Scientists at Vilnius University’s Life Sciences Center (LSC) have uncovered a novel mechanism by which cells can silence specific genes without the need to cut the DNA. This discovery, led by Professor Patrick Pausch, is a significant advancement in gene regulation and has the potential to revolutionize gene therapy and biotechnology. The research, published in Nature Communications, outlines how cells use a natural system to “pause” genes, effectively turning them off without altering their underlying DNA sequence.
The study, conducted by Professor Pausch alongside doctoral student Rimvydė Čepaitė, Dr. Aistė Skorupskaitė, and undergraduate Gintarė Žvejyte, provides a detailed exploration of this gene-silencing process. The team collaborated with an international group of scientists to investigate a specific type IV-A CRISPR system, a previously underexplored part of the CRISPR-Cas family of proteins. Unlike the commonly known CRISPR-Cas9 system, which cuts DNA to make edits, this new CRISPR system silences genes without introducing any breaks in the DNA strand.
Professor Pausch explains that the type IV-A CRISPR system works in a way that is fundamentally different from the “molecular scissors” metaphor typically used to describe CRISPR technologies. Instead of cutting DNA, this system uses an RNA-guided “effector” complex to recruit a specialized enzyme called DinG. This enzyme moves along the DNA, silencing genes in a more controlled, subtle manner. “What’s fascinating about this system is how it identifies where to start silencing the gene. It uses two proteins—Cas8 and Cas5—to locate a very short sequence motif adjacent to the RNA guide’s complementary target DNA. Once these proteins bind to this motif, they melt the double-stranded DNA, allowing the system to interrogate the target sequence,” Pausch explains.
A critical element of this process is the formation of an R-loop, an open DNA structure where RNA binds to the DNA, signaling the system to initiate gene silencing. The term “R-loop” refers to the RNA-DNA hybrid structure that forms during this process. Pausch notes that all DNA-binding CRISPR-Cas systems rely on R-loops to probe the DNA sequence and identify the correct target site. These stable R-loops only form when the DNA sequence matches the RNA guide closely enough, thus providing a precise trigger for gene silencing.
The DinG enzyme plays a crucial role in enhancing the silencing effect. By unwinding the DNA strands, DinG allows the system to exert its silencing influence over a longer sequence of DNA, effectively “pausing” the gene’s activity. This ability to silence genes without cutting the DNA opens up new possibilities for genetic modifications, providing a safer alternative to traditional methods.
This discovery could have significant implications for future gene-editing applications. The ability to silence genes without causing cuts in the DNA could reduce the risks associated with unintended genetic changes, making gene therapy safer and more precise. Professor Pausch believes that this RNA-guided gene silencing system could be a valuable tool for advancing biotechnology and biomedical research. “The fact that our system can traverse the DNA without making cuts is a huge advantage for gene-editing applications. It opens up new avenues for genetic modifications that could one day lead to safer, more effective therapies for genetic diseases,” he says.
The research team’s findings represent a fundamental step forward in the field of gene regulation and offer a promising new approach to genome editing. By providing a method to silence genes without cutting DNA, this study could pave the way for more precise, controlled gene therapies, minimizing the risks and improving the effectiveness of genetic interventions. As the research continues, scientists are excited about the potential applications of this technology, which could ultimately benefit a wide range of industries, from medicine to agriculture.
Source: Vilnius University