicate themselves

Similar to CRISPR, RTR has multiple components: the genetic snippet that contains a mutation , and two proteins, RT and SSAP , that transform the retron into ssDNA and let it insert itself into a dividing cell.

So to make it clearer: retrons carry the genetic code we want to insert; RT makes it into a more compatible form that’s called ssDNA; and SSAP sticks it into DNA as it’s dividing. Basically, a Trojan horse invades the cell and pours out spies that insert themselves into the cell, changing its DNA, with the help of enzymatic magicians.
The two proteins are new to the party.

Previously, scientists have tried to use retrons for gene editing, but the efficiency was extremely low, around 0.1 percent of all bacterial cells infected. The two newcomers quieted down the bacteria’s natural “alarm system” that corrects DNA changes, so they ignore the new DNA bits, and allow edits to enter and pass on to the next generation. One other trick was to disable two genes that encode for proteins that normally destroy ssDNA.
In one test, the team found that over 90 percent of bacterial cells readily admitted the new retron sequence into their DNA. They next went big.

The goal is easy: to find another solution to CRISPR that can influence millions of cells at once, without damaging the cells. In other words, take gene editing into the big data era, through multiple generations.
Compared to CRISPR, the new RLR tool is simpler because it does not require a “guide” tool in addition to an “editing” tool, a retron is basically a two-in-one. Being able to influence multiple genes at once, without physically cutting into them, also makes it an intriguing tool for synthetic biology. The tool’s also got staying power. Instead of a “one and done” CRISPR ethos, it lasts through generations as cells divide.