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A search for new genome-editing tools has led researchers from MIT’s McGovern Institute and the Broad Institute of MIT to identify a distinct class of RNA-guided systems with the potential to expand genetic engineering capabilities. These systems, named TIGR (Tandem Interspaced Guide RNA) systems, use RNA molecules to direct proteins to specific DNA sequences. Their modularity and compact size make them a promising addition to existing genome-editing technologies.
“This is a very versatile RNA-guided system with a lot of diverse functionalities,” said Feng Zhang, who led the study. The TIGR-associated (Tas) proteins share a conserved RNA-binding domain that allows them to interact with RNA guides and direct them to specific genomic sites. Some Tas proteins can cleave DNA, while others appear to interact with additional proteins.
Known for his role in previously adapting CRISPR systems for gene editing, Zhang emphasized the importance of exploring natural diversity for new molecular tools. “Nature is pretty incredible,” he said. “It’s got a tremendous amount of diversity, and we have been exploring that natural diversity to find new biological mechanisms and harnessing them for different applications to manipulate biological processes.”
To identify novel RNA-guided proteins, the research team focused on structural similarities to Cas9, the CRISPR enzyme that binds an RNA guide to target DNA. Searching through hundreds of millions of proteins, they used an iterative approach that identified IS110, a protein previously shown to bind RNA.
As the dataset grew, normal phylogenetic methods became insufficient to analyze the quantity and diversity of candidates. The researchers turned to artificial intelligence, using a protein language model to classify the proteins into evolutionary groups. The TIGR-Tas systems stood out the most. Identified primarily in viruses that infect bacteria, these systems contained regularly spaced repetitive sequences, similar to the guide RNA arrays found in CRISPR systems.
The team eventually discovered over 20,000 Tas proteins, many of which can be programmed to target and cut DNA in human cells. Unlike CRISPR-Cas systems, which require short protospacer adjacent motifs (PAMs) to recognize DNA targets, TIGR-Tas proteins doesn’t have this restriction. “This means theoretically, any site in the genome should be targetable,” said scientific advisor Rhiannon Macrae.
Another distinguishing feature is their “dual-guide system,” which interacts with both strands of the DNA double helix. This interaction enhances specificity and minimizes off-target effects. Additionally, Tas proteins are significantly smaller than Cas9 (about one-quarter of its size), which makes them more amenable to delivery in therapeutic settings.
Zhang’s team is now investigating the natural role of TIGR systems in viruses and assessing their potential for biomedical applications. They have already analyzed the structure of one Tas protein that has shown to work in human cells. Finally, connections between TIGR-Tas systems and certain RNA-processing proteins in human cells suggest broader functional significance that warrants further exploration.
Publication Details
Guilhem Faure et al., TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses. Science 0, eadv9789 DOI:10.1126/science.adv9789
“This is a very versatile RNA-guided system with a lot of diverse functionalities,” said Feng Zhang, who led the study. The TIGR-associated (Tas) proteins share a conserved RNA-binding domain that allows them to interact with RNA guides and direct them to specific genomic sites. Some Tas proteins can cleave DNA, while others appear to interact with additional proteins.
Known for his role in previously adapting CRISPR systems for gene editing, Zhang emphasized the importance of exploring natural diversity for new molecular tools. “Nature is pretty incredible,” he said. “It’s got a tremendous amount of diversity, and we have been exploring that natural diversity to find new biological mechanisms and harnessing them for different applications to manipulate biological processes.”
To identify novel RNA-guided proteins, the research team focused on structural similarities to Cas9, the CRISPR enzyme that binds an RNA guide to target DNA. Searching through hundreds of millions of proteins, they used an iterative approach that identified IS110, a protein previously shown to bind RNA.
As the dataset grew, normal phylogenetic methods became insufficient to analyze the quantity and diversity of candidates. The researchers turned to artificial intelligence, using a protein language model to classify the proteins into evolutionary groups. The TIGR-Tas systems stood out the most. Identified primarily in viruses that infect bacteria, these systems contained regularly spaced repetitive sequences, similar to the guide RNA arrays found in CRISPR systems.
The team eventually discovered over 20,000 Tas proteins, many of which can be programmed to target and cut DNA in human cells. Unlike CRISPR-Cas systems, which require short protospacer adjacent motifs (PAMs) to recognize DNA targets, TIGR-Tas proteins doesn’t have this restriction. “This means theoretically, any site in the genome should be targetable,” said scientific advisor Rhiannon Macrae.
Another distinguishing feature is their “dual-guide system,” which interacts with both strands of the DNA double helix. This interaction enhances specificity and minimizes off-target effects. Additionally, Tas proteins are significantly smaller than Cas9 (about one-quarter of its size), which makes them more amenable to delivery in therapeutic settings.
Zhang’s team is now investigating the natural role of TIGR systems in viruses and assessing their potential for biomedical applications. They have already analyzed the structure of one Tas protein that has shown to work in human cells. Finally, connections between TIGR-Tas systems and certain RNA-processing proteins in human cells suggest broader functional significance that warrants further exploration.
Publication Details
Guilhem Faure et al., TIGR-Tas: A family of modular RNA-guided DNA-targeting systems in prokaryotes and their viruses. Science 0, eadv9789 DOI:10.1126/science.adv9789