Discovered just over a decade ago, CRISPR has revolutionized the biomedical industry thanks to the fact it allows scientists to target diseases – particularly genetic ones – that were previously untreatable by making direct edits to genes. However, despite being versatile, CRISPR has limitations – while it is ideal for breaking problematic genes and making small edits, it is not very useful when it comes to inserting whole genes or large chunks of DNA. Now, though, the recent discovery of a molecular oddity known as bridge RNA, found in bacteria, could lead to a new gene editing technique that can overcome these limitations.

The discovery of bridge RNA: what exactly is it?

The new gene editing technique harnesses the natural ability of mobile genetic sequences – known as “jumping genes” – to cut and paste themselves throughout a genome, and essentially allows scientists to insert, delete, or flip large segments of DNA. 

This new approach is made possible thanks to a molecule called bridge RNA, which was discovered by Patrick Hsu and his team at the Arc Institute in Palo Alto, in collaboration with the University of Tokyo. It is very similar to guide RNA (the molecule associated with CRISPR), but rather than simply recognizing one strand of DNA at a time, it recognizes two at once: the target site for editing and the new gene that will be inserted into it. It then recruits an enzyme called a recombinase to perform the actual edit.

The discovery of bridge RNA came about as a result of Hsu and his team sieving through a diverse class of enzymes that allow mobile DNA elements in bacteria to hop from one location to another. Eventually, they settled on a bacterial transposable element called IS110, which was first discovered 40 years ago. 

In their studies, the team found that when IS110 jumps out of the genome, it forms a circle, as its two flanks come together to create what is known as a canonical bacterial transcriptional promoter. This then leads to the transcription of a previously hidden noncoding RNA (which is only readable when the two flanks of the jumping gene come together to form a circle) that folds into two loops. One of the loops binds to the IS110 element, while the other binds to the area on the genome where it is to be inserted, essentially forming a “bridge” between the two. 

By changing the sequences at either end of this bridge, the researchers were then able to program IS110 to insert a cargo of their choosing where they wanted in the genome. They used the system to insert a piece of DNA that was nearly 5,000 bases long into the genome of the bacterium E. coli with high precision, as well as to excise and invert another piece of DNA from the E. coli genome.

How does bridge RNA overcome CRISPR’s limitations?

As previously mentioned, CRISPR comes with limitations. The tool is most often used to change just one or a few DNA bases and cannot make large edits. Furthermore, it cannot make edits without breaking both strands of DNA and then relying on the cell’s innate DNA repair systems to generate the desired change, opening the door to unintended collateral genetic damage. 

Bridge RNA, on the other hand, allows scientists to make large genetic changes in a more controlled manner than when using CRISPR technology. With bridge RNA, researchers can program both the target and the donor sequence of DNA so they can mix and match any two that they want, whereas the guide RNA in CRISPR-Cas9 systems can specify only the target DNA sequence to be cut, not the one to be added in. 

In a statement to Fierce Biotech, Hsu said: “Bridge editing [cuts and pastes DNA] in a single-step mechanism that recombines and re-ligates the DNA, leaving it fully intact. This is very distinct from CRISPR editing, which creates exposed DNA breaks that require DNA repair and have been shown to create undesired DNA damage responses.” Therefore, by avoiding those, bridge editing “could potentially lead to more precise or safer types of genome edits.”

What are the next steps?

The technique has only been tested in bacteria and in test tube reactions, but Hsu told Endpoints that he already has several ideas for the technology’s practical applications in humans. It could provide a new way to upload genes into cell therapies for cancer and replace broken genes in inherited conditions. Plus, the ability to cut out segments of DNA could help collapse the problematic repetitive mutations responsible for neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and Huntington’s disease. 

The next step for the researchers now will be to study how they can make the technique work in human cells, along with ways to boost its precision and efficiency. They will also look at what other functionalities the IS110 element has that could be used in gene editing.

Hsu is already involved in several biotech companies, including the startup Stylus Medicine, which has an undisclosed amount of funding from RA Ventures and Khosla Ventures, according to its website. Endpoints said that Hsu would not confirm whether bridge recombination was a focus of that company, but its website mentions “a novel class of enzymes to enable the insertion of any-length genetic sequences.” 

We will have to wait and see what happens next, but if bridge RNA can work in humans, it could be even more revolutionary than CRISPR, offering a safer, more accurate, and more flexible approach to making large-scale chromosome changes.

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