Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development

How temporal cues combine with spatial inputs to control gene expression during development is poorly understood. Here, we test the hypothesis that the Drosophila transcription factor E93 controls temporal gene expression by regulating chromatin accessibility. Precocious expression of E93 early in wing development reveals that it can simultaneously activate and deactivate different target enhancers. Notably, the precocious patterns of enhancer activity resemble the wild-type patterns that occur later in development, suggesting that provision of E93 alters the competence of enhancers to respond to spatial cues. Genomic profiling reveals that precocious E93 expression is sufficient to regulate chromatin accessibility at a subset of its targets. These accessibility changes mimic those that normally occur later in development, indicating that precocious E93 accelerates the wild-type developmental program. Further, we find that target enhancers that do not respond to precocious E93 in early wings become responsive after a developmental transition, suggesting that parallel temporal pathways work alongside E93. These findings support a model wherein E93 expression functions as an instructive cue that defines a broad window of developmental time through control of chromatin accessibility. Overall design: FAIRE-seq from Drosophila 3LW wings precociously expressing HA-tagged E93 under control of a wing-specific driver (labeled "E93GOF" below). ChIP-seq against precociously expressed HA-tagged E93 in third-instar wandering (3LW) wing discs; includes a negative control ChIP experiment from wing discs containing the GAL4 driver but not the UAS-E93-3xHA transgene (labeled "VgControl" below). We compare these data to a developmental timecourse of chromatin accessibility as measured by FAIRE-seq in wild-type and E93-mutant wing discs and ChIP-seq for a GFSTF-tagged allele of E93 in otherwise wild-type 24hAPF pupal wings. This series includes re-analyzed samples from: GSE38727, GSE97956 and GSE131981.