Researchers uncover new RNA-guided genome editing system

Fanzor proteins show potential for precise human genome editing, offering an alternative to CRISPR-Cas systems.

Scientists at the McGovern Institute for Brain Research at MIT and the Broad Institute of MIT and Harvard have made a significant discovery – Fanzor. While the name might sound like it belongs to a character that should be battling Godzilla, Fanzor proteins play a key role in a novel RNA-guided genome editing system, and one that opens up new possibilities for more precise DNA editing in human cells compared with the widely used CRISPR/Cas systems.

Published in Nature, this new study provides insights into the structure and functionality of Fanzor proteins, highlighting their potential as therapeutics for human genome editing.

Longevity.Technology: CRISPR-Cas systems, originally identified in prokaryotes such as bacteria, have revolutionized genetic research due to their ability to be easily reprogrammed for targeting different sites in the genome. However, scientists have long speculated about the existence of similar systems in the more complex eukaryotes, the domain that encompass fungi, plants and animals. Researchers now demonstrated the presence of RNA-guided DNA-cutting mechanisms across all kingdoms of life, establishing Fanzor as a promising alternative to existing genome editing tools.

CRISPR – short for Clustered Regularly Interspaced Short Palindromic Repeats – is a powerful gene editing technology that allows scientists to make precise modifications in the DNA of organisms by using a molecule called RNA as a guide to target specific sequences of DNA and make changes at those locations. The compact Fanzor systems introduces a new RNA-guided system that can more easily be potentially enhance the precision and delivery of therapeutics for genome editing.

“CRISPR-based systems are widely used and powerful because they can be easily reprogrammed to target different sites in the genome,” said Zhang, senior author on the study and a core institute member at the Broad, an investigator at MIT’s McGovern Institute, the James and Patricia Poitras Professor of Neuroscience at MIT, and a Howard Hughes Medical Institute investigator. “This new system is another way to make precise changes in human cells, complementing the genome editing tools we already have [1].”

The researchers isolated Fanzor proteins from various organisms, including fungi, algae, amoeba species and a clam called the northern quahog. Through meticulous biochemical characterization, they found that Fanzors are endonuclease enzymes that use non-coding RNAs known as ωRNAs to precisely target specific sites in the genome [2]. This mechanism, observed for the first time in eukaryotes, showcases the versatility and potential of Fanzor proteins for genome editing applications in animals.

Researchers uncover new RNA-guided genome editing system in animals
A Cryo-EM map of a Fanzor protein (gray, yellow, light blue and pink) in complex with ωRNA (purple) and its target DNA (red). Non-target DNA strand in blue.
Photograph: the Zhang lab, Broad Institute of MIT and Harvard/McGovern Institute for Brain Research at MIT

Unlike CRISPR proteins, Fanzor enzymes are encoded within the eukaryotic genome’s transposable elements. Phylogenetic analysis indicates that Fanzor genes have migrated from bacteria to eukaryotes through horizontal gene transfer.

This is also reinforced through previous research; two years ago, Zhang lab members discovered a class of RNA-programmable systems in prokaryotes called OMEGAs, which are often linked with transposable elements, or “jumping genes”, in bacterial genomes and likely gave rise to CRISPR/Cas systems. That work also highlighted similarities between prokaryotic OMEGA systems and Fanzor proteins in eukaryotes, suggesting that the Fanzor enzymes might also use an RNA-guided mechanism to target and cut DNA.

“These OMEGA systems are more ancestral to CRISPR and they are among the most abundant proteins on the planet, so it makes sense that they have been able to hop back and forth between prokaryotes and eukaryotes,” explained co-first author Makoto Saito of the Zhang lab [1].

To evaluate the editing capabilities of Fanzor, the researchers successfully demonstrated its capacity to generate insertions and deletions at targeted genome sites in human cells. Although initially less efficient than CRISPR-Cas systems, the team engineered the Fanzor protein through a combination of mutations, resulting in a tenfold increase in activity. Importantly, unlike some CRISPR systems, Fanzor proteins exhibited minimal “collateral activity,” mitigating the unintended cleavage of nearby DNA or RNA.

Structural analysis conducted by the team revealed similarities between Fanzor and its prokaryotic counterpart, CRISPR-Cas12 protein. However, the interaction between ωRNA and the catalytic domains of Fanzor was found to be more extensive, suggesting the involvement of ωRNA in catalytic reactions. This insight into the molecular structure of Fanzor provides a foundation for further engineering and optimization to enhance its precision and efficiency as a genome editing tool.

 “We are excited about these structural insights for helping us further engineer and optimize Fanzor for improved efficiency and precision as a genome editor,” said co-first author Peiyu Xu [1].

Fanzor shares the hallmark characteristic of CRISPR-based systems – its programmability to target specific genome sites. This feature, combined with the potential for improved efficiency and precision through ongoing research, positions Fanzor as a promising technology for both research and therapeutic applications in the future. Additionally, the prevalence of RNA-guided endonucleases like Fanzor hints at the possibility of discovering more novel RNA-programmable systems, expanding our understanding of genetic mechanisms in different organisms.

The discovery of Fanzor marks a significant milestone in the field of genome editing, offering scientists a potential alternative to CRISPR-based systems for precise manipulation of the human genome.

“Nature is amazing. There’s so much diversity,” said Zhang. “There are probably more RNA-programmable systems out there, and we’re continuing to explore and will hopefully discover more [1].”


Photograph: vectorpocket/Freepik