Abstract: Our understanding of gene function in model organisms has increased dramatically over the last 30 years utilizing new reverse genetic techniques to manipulate gene expression. Selectively changing the expression of a gene in an otherwise wild-type organism allows for much greater understanding of that gene’s function and downstream effects on phenotypes than mutant analysis alone. This is especially important for studying essential genes, pleiotropic genes and genes with tissue, stage, sex or enviroment specific effects. In the Drosophila melanogaster model system, use of the GAL4-UAS system is one such genetic tool for experimental manipulation of gene expression that is used in a large number of studies to date. A recent improvement added a hormone-induced (mifepristone) GAL4 expression system called GeneSwitch making it even more tractable and applicable to many experimental questions. Because the GAL4-UAS system was taken from yeast, mifepristone from mammals and both used in D. melanogaster, it is largely considered to act specifically with few if any off-target effects. To test the effects of GAL4 protein expression and mifepristone exposure on genome-wide gene expression, we performed RNA sequencing (RNA-seq) and identified numerous D. melanogaster genes that are significantly differentially expressed in response to GAL4 and RU486. Our study provides evidence that use of the GeneSwitch GAL4-UAS system requires effective control experiments and provides suggestions for future studies to maximize the utility of this genetic toolkit.
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