Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses

Abstract

Steroid hormones perform diverse biological functions in developing and adult animals. However, the mechanistic basis for their tissue specificity remains unclear. In Drosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its nuclear receptor, a heterodimer of the EcR and Usp proteins. Ligand binding to EcR triggers a transcriptional cascade, including activation of a set of primary response transcription factors. The hierarchical organization of this pathway has left the direct role of EcR in mediating ecdysone responses obscured. Here, we investigate the role of EcR in controlling tissue-specific ecdysone responses, focusing on two tissues that diverge in their response to rising ecdysone titers: the larval salivary gland, which undergoes programmed destruction, and the wing imaginal disc, which initiates metamorphosis. We find that EcR functions bimodally, with both gene repressive and activating functions, even at the same developmental stage. EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. Finally, despite a strong correlation between tissue-specific EcR binding and tissue-specific open chromatin, we find that EcR does not control chromatin accessibility at genomic targets. We conclude that EcR contributes extensively to tissue-specific ecdysone responses. However, control over access to its binding sites is subordinated to other transcription factors. SignificanceHormones affect an incredible array of biological processes in both normal development and in disease. In insects, the steroid hormone ecdysone controls processes ranging from neuronal diversification to morphogenesis. Despite its importance, the mechanisms through which ecdysone generates wide-ranging yet tissue-specific responses remain incompletely understood. Like many hormones, ecdysone triggers a cascade of gene expression. At the top of this hierarchy is a nuclear receptor, EcR, which functions both as a hormone receptor and as a transcription factor. However, EcR is not the only transcription factor that functions in the ecdysone cascade; multiple other transcription factors are induced by ecdysone. As a result, the extent to which EcR plays a direct role in regulating tissue-specific responses to ecdysone remains unclear.