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Thousands of Organisms Possess DNA-Editing Enzyme Fanzor

A picture of venus clams.
The research team analyzed the Fanzor2 enzyme from Venus clams. Credit: Paul Einerhand on Unsplash.
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The discovery of Fanzors

Earlier this year, researchers led by Dr. Feng Zhang at the McGovern Institute for Brain Research reported the discovery of a programmable RNA-guided system in eukaryotes. The system’s components include an RNA-guided endonuclease, Fanzor, which can cut DNA at targeted sites. Fanzor enzymes can be likened to a eukaryotic version of the bacterial endonucleases harnessed in CRISPR-Cas genome editing technologies.

Zhang and colleagues utilized a suite of scientific tools, including biochemical and genetic studies, to characterize the Fanzor system. “The Fanzor protein is a kind of molecular scissors that can cut DNA. Fanzor interacts very closely with a special piece of RNA, called an omegaRNA, and this omegaRNA contains a section, called the guide. When the guideRNA sequence and the target DNA match up, they ‘zip together’ and Fanzor can then recognize and cut that specific piece of DNA,” Zhang told Technology Networks.

The discovery of a programmable RNA-guided system in eukaryotes creates a “whole new kind of playground to work in,” according to McGovern Fellow Dr. Jonathan Gootenberg. Eukaryotes are organisms whose cell has a nucleus and other cellular organelles that are neatly enclosed by a plasma membrane. Animals, plants, fungi and the majority of multicellular organisms are examples of eukaryotes. Hundreds of Fanzors had been discovered across this wide domain of creatures, but as McGovern Research Fellow Dr. Omar Abudayyeh described, “the more we can find, the better.”

In a new study, Abudayyeh and Gootenberg led a team of scientists on a quest to identify and characterize Fanzor enyzmes in large-scale genetic databases. Their genetic mining venture, published in Science Advances, outlines the discovery of over 3,600 Fanzors in eukaryotes, including algae, snails, amoebas and the viruses that infect them.

Fanzors evolved new features to survive and thrive in eukaryotes

Five distinct families of Fanzors could be identified from the study data. By comparing the biological makeup of these families, Abudayyeh and colleagues could track their evolutionary history. Fanzors most likely evolved from proteins called TnpB, which are encoded in transposons – mobile genetic elements often nicknamed “jumping genes”. In Nature, the McGovern team hypothesized that the TnpB gene may have “jumped” from bacteria to eukaryotes in a genetic “shuffling” many years ago. Abudayyeh and Gootenburg’s new study and genetic tracing implies that this event likely occurred several times, with Fanzors “jumping” from viruses and symbiotic bacteria. Their analyses also suggest that once these genes had made their way into eukaryotes, they evolved new features that promoted their survival, including the ability to enter a cell’s nucleus and access its DNA.

Graduate student and lead author Kaiyi Jiang identified that Fanzors have a DNA-cutting site that is different from its bacterial ancestors, which allows the molecular scissors to cut more precisely.

Precision is an important feature to ensure the efficiency and safety of genome-editing tools. “Further refinements to improve their targeting efficiency could make them [Fanzor proteins] a valuable new technology for human genome editing,” Zhang said previously. “We are excited to see how the trajectory unfolds, and we are continuing to work to develop Fanzor into a valuable new technology for human genome editing. Going forward, we are continuing to study the biology of Fanzor proteins and exploring ways that we can engineer them for use as molecular technologies.”

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Gootenberg echoed Zang and hopes that the collective works on Fanzor enzymes will help to create a new suite of sophisticated genome-editing tools: “It’s a new platform, and they have many capabilities,” he said.

Reference: Jiang K, Lim J, Sgrizzi S, et al. Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses. Sci Adv. 9(39):eadk0171. doi:10.1126/sciadv.adk0171

This article is a rework of a press release issued by the Massachusetts Institute of Technology. Material has been edited for length and content.