UC San Diego

Understanding the molecular mechanisms responsible for various biological phenomena often involves demonstrating necessity or sufficiency of gene function in specific cells. Such studies gain strength from confirmation that molecules of interest are normally expressed where they are hypothesized to function. However, such efforts are often limited by the availability of high quality probes. To overcome this problem in vertebrates, RNAscope was recently developed as a high-sensitivity alternative to in situ hybridization. In the present study I describe the development of RNAscope for use in whole mount adult fly brains. I demonstrate that RNAscope can achieve high signal, low background and good spatial resolution of mRNAs. I further demonstrate that RNAscope can be used in multiplex format for simultaneous detection of up to three types of transcripts, or for a single type of transcript combined with immunohistochemistry. Lastly, I show that RNAscope can be used to assay the spatial distinctness and plasticity of neurotransmitter identity in the nervous system. Collectively these results should open up new opportunities for quantitative gene expression studies in the adult fly brain.