Gene expression is a tightly regulated process that eventually determines cell fate. The regulation of this process relies on short gene regulatory sequences, enhancers, whose activity fluctuates until the on or off state is fixed. Based on the G‐TRACE analysis system, we show here that a set of nervous system specific enhancers (elav, D42, OK6) have ectopic activity in epithelial tissues early in development. This ectopic activity is variable, unstable and mainly influenced by the primary sequence of the enhancer and the insertion site in the chromosome.
In addition, the LN2 enhancer from the sex lethal (sxl) gene showed sex dependent features in its ectopic expression. Although variable and unstable, the non‐canonical expression of enhancers seems to be regulated in terms of tissue and extent. The factors that determine enhancer activity are relevant for transgenic animal models and the engineering of biotechnology tools. As well as for the interpretation of many current developmental biology studies in which Gal4 lines are used. In addition, since all 12 neural enhancers analyzed here showed unstable expression, we argue that this general phenomenon may be relevant for evolutionary change.