The Core Promoter has an active role in interpreting patterning information

Abstract Precise spatiotemporal control of gene expression is conventionally attributed to distal enhancers. The extent to which different core promoters actively shape transcriptional output from enhancers remains unclear, especially in the context of genes that contain alternate promoters. We have explored these questions using the Drosophila grainy head ( grh ) locus, and tested the activities conferred by its alternate promoters in combination with a well characterised Notch responsive enhancer. We find that, of the alternate promoters tested, only the grh short promoter is competent to drive neuroblast-specific expression. Notably, when paired with identical enhancers, grh -short and grh -medium promoters drive distinct expression patterns. The activity of other core promoters, such as hsp70, is also selective. Together the results establish that the core promoter acts alongside enhancers to confer specificity and robustness on gene expression profiles.