Problems associated with reporter assays in RNAi studies

Reporter assays represent a facile tool for studies of RNA interference and are routinely used in functional tests or mechanistic studies of siRNAs and miRNAs. Unfortunately some reporter assays were developed without careful consideration when they were adopted from studies of transcriptional regulation using promoter-reporter gene fusions. Here we report on some problems in the use of reporter systems for studies of RNA interference and make some suggestions for avoiding such problems in future studies.