Employing proximity-dependent ligation techniques to estimate EcR/Usp molecular partners in Drosophila
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ABSTRACT:
PROVIDER: PRJNA579279 | ENA |
REPOSITORIES: ENA
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Project description:The subject of the current study is the finding of possible molecular partners of Drosophila EcR receptor. Two labelling enzymes (BioID2 and APEX2) were fused to EcR or Usp to biotin label the surrounding proteins. All fused proteins were expressed using the Act5C promoter in Drosophila S2 cells. To ensure functionality of the generated proteins, we verified their ability to bind EcR and Usp sites in the Drosophila genome with the ChIP-Seq. Our results demonstrate that EcR and Usp fusions can be recruited to genomic sites endogenous for the EcR/Usp proteins. Conversely, unfused BioID2 and APEX2 enzymes do not bind to EcR/Usp sites. A more in-depth study was conducted to clarify the association of EcR/Usp with one of the detected proteins, CP190, a well-described cofactor of Drosophila insulators. ChIP-Seq experiments revealed an enrichment of CP190 binding on transcription start and end sites of 20E-dependent genes but not at EcR/Usp-bound enhancers.
2020-03-17 | GSE139316 | GEO
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
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
2010-06-05 | E-GEOD-540 | biostudies-arrayexpress
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
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 | GSE202808 | GEO
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 | GSE202807 | GEO
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
Project description:We compared ecdysone receptor (EcR)-dependent gene expression in the Drosophila fat body on 0.15 M sucrose and 0.5 M sucrose high-sugar diets in order to gain insight into the role of this gene during caloric overload. Phenotypic analyses showed an increased severity of EcR RNAi phenotypes with increasing dietary sugar concentration. Because EcR is a transcription factor, we performed RNA-seq studies to identify transcriptional targets that might underlie insulin resistance downstream of EcR RNAi.
2018-02-10 | GSE110432 | GEO
Project description:In Drosophila, male-specific FRU (FRUM) is required to establish the potential for courtship behaviors, but the downstream effectors of FRUM during development are largely unknown. A microarray-based approach identified genes that are differentially expressed as a consequence of FRUM in pupae, in both whole body and CNS tissues. Genes were also identified that are sex-differentially expressed in CNS tissues. The FRUM-regulated sets were significantly overrepresented with genes also regulated by the ecdysone regulatory pathway. Two EcR isoforms (EcRA and EcRB1) are expressed in FRUM-expressing neurons during distinct periods of metamorphosis. Males with abrogated EcRA function in FRUM-expressing neurons aggressively court other males. Transcriptional profiles of mutants with abrogated EcRA function in the fru circuit demonstrate that EcR and FRUM regulate common gene sets, including the early gene broad. These results demonstrate a novel role for EcR in specifying male courtship behavior through its actions specifically in the FRUM neural circuitry.
2009-09-21 | GSE11752 | GEO
Project description:In Drosophila, male-specific FRU (FRUM) is required to establish the potential for courtship behaviors, but the downstream effectors of FRUM during development are largely unknown. A microarray-based approach identified genes that are differentially expressed as a consequence of FRUM in pupae, in both whole body and CNS tissues. Genes were also identified that are sex-differentially expressed in CNS tissues. The FRUM-regulated sets were significantly overrepresented with genes also regulated by the ecdysone regulatory pathway. Two EcR isoforms (EcRA and EcRB1) are expressed in FRUM-expressing neurons during distinct periods of metamorphosis. Males with abrogated EcRA function in FRUM-expressing neurons aggressively court other males. Transcriptional profiles of mutants with abrogated EcRA function in the fru circuit demonstrate that EcR and FRUM regulate common gene sets, including the early gene broad. These results demonstrate a novel role for EcR in specifying male courtship behavior through its actions specifically in the FRUM neural circuitry. All microarrays were dual channel with direct comparisons of male versus female, wild type versus mutant, or experimental versus control. For each experiment, four to eight independent biological samples were analyzed using a dye-swap design. Samples consisted of whole body pupae or dissected CNS collected either at 0 hour After Pupal Formation (APF), 48 hour APF, or 0-24 hour adults.
2009-09-21 | E-GEOD-11752 | biostudies-arrayexpress