Knockdown of Chimeric RNA by RNAi.
Knockdown assays are widely used to study the functions of a gene of interest. RNA interference (RNAi) describes a set of well-known methods used to reduce the expression of a target gene by degrading its mRNA with short hairpin RNAs (shRNAs) or short interfering RNAs (siRNAs). Knockdown of chimeric RNAs present different challenges than standard RNAi targeting for regular genes. Most specifically, sequence homology restricts the targeting region to the chimeric junction and can result in off-target effects on the parental genes. In this chapter, we provide guidelines and procedures for RNAi design of chimeric RNAs, knockdown of chimeric RNAs, downstream experiments for chimeric RNA functional studies and necessary controls to accompany each set of experiments.