During Drosophila development, regulation of transcriptional activity is required to control coordinated and rapid tissue morphogenesis. One such mechanism is the use of shadow enhancers, whereby two or more enhancers regulate the same gene with similar spatiotemporal activity. Shadow enhancers are thought to provide robustness to transcriptional patterning, although the biological significance is not clear. In this study, Peter Whitney, Christine Rushlow and colleagues aim to address this by characterising transcription of the short gastrulation (sog) gene during Drosophila blastoderm development. sog is regulated by a shadow enhancer pair consisting of upstream distal and intronic proximal enhancers. Using CRISPR editing, the authors selectively remove one or both enhancers and assess subsequent changes in sog expression in the developing blastoderm. Here, each enhancer differs in sog spatial expression, timing of activation and transcriptional kinetics. Interestingly, whilst activation of both enhancers produces an additive effect in overlapping domains, repression of the proximal enhancer of sog by Snail (Sna) is augmented in the presence of the distal domain, suggesting a synergistic effect. Furthermore, altering sog expression by perturbing shadow enhancers results in changes in dorso-ventral patterning. Together, these results suggest that shadow enhancers are not redundant, but regulate different transcriptional parameters, allowing tuning of selective aspects of gene expression during development.
