RNA interference (RNAi) is widely used in high-throughput reverse genetics
screens for basic research and drug discovery. However, this technique is known to
produce “off-target” effects, or phenotypic results caused by an RNAi reagent’s
knockdown of unintended genes rather than the gene of interest. Off-target effects are
regulated through multiple mechanisms within the cell, and their presence can greatly
complicate the interpretation of experimental data. We review the biology of offtargeting
and discuss both bioinformatics and experimental approaches to reduce RNAi
reagents’ off-target effects. Since such techniques cannot completely eliminate offtarget
effects, we also discuss analysis methods developed to identify off-target effects
in RNAi screening data and, in some cases, even leverage them to uncover novel
biological functionality.
Keywords: bioinformatics, miRNA, mRNA, off-target effects, off-targets, pools,
RNAi, screening, seeds, silencing, siRNA.
