No CRISPR, no problem: 'Jumping gene' system could be bridge to complex gene editing

A new gene editing technique derived from bacterial “jumping genes” can add, remove, recombine and invert DNA sequences, potentially overcoming some of the limitations of CRISPR. 

The approach is made possible by a molecule called bridge RNA, the discovery of which came about through a joint effort led by scientists at the Arc Institute in Palo Alto, California, in collaboration with the University of Tokyo. They described their work in a pair of papers published June 26 in Nature. 

“We're excited about the many potential applications that lie ahead,” Patrick Hsu, Ph.D., senior author, told Fierce Biotech in an email. Eventually, the mechanism could be used in cell and gene therapy to, for instance, insert chimeric antigen receptors or missing genes, he said. 

“There are also many functional genomics applications, including possibilities for diseases caused by repeat expansions or genetic translocations which could be addressed by precisely excising or inverting the problematic DNA segments, allowing scientists to target genetic abnormalities,” Hsu added.

CRISPR has only been around for a decade, but it has revolutionized biomedical research by making it possible for scientists to edit genes in cells and other organisms, offering them a window into how genetic changes cause disease and explore potential treatments. The technology is now being used as a therapy, too: In December 2023, the FDA approved Vertex Pharmaceuticals and CRISPR Therapeutics’ Casgevy for sickle cell disease. The next month, Casgevy got the green light for use in the blood disorder beta thalassemia as well. 

But there are limits to CRISPR’s utility. It can’t make edits without breaking both strands of DNA—a potential route of toxicity—and isn’t useful for inserting whole genes or even large chunks of DNA. It’s also not always as accurate as scientists would like. Biotechs like Tessera Therapeutics, Prime Medicine and more are racing to improve on those shortfalls with gene writing, prime editing and other technologies.  

Developments based on the Arc Institute team’s newly identified molecule could eventually join them. Bridge RNA is a lot like the guide RNA (gRNA) component of CRISPR-Cas9 systems. However, rather than recognizing one strand of DNA at a time as CRISPR gRNA does, bridge RNA recognizes two—the target DNA and the gene that will be inserted into it. Once it’s bound to both, it brings in a DNA recombinase to do the editing. 

Bridge RNA’s bispecificity is the key to its utility. Researchers can program both the target and the donor sequence of DNA so they can mix and match any two they want. In contrast, the gRNA in CRISPR-Cas9 systems can specify only the target DNA sequence to be cut, not the one to be added in. Inserting a gene with CRISPR requires using a separate component called a homology-directed repair template and the host cell’s own DNA repair mechanisms. 

“Bridge editing [cuts and pastes DNA] in a single-step mechanism that recombines and re-ligates the DNA, leaving it fully intact,” Hsu explained in an email to Fierce. “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.” By avoiding those, bridge editing “could potentially lead to more precise or safer types of genome edits,” he added. 

The Hsu lab’s discovery came about through the study of a bacterial transposable element, or jumping gene, called IS110. The researchers found for the first time that when it “jumps” out of the genome, it circularizes itself, bringing together its far left and far right ends to create what's known as a canonical bacterial transcriptional promoter. This leads to the transcription of a previously hidden noncoding RNA that folds into two loops. One of the loops binds to the IS110 element itself while the other binds to the area on the genome where it is to be inserted—in other words, forming a “bridge” between the two. 

The studies in the new papers showed that it’s possible to program each end of the bridge RNA to link two sequences of DNA and manipulate them, at least in bacteria. The Arc Institute team used the bridge RNA system to insert a large piece of DNA into the genome of an E. coli bacterium with high precision as well as to excise and invert E. coli DNA. 

Next, the researchers will study how to make the technique work in human cells, along with ways to boost its precision and efficiency. They’ll also look at what other functionalities the IS110 element has that could be used in gene editing.