The ecdysone pathway was among the first experimental systems employed to study the
impact of steroid hormones on the genome. In Drosophila and other insects, ecdysone
coordinates developmental transitions, including wholesale transformation of the larva
into the adult during metamorphosis. Like other hormones, ecdysone controls gene expression
through a nuclear receptor, which functions as a ligand-dependent transcription factor.
Although it is clear that ecdysone elicits distinct transcriptional responses within
its different target tissues, the role of its receptor, EcR, in regulating target
gene expression is incompletely understood. In particular, EcR initiates a cascade
of transcription factor expression in response to ecdysone, making it unclear which
ecdysone-responsive genes are direct EcR targets. Here, we use the larval-to-prepupal
transition of developing wings to examine the role of EcR in gene regulation. Genome-wide
DNA binding profiles reveal that EcR exhibits widespread binding across the genome,
including at many canonical ecdysone response genes. However, the majority of its
binding sites reside at genes with wing-specific functions. We also find that EcR
binding is temporally dynamic, with thousands of binding sites changing over time.
RNA-seq reveals that EcR acts as both a temporal gate to block precocious entry to
the next developmental stage as well as a temporal trigger to promote the subsequent
program. Finally, transgenic reporter analysis indicates that EcR regulates not only
temporal changes in target enhancer activity but also spatial patterns. Together,
these studies define EcR as a multipurpose, direct regulator of gene expression, greatly
expanding its role in coordinating developmental transitions.