Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736303 | ENA |
REPOSITORIES: ENA
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Project description:The intricate regulation of gut homeostasis is dependent on a fine-tuned regulation of the host defense to avoid detrimental immune activation. We have previously applied Drosophila to show that mutants of the short isoform of the POU transcription factor Pdm1/nubbin (nub) have a constitutively active immune response, altered gut microbiota and shortened lifespan. Here, we studied the role of Nub-PB, the larger isoform derived from the nub gene. Both Nub protein isoforms contain the C-terminal POU and Homeo domains whereas Nub-PB encompasses a longer N-terminal end. Microarray analysis revealed that targeted misexpression of Nub-PB in immunocompetent organs triggers a strong and broad expression of immune genes in a comparable manner to Nub-PD mutants. The seemingly antagonistic functions of the two isoforms were confirmed by co-overexpression of both forms, which resulted in normal expression levels of antimicrobial peptide (AMP) genes. Cell line experiments demonstrated a synergistic activation of AMPs by the combined transfection with Nub-PB and NF-kB/Relish. In agreement with this finding, Relish was indispensable for Nub-PB-driven diptericin expression, suggesting that Nub-PB acts as a Relish co-activator. Moreover, Nub-PB triggered strong expression of gut-specific drosomycin-like genes in a JAK/STAT pathway-dependent manner. Using RNA interference, we found that Nub-PB influences antimicrobial peptide expression in gut but not fat body tissues. Moreover, Nub-PB expression levels in gut enterocytes correlated with the gut bacterial load as well as host lifespan, suggesting a profound role in host immunity. Surprisingly, Nub-PB-overexpression caused a hypersensitive infection phenotype as flies succumbed within 24 h to orally administered Erwinia carotovora carotovora 15. Nub-PB thus appears to be a central activator of gut immunity that requires tight control, executed at least in part, by isoform antagonism to maintain immune homeostasis.
2018-03-10 | GSE100604 | GEO
Project description:The microbial population that live within the gut of animals influences their physiology. We used axenic and recolonized flies to identify genes whose expression is modulated by the presence of a bacterial flora in the gut. We identified several up regulated genes, most of which are described as enriched in the midgut, and related either to immunity or to metabolism. This work also suggests that most microbiota regulated genes are Relish dependent.
2014-03-26 | GSE56173 | GEO
Project description:The microbial population that live within the gut of animals influences their physiology. We used axenic and recolonized flies to identify genes whose expression is modulated by the presence of a bacterial flora in the gut. We identified several up regulated genes, most of which are described as enriched in the midgut, and related either to immunity or to metabolism. This work also suggests that most microbiota regulated genes are Relish dependent. We raised axenic Flies and either : (1) kept them germ free or (2) recolonized their environment with a set of 4 known commensal bacteria of lab-raised drosophila (Commensalibacter intestini, Lactobacillus plantarum, Lactobacillus brevis, Acetobacter pomorum). Flies were maintained in their respective (axenic or recolonized) environment from emergence to 7 days of age. Then females were collected, and total RNA extraction was performed on groups of 20 whole bodies.
2014-03-26 | E-GEOD-56173 | biostudies-arrayexpress
Project description:This project’s aim was to compare the transcriptional profiles of olfactory sensory neurons in Drosophila melanogaster in order to identify novel genes that specify neuron-specific functions/phenotypes or may otherwise be involved in the development of the olfactory system. The isolation of sufficient numbers of intact olfactory sensory neurons (OSN) from the antenna of Drosophila melanogaster has so far limited single-cell transcriptomic approaches being applied to the adult fly antenna. Targeted DamID (TaDa) provides an alternative approach for profiling transcriptional activity in a cell-specific manor that bypasses the need for isolating OSN. Using the Gal4/UAS system, we applied TaDa to seven OSN populations and compared differences in Pol II occupancy for genes across these datasets.
2021-03-17 | E-MTAB-8935 | biostudies-arrayexpress
Project description:Cell-type specific transcriptional profiling is key to understanding cell fate specification, function and adaptation. This is particularly advantageous for studying specific cell types from complex tissues. In this study, we have used ‘TaDa’ (Targeted DamID), a technique that enables profiling of rare cell populations or cells difficult to isolate by conventional methods. Furthermore, TaDa profiling occurs in vivo and isn’t subject to artefacts arising from disruption of the tissues and cell sorting. Here, we profile the genome-wide binding of RNA polymerase II (Pol II) in terminal tracheal cells (TTCs) that are tightly associated with intestinal tissue from adult Drosophila. We compare terminal tracheal transcriptome from control to regenerative intestine in adult fly. Our data reveal new tracheal intrinsic mechanisms that are essential, in this gut-trachea communication, for regulating intestinal stem cell proliferative activity in context of damage. Our study represents the first analysis of terminal tracheal cell transcriptional profiling in context of homeostasis and regenerative adult intestine and provide new insight into the regulatory programs that underlie the complex interactions between gut-neighbourhood.
2020-12-21 | GSE163570 | GEO
Project description:Targeted DamID (TaDa) is an increasingly popular method of generating cell-type specific DNA binding profiles in vivo. Although sensitive and versatile, TaDa requires the generation of new transgenic fly lines for every protein that is profiled, which is both time-consuming and costly. Here, we describe the FlyORF-TaDa system for converting an existing FlyORF library of inducible open reading frames (ORFs) to TaDa lines via a genetic cross, with recombinant progeny easily identifiable by eye colour. Profiling the binding of the H3K36me3-associated chromatin protein MRG15 in larval neural stem cells using both FlyORF-TaDa and conventional TaDa demonstrates that new lines generated using this system provide accurate and highly-reproducible DamID binding profiles. Our data further show that MRG15 binds to a subset of active chromatin domains in vivo. Courtesy of the large coverage of the FlyORF library, the FlyORF-TaDa system enables the easy creation of TaDa lines for 74% of all transcription factors and chromatin modifying proteins within the Drosophila genome.
2021-01-31 | GSE159632 | GEO
Project description:To identify genes regulated by Relish in both the absence and presence of TBI in Drosophila, we compared genome-wide mRNA expression of control flies, as well as flies that were heterozygous or homozygous for a null allele of relish with and without injury.
2020-08-29 | GSE157102 | GEO
Project description:Cell-type specific transcriptional profiling is key to understanding cell fate specification and function. In order to achieve this it has been necessary, to date, to isolate specific cell types from complex tissues. We have developed 'TaDa', a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation or affinity purification. The method is simple, sensitive, highly reproducible and is in principle transferable to any model system. Here we show that TaDa can be used to identify transcribed genes in a cell-type specific manner. We profile the genome-wide binding of RNA polymerase II (Pol II) in adjacent, clonally related neural stem cells in intact Drosophila brains. Our data reveal the activity of non-canonical metabolic pathways in proliferating neuroepithelial cells, and highlight a possible role for the retinal determination gene regulatory network in patterning neural stem cell fates. We also identify temporal differences in the activity of signalling pathways that control neuroepithelial cell fate by profiling Pol II occupancy at two different stages of brain development. Using RNA Pol II TaDa to profile, in a cell-type specific manner, the transcriptional state of neuroepithelial cells at two stages of larval brain development. Closely related asymmetrically dividing neural stem cells (neuroblasts) were also profiled, in order to compare the transcriptomes of two different types of neural stem cells. 3 biological relicates were performed for 3rd instar neuroepithelial cells (with one dye-swap). 2 biological relicates were performed for 3rd instar neuroblasts (with dye-swap). 2 biological relicates were performed for 1st instar neuroepithelial cells (with dye-swap). As additional supporting evidence for the Pol II TaDa technique, 2 biological relicates were performed for 3rd instar salivary glands (with dye-swap) in order to compare with previous Pol II-ChIP data for this tissue [PMID 22821985].
2013-06-21 | E-GEOD-46803 | biostudies-arrayexpress
Project description:Integration of metabolic, stress and immune responses plays a fundamental role during animal development to maintain energy homeostasis while ensuring growth and proper developmental timing. Perturbation of metabolic and immune signaling circuits has detrimental consequences to animal development including growth retardation, organ malfunction and emergence of the metabolic syndrome. Here, we demonstrate that the Drosophila basic region-leucine zipper (bZIP) protein, Activating transcription factor 3 (Atf3), safeguards a balance of metabolic and immune system responses during fly development. Loss of Atf3 function results in lethality during late-larval and pupal stages. Atf3-deficient larvae exhibit phenotypes resembling the metabolic syndrome in mammals. Excessive accumulation of lipids in the larval fat body and gut is accompanied by altered expression of genes involved in lipid metabolism. Moreover, the fat body of atf3 mutants becomes infiltrated by hemocytes. The major pro-inflammatory pathways signaling through JNK and Imd are hyperactivated in atf3 mutants, causing ectopic expression of antimicrobial peptide genes. Suppression of the immune response, achieved by reducing the gene dose of the transcription factors FOXO or NF-kappaB/Relish, significantly improves lipid metabolism and normalizes gene expression profile of atf3 mutants. In addition, heterozygosity of relish partially rescues lethality of the atf3 mutants. Our data thus identify Atf3 as an essential player that links metabolic and immune system homeostasis during animal development. Examination of mRNA levels from four genotypes of male, 3rd instar Drosophila melanogaster larvae. mRNA levels from four genotypes relative to y w control were determined using two biological replicates per genotype. Genome build: BDGP R5/dm3, April 2006
2012-11-05 | E-GEOD-36377 | biostudies-arrayexpress