Knockdown of Chimeric RNA by RNAi

Knockdown experiments are commonly employed to examine the functions of a gene of interest. A group of well-known techniques known as RNA interference (RNAi) is used to lower the expression of a target gene by using short hairpin RNAs (shRNAs) or short interfering RNAs (siRNAs) to degrade the target gene's mRNA. The issues associated with chimeric RNA knockdown differ from those associated with traditional RNAi targeting of normal genes. Sequence homology, in particular, limits the targeting region to the chimeric junction and may have unintended consequences for the parental genes. This chapter includes instructions on how to study chimeric RNAs using RNA interference (RNAi), how to knock down chimeric RNAs, how to conduct downstream tests for chimeric RNA functional studies, and what controls are required for each set of experiments.