RNAi microarray by reverse transfection of siRNA and shRNA for functional genomics

RNA interference (RNAi) is a widely used method for gene function analyses in a variety of organisms. Establishment of a large-scale, high-throughput platform for analysing gene function may require development of an RNAi microarray system using reverse transfection. Here, we show that shRNA is more effective in microarray gene silencing compared to siRNA. Endogenous mammalian genes are suppressed efficiently if highly functional class I sequences were used for siRNAs produced via shRNAs. Furthermore, the method appears applicable for functional genomics. Indeed, apoptotic cell death induced by staurosporine and actinomycin D was found to be blocked by shRNA against apoptotic protease-activating factor-1 and caspase-3, both of which are required in the cytochrome c-dependent apoptosis cascade.