Double-stranded RNA structures that can initiate RNA interference. Image Credit: Daphne Knudsen-Palmer (CC BY 4.0)
A variety of diseases are treated with therapeutics that switch off genes via a mechanism called RNA interference (or RNAi for short). Each gene has the instructions cells need to build a particular protein. To achieve this, the DNA sequence must first be copied into a single-stranded mRNA molecule than can be translated into protein.
RNAi interferes with this process by generating a double-stranded RNA molecule which contains the same DNA sequence as the gene being turned off. A set of proteins (known as regulators) then progressively trigger a series of events that allow the double-stranded RNA to be processed into short pieces that interact with the mRNA and target it for degradation.
While cells use RNAi to regulate the expression of their own genes, researchers can also artificially switch off genes by synthesizing double-stranded RNA molecules in the laboratory. However, some genes are trickier to turn off than others, and why this happens is poorly understood.
To investigate, Knudsen-Palmer et al. studied how two genes (bli-1 and unc-22) are switched off by RNAi in the roundworm Caenorhabditis elegans. A previous study discovered that bli-1 and unc-22 require different regulators for their expression to be disrupted. Knudsen-Palmer et al. found that this was because the RNAi process involves an intersecting network of multiple regulators, rather than a linear pathway of regulators working one after the other. For example, bli-1 requires three regulators (MUT-16, RDE-10 and NRDE-3), whereas unc-22 only needs any two of these regulators to be switched off.
Further experiments revealed that which regulators are required depends on how the gene being silenced is naturally regulated in the cell. Analysis through a computational model showed that the regulators needed for RNAi could be altered in many ways, including by changing the regions that regulators bind to on the mRNA of the target gene.
These findings provide new insights into why some genes respond differently to double-stranded RNA molecules. They also suggest that testing how natural regulation of a target gene influences its response to the RNAi process could potentially lead to better therapeutics.
