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Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses [CUT&RUN]

ABSTRACT: In Drosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its 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. We find that EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. 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.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE202807 | GEO | 2022/09/12

REPOSITORIES: GEO

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Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses [RNA-seq]

Project description:In Drosophila, the ecdysone steroid hormone is essential for coordinating developmental timing across physically separated tissues. Ecdysone directly impacts genome function through its 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. We find that EcR DNA binding profiles are highly tissue-specific, and transgenic reporter analyses demonstrate that EcR plays a direct role in controlling enhancer activity. 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.

2022-09-12 | GSE202809 | GEO

Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses [FAIRE-seq]

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Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila

Project description:Ecdysone signaling has long been studied as a paradigm for how hormones can synchronize development events in tissues throughout the animal. At the genetic level, ecdysone acts through its receptor, EcR, which has been classically thought to act at a relatively small number of canonical, ecdysone-responsive genes which then go on to activate the effectors of cellular processes. However, in spite of the decades of work studying EcR, the understanding of how EcR promotes changes in gene expression genome-wide in vivo remains incomplete. To examine EcR’s role in promoting changes in gene expression, we use a tissue-specific GAL4 driver to knockdown EcR throughout wing development and perform RNAseq on both WT wings and EcR-RNAi wings at -6h after puparium formation (APF) and +6hAPF. We find that EcR is required to promote thousands of gene expression changes genome-wide. To determine whether EcR is directly effecting these changes, we perform CUT&RUN in wings to identify EcR binding sites genome-wide. We find that EcR directly binds thousands of sites genome-wide, including many genes important for wing development. Collectively, these data suggest that EcR does not only act the top of a signaling cascade, but, instead, directly effects the response to ecdysone at multiple levels.

2019-04-24 | GSE124254 | GEO

Drosophila Ecdysone Receptor Study

2008-05-01 | GSE9156 | GEO

Drosophila Ecdysone Receptor Study

Project description:We used the DamID method to systematically identify the binding sites of Ecdysone Receptor and its heterodimeric partner USP across the whole genome in Drosophila Kc cells. We find that the EcR sites are a subset of the USP sites and that only a proportion are ecdysone regulated from an accompanying ecdysone profiling study. The role of EcR/USP in the ecdysone network appears to be coordinated by the recruitment of many transcription factors as well as signaling molecules. Keywords: DamID, chromatin profiling, DNA microarray In this study we mapped the genomic binding sites of steroid hormone nuclear receptor EcR and USP in Kc167 cells using the DamID method. DamID involves the low level expression of a fusion protein consisting of DNA adenine methyltransferase (Dam) and a chromatin protein of interest. This fusion protein is targeted to the native binding sites of the chromatin protein, where Dam methylates adenines in the surrounding DNA. The methylated DNA fragments were isolated and amplified by selective PCR, labeled with a fluorescent dye and hybridized to whole genome tiling microarrays. In this study,experiments were done with samples obtained from independent experiments and include dye swaps.

2008-05-01 | E-GEOD-9156 | biostudies-arrayexpress

The ecdysone receptor promotes or suppresses proliferation according to ligand level

Project description:Steroid hormones control various cellular activities in a context-dependent manner. For example, ecdysone, which acts through a type II nuclear receptor, has seemingly opposite effects in Drosophila wing precursors, promoting proliferation during larval stages, and triggering proliferation arrest at pupariation. We find that wing precursors proliferate normally in the complete absence of the ecdysone receptor (EcR), whether ecdysone is present or not, suggesting that ecdysone overrides a default anti-proliferative activity of the receptor. By contrast, termination of proliferation by high concentration of 20E at the end of larval life requires ligand-induced transcriptional activation by the receptor. The switch from one mode of regulation to the other is determined by ligand level, as measured with a calibrated EcR transcriptional reporter and ex vivo proliferation assays. Accordingly, RNA Seq analysis uncovers distinct transcriptional responses to different doses of ecdysone. Some genes are only activated at high doses (high threshold targets) and likely to comprise genes that stop proliferation at pupariation, when ecdysone titres are high. We find that other target genes respond to all physiological concentrations of ecdysone. Some of these genes are known to promote proliferation and could therefore contribute to the pro-proliferation activity of low-level ecdysone. Finally, we show mathematically and with synthetic reporters that relatively simple combinations of regulatory elements can recapitulate the behaviour of both types of target genes.

2023-08-24 | GSE236166 | GEO

Finding binding sites for nuclear receptors in S2 Schneider cells

Project description:The subject of the current study is the finding of possible molecular partners of drosophila EcR receptor. The whole-genome experiments revealed that the sites of EcR receptor are partially overlapped with ERR binding sites. As ERR receptor specifically binds regulatory regions of glycolytic genes and genes of glycogen metabolism, the presence of EcR on ERR targets signifies involvement of the ecdysone signaling in regulation of carbohydrate metabolism.

2019-07-16 | GSE122810 | GEO

EcR mutant midgut comparison

Project description:Comparisons between EcR mutant midgut and a reference control sample from mixed-stage normal midgut Keywords = Drosophila, ecdysone, network, genomic, microarray, organogenesis, EcR, midgut, central nervous system, salivary gland, epidermis, imaginal disc, development Keywords: other

2003-07-23 | GSE540 | GEO

EcR mutant midgut comparison

2010-06-05 | E-GEOD-540 | biostudies-arrayexpress

Transcription profiling of human RKO cells after induction of KLF4 for different lengths of time

Project description:A stably transfected inducible system for KLF4 was established in RKO cells as previously described (Chen et al., 2001; Chen et al., 2003). This cell line, called EcR-RKO/KLF4, contains stably transfected receptors for the insect hormone, ecdysone (EcR), and a full-length mouse KLF4 cDNA driven by a promoter that responds to ecdysone and its analogue, ponasterone A. Cells were treated with 5 ÂµM ponasterone A (PA), for various time durations. To control for the experiment, the vehicle, ethanol, was added for the same periods of time.

2007-06-21 | E-GEOD-3113 | biostudies-arrayexpress

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