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Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE149721 | GEO | 2020/06/30

REPOSITORIES: GEO

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RNA-sequencing following Psi or Myc knockdown in Drosophila larval wing tissue

Project description:RNA-seq analysis of gene expression changes following the depletion of P-element somatic inhibitor (Psi) or Myc via RNAi in wing discs of mid-third instar larvae, compared with control. Differential splicing analysis was also performed on the Psi RNAi dataset.

2020-06-30 | GSE149719 | GEO

Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue

Project description:Identification of genome-wide binding sites of Psi, Myc and Pol and gene expression following Psi or Myc knockdown in Drosophila larval wing tissue

| PRJNA629796 | ENA

RNA-sequencing following Psi or Myc knockdown in Drosophila larval wing tissue

Project description:RNA-sequencing following Psi or Myc knockdown in Drosophila larval wing tissue

| PRJNA629805 | ENA

Identification of genome-wide binding sites of Psi, Myc and Pol in Drosophila imaginal wing discs using Targeted DamID

Project description:Targeted DamID was performed to identify binding targets of P-element somatic inhinitor (Psi), Myc and RNA Polymerase (using the RpII18 subunit common to all 3 polymerases). Scalloped(sd)-GAL4 was used to restrict expression to the wing disc.

2020-06-30 | GSE149718 | GEO

Identification of genome-wide binding sites of Psi, Myc and Pol in Drosophila imaginal wing discs using Targeted DamID

Project description:Identification of genome-wide binding sites of Psi, Myc and Pol in Drosophila imaginal wing discs using Targeted DamID

| PRJNA629803 | ENA

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila.

Project description:BackgroundInsulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified.ResultsWe used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites.ConclusionTaken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture.

| S-EPMC2374998 | biostudies-literature

Psi promotes Drosophila wing growth via direct transcriptional activation of cell cycle targets and repression of growth inhibitors.

Project description:The first characterised FUSE Binding Protein family member, FUBP1, binds single-stranded DNA to activate MYC transcription. Psi, the sole FUBP protein in Drosophila, binds RNA to regulate P-element and mRNA splicing. Our previous work revealed pro-growth functions for Psi, which depend, in part, on transcriptional activation of Myc. Genome-wide functions for FUBP family proteins in transcriptional control remain obscure. Here, through the first genome-wide binding and expression profiles obtained for a FUBP family protein, we demonstrate that, in addition to being required to activate Myc to promote cell growth, Psi also directly binds and activates stg to couple growth and cell division. Thus, Psi knockdown results in reduced cell division in the wing imaginal disc. In addition to activating these pro-proliferative targets, Psi directly represses transcription of the growth inhibitor tolkin (tok, a metallopeptidase implicated in TGFβ signalling). We further demonstrate tok overexpression inhibits proliferation, while tok loss of function increases mitosis alone and suppresses impaired cell division caused by Psi knockdown. Thus, Psi orchestrates growth through concurrent transcriptional activation of the pro-proliferative genes Myc and stg, in combination with repression of the growth inhibitor tok.

| S-EPMC10110491 | biostudies-literature

Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs.

Project description:BACKGROUND: Regeneration is the ability of an organism to rebuild a body part that has been damaged or amputated, and can be studied at the molecular level using model organisms. Drosophila imaginal discs, which are the larval primordia of adult cuticular structures, are capable of undergoing regenerative growth after transplantation and in vivo culture into the adult abdomen. RESULTS: Using expression profile analyses, we studied the regenerative behaviour of wing discs at 0, 24 and 72 hours after fragmentation and implantation into adult females. Based on expression level, we generated a catalogue of genes with putative role in wing disc regeneration, identifying four classes: 1) genes with differential expression within the first 24 hours; 2) genes with differential expression between 24 and 72 hours; 3) genes that changed significantly in expression levels between the two time periods; 4) genes with a sustained increase or decrease in their expression levels throughout regeneration. Among these genes, we identified members of the JNK and Notch signalling pathways and chromatin regulators. Through computational analysis, we recognized putative binding sites for transcription factors downstream of these pathways that are conserved in multiple Drosophilids, indicating a potential relationship between members of the different gene classes. Experimental data from genetic mutants provide evidence of a requirement of selected genes in wing disc regeneration. CONCLUSIONS: We have been able to distinguish various classes of genes involved in early and late steps of the regeneration process. Our data suggests the integration of signalling pathways in the promoters of regulated genes.

| S-EPMC2939566 | biostudies-literature

The miRNA machinery targets Mei-P26 and regulates Myc protein levels in the Drosophila wing.

Project description:MicroRNAs (miRNAs) have been implicated in cell-cycle regulation and in some cases shown to have a role in tissue growth control. Depletion of miRNAs was found to have an effect on tissue growth rates in the wing primordium of Drosophila, a highly proliferative epithelium. Dicer-1 (Dcr-1) is a double-stranded RNAseIII essential for miRNA biogenesis. Adult cells lacking dcr-1, or with reduced dcr-1 activity, were smaller than normal cells and gave rise to smaller wings. dcr-1 mutant cells showed evidence of being susceptible to competition by faster growing cells in vivo and the miRNA machinery was shown to promote G(1)-S transition. We present evidence that Dcr-1 acts by regulating the TRIM-NHL protein Mei-P26, which in turn regulates dMyc protein levels. Mei-P26 is a direct target of miRNAs, including the growth-promoting bantam miRNA. Thus, regulation of tissue growth by the miRNA pathway involves a double repression mechanism to control dMyc protein levels in a highly proliferative and growing epithelium.

| S-EPMC2876971 | biostudies-literature

Expression data of Drosophila 3rd instar larval wing discs taken from strains selected for wing shape.

Project description:We measured gene expression across the whole genome in a panel of lines selected for a wing shape trait (angular offset). The lines were created in separate experiments, originating from two widely separated populations, and including multiple replicates of one population, but all were created using the same selection regime and trait. Here we evaluate the data with two objectives: 1) to identify candidate wing shape genes for future testing and validation, and 2) to assess variation among lines in the outcome of identical selection regimes We used microarrays to detail the global programme of gene expression underlying the phenotypic differences among strains selected for wing shape angular offset. Keywords: strain comparison

2008-01-02 | GSE9107 | GEO

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