Orateur
Description
Developmental enhancers are regulatory elements that establish precise spatio-temporal patterns of gene expression, yet how they selectively regulate one gene over its neighbors remains unclear. Current hypotheses suggest that such specificity arises from the 3D organization of the genome or from the sequence of the core promoter. Here, we provide evidence that the core promoter acts in concert with sequences directly upstream to it to provide such specificity.
To reach this conclusion, we first dissected the activity of the E3 enhancer of twist in Drosophila melanogaster. Although E3 was previously characterized as an embryonic mesodermal enhancer, our reporter assays revealed its surprisingly complex activity profile. E3 is active in tissues and developmental stages where twist is not expressed, including in non-mesodermal tissues derived from other germ layers, indicating that E3 is a pleiotropic enhancer. We further discovered that E3 drives the expression of at least three more unrelated (non-paralogous or not in the same pathway) genes, each in a different spatial and temporal context.
While E3 drives a broad and complex expression pattern, each of its target genes is only expressed in a particular spatio-temporal window. How is this achieved? We showed that these differences cannot be due to context-dependent chromatin looping or selective promoter accessibility. Instead, they arise from the action of each gene’s core promoter and promoter-proximal sequences. These sequences act as “gatekeepers” to restrict enhancer input into precise tissue- and stage-specific transcription, thus functioning as active interpreters rather than passive recipients of enhancer signals. We propose that promoter-proximal gatekeepers belong to an emerging class of non-canonical regulatory elements that provide a critical but under-appreciated layer of regulatory specificity within complex gene expression programs.