TY - JOUR T1 - Single molecule fluorescence <em>in situ</em> hybridisation for quantitating post-transcriptional regulation in <em>Drosophila</em> brains JF - bioRxiv DO - 10.1101/128785 SP - 128785 AU - Lu Yang AU - Joshua S. Titlow AU - Darragh Ennis AU - Carlas Smith AU - Jessica Mitchell AU - Florence L. Young AU - Scott Waddell AU - David Ish-Horowicz AU - Ilan Davis Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/21/128785.abstract N2 - RNA in situ hybridization can be a powerful method to investigate post-transcriptional regulation, but analysis of intracellular mRNA distributions in thick, complex tissues like the brain poses significant challenges. Here, we describe the application of single-molecule fluorescent in situ hybridization (smFISH) to quantitate primary transcription and post-transcriptional regulation in whole-mount Drosophila larval and adult brains. Combining immunofluorescence and smFISH probes for different regions of a single gene, i.e., exons, 3’UTR, and introns, we show examples of a gene that is regulated post-transcriptionally and one that is regulated at the level of transcription. We also show that the method can be used to co-visualise a variety of different transcripts and proteins in neuronal stems cells as well as deep brain structures such as mushroom body neuropils. Finally, we introduce the use of smFISH as asensitivealternative to conventional antibody labelling to mark specific neural stem cell populations in the brain. ER -