Abstract
Since the discovery that the triggers for RNA interference (RNAi), small interfering RNAs, could mediate silencing in mammalian cells without triggering a toxic response, RNAi has become the standard tool for sequence-specific knockdown of gene expression in molecular biology. This is due in part to the development of methods for promoter-based expression of RNAi triggers that can mediate stable silencing in mammalian cells. Numerous systems with slightly different characteristics exist, but despite incredible progress in a field that moves very rapidly, challenges still remain. The biggest challenge is to successfully and safely apply RNAi in vivo. Aside from potential issues of delivery, which is one of the most important considerations, successful application of short hairpin RNAs (shRNAs) in vivo requires expression systems that yield potent and specific knockdown of the target in the absence of toxicity. With a couple of exceptions, the current systems available for shRNA expression have not generally resulted in unexpected toxicities, while still providing strong knockdown of the intended targets; however, we do not know enough about how sequence-specific off-target effects will affect various cell and tissue types, or to what extent ectopic expression of RNAi triggers will perturb the endogenous RNAi mechanisms.