Reporter-Based Assays for Analyzing RNA Interference in Mammalian Cells

Abstract

RNA interference (RNAi) is a process whereby small RNAs serve as effectors to direct posttranscriptional regulation of gene expression. The effector small RNAs can arise from various sources including plasmids that express short-hairpin RNAs (shRNAs) or microRNA (miRNAs), or alternatively, from synthetic small-interfering RNAs (siRNAs). These small RNAs enter a protein complex that binds directly to mRNA targets and this results in transcript-specific inhibition of protein expression. Though the key core components of the mammalian RNAi processing and effector complexes have been identified, accessory and regulatory factors are less well-defined. Reporter assays that can quantitatively assess RNAi activity can be used to identify modulators of RNAi. We present two methods to quantitatively analyze RNAi activity that have overlapping and distinct utility. The first method uses an eGFP reporter in transiently transfected cells to identify RNAi modulators. The second method uses cells that express luciferase-based reporters in a stable fashion. This assay can easily be conducted in 96-well plate format. Both methods can be used to identify novel proteins or small molecules that modulate RNAi activity.