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Xrp1 governs the stress response program to spliceosome dysfunction

ABSTRACT: We investigated the changes in gene expression in response to reduced levels of Ecdysoneless (Ecd), and the role of Xrp1 in induction of transcriptional changes upon loss of Ecd in the developing wing disc of Drosophila. To do this we utilized the GAL4/UAS system to express UAS-ecd-RNAi alone and in combination with UAS-xrp1-RNAi in the nubbin-domain (nub-Gal4, UAS-mRFP, UAS-ecd-RNAi and nub-Gal4, UAS-mRFP, UAS-ecd-RNAi, xrp1-RNAi) of the wing disc and used nub-Gal4, UAS-mRFP wing discs as controls. We quantified transcriptomic expression analysis from four biological replicates for both experimental groups

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE213298 | GEO | 2024/01/31

REPOSITORIES: GEO

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Xrp1 governs the stress response program to spliceosome dysfunction

Project description:We investigated the changes in gene expression in response to reduced levels of Ecdysoneless (Ecd) in the developing wing disc of Drosophila. To do this we utilized the GAL4/UAS system to express UAS-ecd-RNAi in the nubbin-domain (nub-Gal4, UAS-mRFP, UAS-ecd-RNAi) of the wing disc and used Nub-Gal4/+ wing discs as controls. We quantified transcriptomic expression analysis from four biological replicates for both experimental groups

2024-01-31 | GSE203127 | GEO

Gene expression regulated by transcription factor MiT in Drosophila

Project description:To understand the role of MiT in Drosophila, we set out to identify critical gene targets by looking at changes in the WT transcriptome induced by either gain or loss of MiT function. Mutant hindgut and malpighian tubules provided loss-of function tissue and nub-Gal4-driven expression of MiT in the wing epithelium was used for gain-of-function. In the wing disc experiment, 543 genes were upregulated by exogenous MiT, and 359 genes were downregulated (>1.4 fold; P value < 0.01). In the larval HG+MT, 897 genes were downregulated and 898 were upregulated (>1.4 fold; P value < 0.01) after MiT. Among these genes, 85 were both upregulated in wing discs and downregulated in mutant HG+MT, and are the common genes that regulated by MiT in both tissues. We set out to identify potential targets of MiT by comparing the transcriptional profiles of wing discs with and without MiT overexpression (nub-Gal4 UAS-MiT versus nub-Gal4), and separately the profiles of HG+MT tissue from WT and MiT mutant (MiTTZ2/Df(4)TZ). Then, we focused on genetic loci that were upregulated by gain of MiT in the wing and downregulated by loss of MiT in the HG+MT.

2015-08-01 | E-GEOD-58416 | biostudies-arrayexpress

Gene expression changes in Su(H) induced wing disc hyperplasia

Project description:The outcome of Notch activation of proliferation depends on cellular context. In Drosophila wing discs Notch pathway overactivation results in hyperplasia. To understand the mechanisms we have used genomic strategies to indetify the Notch-S(H) target genes directly regulated in wing disc hyperplasia. These data are the results from expression profiling the RNAs from hyperplastic wing discs overexpressing Su(H). Direct comparison of Giant third instar lavae wing imaginal disc (UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver) vs control (UAS-NLS-GFP expressed by the patched[559.1]-Gal4 driver). 3 Biological replicates, the 3rd replicate was performed as a dye-swap.

2013-12-31 | E-GEOD-41427 | biostudies-arrayexpress

Gene expression changes in Nicd induced wing disc hyperplasia

Project description:The outcome of Notch proliferation on proliferation depends on the context. In Drosophila wing imaginal discs Notch activation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand te underlying mechanisms we have used genomic strategies to identify the Notch-Su(H) target genes during wing discs hyperplasis. these data are the results from expression profiling the RNAs from hyperplastic wing discs overexpressing Nicd. Direct comparison of third instar lavae wing imaginal disc Nicd (abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B) vs control (abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with FRT82B ). 4 Biological replicates, the 2nd replicate was performed as a dye-swap.

2013-12-31 | E-GEOD-41428 | biostudies-arrayexpress

Su(H) bound regions in Nicd induced wing-disc hyperplasia

Project description:The outcome of Notch activation on proliferation depends on cellular context. In Drosophila wing discs Notch activation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand the underlying mechanisms we have used genomic strategies to identify the Notch-Su(H) target genes directly activated during wing disc hyperplasia. These data are the results from ChIP-Chip experiments to identify genomic regions occupied by Su(H) in hyperplastic Nicd-expressing Drosophila wing discs. 2 independent replicates; Immunoprecipitation perfomed with Su(H) antibody on chromatin isolated from wing discs overexpressing Nicd (abxUbxFLPase; Act>y>Gal4, UAS GFP; FRT82B tubGal80 with UAS-Nicd; FRT82B) and compared to the total input DNA.

2013-12-31 | E-GEOD-41426 | biostudies-arrayexpress

SmD3 protein interactome in Drosophila melanogaster wing imaginal discs

Project description:Screening for binding partners of the splicing factor SmD3 and changes in interaction upon depletion of the protein Ecdysoneless (Ecd) in the nubbin domain of third-instar larval wing imaginal discs.

2021-09-09 | PXD019761 | Pride

The Drosophila functional Smad suppressing element fuss, a homologue of the human Skor genes, retains prooncogenic properties of the Ski/Sno family

Project description:To detect dysregulated genes upon overexpression of the functional smad suppressing element (fuss) in Drosophila melanogaster, we overexpressed fuss with the GMR-Gal4 line in developing eye discs and with the nub-Gal4 driverline in developing wing discs. The offspring of crossings of the driver lines GMR-Gal4 or nub-Gal4 with w1118 were used as controls. Libraries were generated from total RNA and sequenced on a Illumina HiSeq 1000. Via differential gene expression analysis we discovered the genes which are dysregulated by fuss overexpression compared to controls.

2022-01-05 | GSE165738 | GEO

Gene expression regulated by transcription factor MiT in Drosophila

2015-08-01 | GSE58416 | GEO

Su(H) bound regions in Su(H) induced wing-disc hyperplasia

Project description:The outcome of Notch activation on proliferation depends on cellular context. In Drosophila wing discs Notch activation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand the underlying mechanisms we have used genomic strategies to identify the Notch-Su(H) target genes directly activated during wing disc hyperplasia. These data are the results from ChIP-Chip experiments to identify genomic regions occupied by Su(H) in hyperplastic Su(H)-expressing Drosophila wing discs. 3 independent replicates. Immuno Precipitation perfomed with Su(H) antibody on chromatin isolated from wing discs overexpressing Su(H) (UAS-GFP:Su(H) expressed by the patched[559.1]-Gal4 driver) and compared to the total input DNA. Samples from replicate #1 and #2 were labelled with Cy5 and replicate #3 as dye-swap with Cy3.

2013-12-31 | E-GEOD-41425 | biostudies-arrayexpress

Microarray comparison of anterior and posterior Drosophila wing imaginal disc cells

Project description:Signaling between cells in the Anterior (A) and Posterior (P) compartments directs Drosophila wing disc development and is dependent on expression of the homeodomain transcription factor Engrailed (En) in P cells. Downstream of en, posteriorly expressed Hedgehog (Hh) protein signals across the A/P border to establish a developmental organizer that directs pattern formation and growth throughout the wing primordium. Here we extend investigations of the processes downstream of en by using expression array analysis to compare A and P cells. 102 candidate genes were identified that express differentially in the A and P compartments; four were characterized: Stubble (Sb) expression is restricted to A cells due to repression by en. CG15905, CG16884, and CG10200/hase und igel (hui) are expressed in A cells downstream of Hh signaling; and RNA interference for hui, Stubble, and CG16884 revealed that each is essential to wing development. We carried out a global screen for genes with compartment-specific expression using expression array hybridization to compare transcript levels in A and P wing disc cells. GFP-labeled wing imaginal discs (ptc-Gal4/UAS-GFP and hh-Gal4/UAS-GFP) were micro-dissected under a fluorescence dissecting microscope. RNA isolation, amplification and microarray procedures were previously described (Klebes et al., 2002; Klebes et al., 2005; Klebes and Kornberg, 2008). In brief, hybridization probes were generated by two rounds of T7-catalyzed linear RNA amplification and labeled with Cy3 and Cy5 dyes. Reciprocally labeled probes (M-bM-^@M-^Xdye flipM-bM-^@M-^Y) were hybridized to custom produced glass microarrays (GPL2581) that contained approximately 14,000 100-600 bp exon sequences that were generated by PCR. Signal intensities were collected with a GenePix 4000B Scanner and processed with GenePix software (Molecular Devices) and global median normalized with NOMAD (http://ucsf-nomad.sourceforge.net/).

2013-05-04 | E-GEOD-46601 | biostudies-arrayexpress

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