For more than 20 years, scientists have understood that cells rely on RNA interference to regulate gene expression. Yet how the molecular complex responsible for carrying out that job gets built has remained largely unknown. A new study is the first to detail how a specific protein oversees each step of that assembly process.
The study, published May 26, 2026 in Molecular Cell, centers on the RNA-induced silencing complex, or RISC—the molecular machinery responsible for suppressing gene expression. The research shows that a managing protein called Argonaute2 undergoes a four-step process to convert a precursor complex into a mature RISC.
“This mechanism has been a black box for a quarter century, since the discovery of RNA interference,” said senior author Kotaro Nakanishi from The Ohio State University. "Visualizing the mechanism is very important—pharmaceutical companies may appreciate our 3D structures because they can optimize or design a new drug based on them.”
Nakanishi and colleagues conducted biochemical assays and cryogenic-electron microscopy using Argonaute2 as a model. The process begins when Argonaute2 is incubated with a specific siRNA duplex. From there, the protein loads the double-stranded RNA and selects one strand to serve as a guide. It then unwinds the duplex and ejects the “passenger” strand that is no longer needed.
That ejection step produced one of the study’s most notable findings: the messenger RNA (mRNA) being targeted for interference also plays a role in completing the final assembly step. The team named this step TAPE—target-assisted passenger ejection. While mRNAs have generally been viewed as targets of microRNA and siRNA, the study suggests they can also bind precursor RISCs and help facilitate passenger removal during RISC maturation.
“It’s complicated, but it also makes sense to me that if the cell is targeting predominant mRNAs, these targeted mRNAs also facilitate formation of the RISC,” Nakanishi said.
The findings are expected to support development of therapeutic siRNAs and cityRNAs (cleavage-inducing tiny RNAs) that could be designed to silence problematic genes linked to disease. “Now we can provide a robust structural basis or foundation to design or optimize siRNAs,” Nakanishi added.
His lab is now applying the same techniques to examine how the other three Argonaute proteins assemble RISCs.
The study, published May 26, 2026 in Molecular Cell, centers on the RNA-induced silencing complex, or RISC—the molecular machinery responsible for suppressing gene expression. The research shows that a managing protein called Argonaute2 undergoes a four-step process to convert a precursor complex into a mature RISC.
“This mechanism has been a black box for a quarter century, since the discovery of RNA interference,” said senior author Kotaro Nakanishi from The Ohio State University. "Visualizing the mechanism is very important—pharmaceutical companies may appreciate our 3D structures because they can optimize or design a new drug based on them.”
Nakanishi and colleagues conducted biochemical assays and cryogenic-electron microscopy using Argonaute2 as a model. The process begins when Argonaute2 is incubated with a specific siRNA duplex. From there, the protein loads the double-stranded RNA and selects one strand to serve as a guide. It then unwinds the duplex and ejects the “passenger” strand that is no longer needed.
That ejection step produced one of the study’s most notable findings: the messenger RNA (mRNA) being targeted for interference also plays a role in completing the final assembly step. The team named this step TAPE—target-assisted passenger ejection. While mRNAs have generally been viewed as targets of microRNA and siRNA, the study suggests they can also bind precursor RISCs and help facilitate passenger removal during RISC maturation.
“It’s complicated, but it also makes sense to me that if the cell is targeting predominant mRNAs, these targeted mRNAs also facilitate formation of the RISC,” Nakanishi said.
The findings are expected to support development of therapeutic siRNAs and cityRNAs (cleavage-inducing tiny RNAs) that could be designed to silence problematic genes linked to disease. “Now we can provide a robust structural basis or foundation to design or optimize siRNAs,” Nakanishi added.
His lab is now applying the same techniques to examine how the other three Argonaute proteins assemble RISCs.