Genome wide analysis of self-renewal in Drosophila neural stem cells by transgenic RNAi
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Anja Fischer
PROVIDER: E-MEXP-3112 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The balance between stem cell self-renewal and differentiation is precisely controlled to ensure tissue homeostasis and prevent tumorigenesis. Here we use genome-wide transgenic RNAi to identify 620 genes potentially involved in controlling this balance in Drosophila neuroblasts. We quantify all phenotypes and derive measurements for proliferation, lineage, cell size, and cell shape. We identify a set of transcriptional regulators essential for self-renewal and use hierarchical clustering and integration with interaction data to create functional networks for the control of neuroblast self-renewal and differentiation. Our data identify key roles for the chromatin remodeling Brm complex, the spliceosome, and the TRiC/CCT-complex and show that the alternatively spliced transcription factor Lola and the transcriptional elongation factors Ssrp and Barc control self-renewal in neuroblast lineages. As our data are strongly enriched for genes highly expressed in murine neural stem cells, they are likely to provide valuable insights into mammalian stem cell biology as well.
| S-EPMC3093620 | biostudies-literature
Project description:Drosophila neuroblasts have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type specific gene expression data. Here, we describe a methodology to isolate large numbers of pure neuroblasts and differentiating neurons that retain both cell cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted neuroblast specific transcription factors, which can be arranged in a network containing hubs for Notch signaling, growth control and chromatin regulation. Overexpression and RNAi for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klu function causes premature differentiation while overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for Drosophila developmental neurobiology and we describes methodology that can be applied to other invertebrate stem cell lineages as well. comparison of transcriptomes of Drosophila melanogaster larval neuroblasts and their differentiated daughter cells (neurons)
2012-08-21 | E-GEOD-38764 | biostudies-arrayexpress
Project description:The analysis presented here aims at exposing single-cell transcriptome profiles of Drosophila larval brain type II neural stem cells (NSCII) and of their intermediate neural progenitor (INP) cell progeny during normal development and upon brain tumour initiation using the brain tumour (brat) mutant model. We have used brains 24 hours after larval hatching (ALH), a developmental stage when brat INPs (b_INP) have transformed into brain tumour initiating cells, expressing aberrantly the self-renewal transcription factor Deadpan unlike their iINP control counterparts (c_iINP), but have not yet started to overproliferate. iINP will acquire expression of proneural Asense (Ase) becoming mature INPs (m_INPs), yet brat INPs never express Ase and will lead to massive tumour growth (Bello et al., 2008; Boone and Doe, 2008; Bowman et al., 2008). NSCIIs, adjacent smaller iINPs and one mature INP were individually harvested from live freshly dissected brains expressing membrane tagged GFP specifically in NSCII lineages, and single cell transcriptomes obtained as previously described (Bossing et al., 2012; Barros & Bossing, 2022). PCRs confirmed iINPs and INP samples to lack or show ase expression, respectively. Single cell cDNAs were hybridised on whole-genome microarrays in pairs and data processed as indicated below. References: Bello, B.C., Izergina, N., Caussinus, E., and Reichert, H. (2008). Amplification of neural stem cell proliferation by intermediate progenitor cells in Drosophila brain development. Neural Dev 3, 5. Bowman, R.L., Wang, Q., Carro, A., Verhaak, R.G., and Squatrito, M. (2017). GlioVis data portal for visualization and analysis of brain tumor expression datasets. Neuro Oncol 19, 139-141. Boone, J.Q., and Doe, C.Q. (2008). Identification of Drosophila type II neuroblast lineages containing transit amplifying ganglion mother cells. Dev Neurobiol 68, 1185-1195. Bossing, T., Barros, C.S., Fischer, B., Russell, S., and Shepherd, D. (2012). Disruption of microtubule integrity initiates mitosis during CNS repair. Dev Cell 23, 433-440. Barros C.S. & Bossing, T. (2022). Direct isolation of single cells from living brains of Drosophila melanogaster without dissociation for transcriptome analysis. STAR Protoc. Dec 16;3(4):101735.
2023-11-10 | GSE190133 | GEO
Project description:We compared four transcription factor knockdowns using transgenic RNAi expressed in the larval fat body. FOXO, Tfb1, p53, and Stat92E-dependent gene expression in the Drosophila fat body was quantified on control and high-sugar diets in order to generate expression profiles via RNA-seq. These expression data were used to build a gene regulatory network to predict novel roles for these and other genes during caloric overload.
2018-03-13 | GSE111728 | GEO
Project description:Drosophila neuroblasts have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type specific gene expression data. Here, we describe a methodology to isolate large numbers of pure neuroblasts and differentiating neurons that retain both cell cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted neuroblast specific transcription factors, which can be arranged in a network containing hubs for Notch signaling, growth control and chromatin regulation. Overexpression and RNAi for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klu function causes premature differentiation while overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for Drosophila developmental neurobiology and we describes methodology that can be applied to other invertebrate stem cell lineages as well.
2012-08-21 | GSE38764 | GEO
Project description:Myofiber atrophy occurs with aging and in many diseases but the underlying mechanisms are incompletely understood. Here, we have used >1,100 muscle-targeted RNAi interventions to comprehensively assess the function of 447 transcription factors in the developmental growth of body wall skeletal muscles in Drosophila. This screen identifies new regulators of myofiber atrophy and hypertrophy, including the transcription factor Deaf1. Deaf1 RNAi increases myofiber size whereas Deaf1 overexpression induces atrophy. Consistent with its annotation as a Gsk3 phosphorylation substrate, Deaf1 and Gsk3 induce largely overlapping transcriptional changes that are opposed by Deaf1 RNAi. The top category of Deaf1-regulated genes consists of glycolytic enzymes, which are suppressed by Deaf1 and Gsk3 but are upregulated by Deaf1 RNAi. Similar to Deaf1 and Gsk3 overexpression, RNAi for glycolytic enzymes reduces myofiber growth. Altogether, this study defines the repertoire of transcription factors that regulate developmental myofiber growth and the role of Gsk3/Deaf1/glycolysis in this process.
2021-12-10 | GSE174637 | GEO
Project description:Purpose: The goal of this RNA-Seq is to analyze the transcriptomes from wild type and TFAM RNAi fat body samples at 96 hr AEL (after egg laying) and to identify the differentially expressed genes. Methods: Drosophila larval fat bodies were isolated from wild type and TFAM RNAi (r4-gal4) animals at 96 hrs AEL (after egg laying) of development. mRAN profiles were generated by Next Generation Sequencing Facilities. Results: RNA Seq differential expression analysis identified a significant change in 1758 transcripts, with 1213 transcripts showing reduced expression levels and 545 transcripts with elevated expression levels.
2022-03-19 | GSE198604 | GEO
Project description:Existing transgenic RNAi resources in Drosophila utilize the expression of long double stranded hairpin RNAs and are powerful tools for the identification and characterization of genes involved in various processes. However, they are ineffective to knockdown genes during oogenesis, an important model system for the study of numerous fundamental questions in biology. Here, we show that short hairpin RNAs (shRNAs), modeled on an endogenous microRNA, are extremely effective at silencing gene expression during oogenesis. We also describe our progress towards building a genome-wide shRNA resource.
2011-03-26 | GSE27039 | GEO
Project description:The Drosophila TRIM-NHL protein Brain tumor (Brat) plays important roles during early embryogenesis, in cell fate decisions, during neurogenesis and in mature neurons. Brat is an RNA-binding protein and functions as translational repressor. However, which RNAs Brat regulates and how RNA-binding specificity is achieved, is unknown. Using RNA-Immunoprecipitation we identify Brat-bound mRNAs in Drosophila embryos and define a consensus binding motif. Microarrays were used to profile Brat-associated RNAs from fly embryos.
2015-11-13 | GSE71663 | GEO
Project description:Effect of transgenic RNAi on wandering third instar larval fat body gene expression in Drosophila melanogaster
| PRJNA437974 | ENA