Genome editing mechanism developed from protein found in complex organisms

A new genome editing mechanism has been developed for the first time from a protein found in eukaryotes.

The new system is similar to the CRISPR genome editing approach, which is derived from prokaryote organisms, such as bacteria. CRISPR allows editing of specific regions in the genome, through the use of small RNA guides that direct an enzyme called Cas9 to cut DNA. The new technique is based on a protein called Fanzor, that is common in some eukaryotes, such as animals, plants and fungi. Fanzor proteins can be programmed to target specific genetic loci and introduce changes into the human genome.

'CRISPR-based systems are widely used and powerful because they can be easily reprogrammed to target different sites in the genome... This new system is another way to make precise changes in human cells, complementing the genome editing tools we already have,' said Professor Feng Zhang, from the Broad Institute in Cambridge, Massachusetts, and senior author of the study.

The group initially identified a class of RNA programmable systems called 'OMEGAs' that were likely evolutionary precursors to CRISPR/Cas. This work led to the discovery of similarities between OMEGA systems in prokaryotes and Fanzor proteins in eukaryotes, suggesting that Fanzor genes may have migrated from bacteria to eukaryotes.

In the study published in Nature, researchers from the Massachusetts Institute of Technology (MIT) showed that Fanzor proteins are enzymes that cut DNA using non-coding RNAs to target specific sites in the genome. Fanzor proteins target RNA loops that guides them to cleave DNA motifs – short, recurring patterns in DNA. The researchers demonstrated that Fanzor proteins can generate insertions and deletions at specific genomic targets in human cells. They are more easily delivered to human cells and tissues, as they of much smaller size than bacterial Cas proteins.

Initially, the system was less efficient than CRISPR/Cas, but through systematic engineering and introducing various mutations into the gene, activity was increased ten-fold. An additional advantage of Fanzor proteins is reduced degradation activity in nearby DNA or RNA that can be observed in some CRISPR and OMEGA systems. However, like CRISPR/Cas, each Fanzor system needs to be designed for its specific cleavage site, with different key characteristics dependent on the target.

'This is exciting work describing the diversity of RNA-guided DNA nucleases in eukaryotes and their potential for gene editing. There is a playbook for translating these discoveries into tools, and time will tell how Fanzors stack up against the existing gene editing toolbox,' Dr Janice Chen chief technology officer and cofounder of Mammoth Biosciences, California, who was not involved with the studies, told GenomeWeb.

In a second, independent study, Professor Zhang's former students Dr Omar Abudayyeh and Dr Jonathan Gootenberg, from MIT, also investigated RNA-guided cleavage systems in eukaryotes, based on Fanzor proteins. They have published their findings as a preprint in bioRxiv that has not yet been peer-reviewed. Patents have been filed from both groups and both groups believe that Fanzor proteins have the potential to be used as part of a more efficient, valuable new approach for human genome editing.