| RNAi pathway | FBgn0002939
| ninaD | np | np |
No effect on dsRNA uptake
| no |
ReferenceDouble-stranded RNA is internalized by scavenger receptor-mediated endocytosis in Drosophila S2 cells. Ulvila et al.,
2006
Double-stranded RNA (dsRNA) fragments are readily internalized and processed by Drosophila S2 cells, making these cells a widely used tool for the analysis of gene function by gene silencing through RNA interference (RNAi). The underlying mechanisms are insufficiently understood. To identify components of the RNAi pathway in S2 cells, we developed a screen based on rescue from RNAi-induced lethality. We identified Argonaute 2, a core component of the RNAi machinery, and three gene products previously unknown to be involved in RNAi in Drosophila: DEAD-box RNA helicase Belle, 26 S proteasome regulatory subunit 8 (Pros45), and clathrin heavy chain, a component of the endocytic machinery. Blocking endocytosis in S2 cells impaired RNAi, suggesting that dsRNA fragments are internalized by receptor-mediated endocytosis. Indeed, using a candidate gene approach, we identified two Drosophila scavenger receptors, SR-CI and Eater, which together accounted for more than 90% of the dsRNA uptake into S2 cells. When expressed in mammalian cells, SR-CI was sufficient to mediate internalization of dsRNA fragments. Our data provide insight into the mechanism of dsRNA internalization by Drosophila cells. These results have implications for dsRNA delivery into mammalian cells.
Screen detailsStable Id:
GR00068-A-0
Screen title:
RNAi pathway
Assay:
RNAi activity
Method:
Viability and FACS
Scope:
Screen type:
Cell-based
Species:
Drosophila melanogaster
Biosource:
Cell line
Biomodel:
S2
Library:
, Custom-made library
Reagent type:
dsRNA
Score type:
np
Cutoff:
np
Notes:
|
| Cell size and cell-cycle regulation (1) | FBgn0002939
| ninaD | RE41741 | sp |
none
| no |
ReferenceIdentification of pathways regulating cell size and cell-cycle progression by RNAi. Bjӧrklund et al.,
2006
Many high-throughput loss-of-function analyses of the eukaryotic cell cycle have relied on the unicellular yeast species Saccharomyces cerevisiae and Schizosaccharomyces pombe. In multicellular organisms, however, additional control mechanisms regulate the cell cycle to specify the size of the organism and its constituent organs. To identify such genes, here we analysed the effect of the loss of function of 70% of Drosophila genes (including 90% of genes conserved in human) on cell-cycle progression of S2 cells using flow cytometry. To address redundancy, we also targeted genes involved in protein phosphorylation simultaneously with their homologues. We identify genes that control cell size, cytokinesis, cell death and/or apoptosis, and the G1 and G2/M phases of the cell cycle. Classification of the genes into pathways by unsupervised hierarchical clustering on the basis of these phenotypes shows that, in addition to classical regulatory mechanisms such as Myc/Max, Cyclin/Cdk and E2F, cell-cycle progression in S2 cells is controlled by vesicular and nuclear transport proteins, COP9 signalosome activity and four extracellular-signal-regulated pathways (Wnt, p38betaMAPK, FRAP/TOR and JAK/STAT). In addition, by simultaneously analysing several phenotypes, we identify a translational regulator, eIF-3p66, that specifically affects the Cyclin/Cdk pathway activity.
Screen detailsStable Id:
GR00048-A-1
Screen title:
Cell size and cell-cycle regulation (1)
Assay:
Cell size, DNA content and viability
Method:
Flow cytometry
Scope:
Kinases, phosphatases and selected genes
Screen type:
Cell-based
Species:
Drosophila melanogaster
Biosource:
Cell line
Biomodel:
S2
Library:
Custom-made, DGC1, DGC2 and PHOSPHO
Reagent type:
dsRNA
Score type:
Complex, sp
Cutoff:
Complex criteria
Notes:
Additional information about the primary sccreen (pooled library) and a secondary screen (number of binucleate cells)
|
| Muscle morphogenesis and function (1) | CG31783
| ninaD | | np |
none
| no |
ReferenceSystematic genetic analysis of muscle morphogenesis and function in Drosophila. Schnorrer et al.,
2010
Systematic genetic approaches have provided deep insight into the molecular and cellular mechanisms that operate in simple unicellular organisms. For multicellular organisms, however, the pleiotropy of gene function has largely restricted such approaches to the study of early embryogenesis. With the availability of genome-wide transgenic RNA interference (RNAi) libraries in Drosophila, it is now possible to perform a systematic genetic dissection of any cell or tissue type at any stage of the lifespan. Here we apply these methods to define the genetic basis for formation and function of the Drosophila muscle. We identify a role in muscle for 2,785 genes, many of which we assign to specific functions in the organization of muscles, myofibrils or sarcomeres. Many of these genes are phylogenetically conserved, including genes implicated in mammalian sarcomere organization and human muscle diseases.
Screen detailsStable Id:
GR00134-A-1
Screen title:
Muscle morphogenesis and function (1)
Assay:
Posture, locomotion, flight and viability
Method:
Visual inspection
Scope:
Genome-wide
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Tissue
Biomodel:
Mef2-GAL4
Library:
VDRC, np
Reagent type:
UAS-IR construct
Score type:
rp
Cutoff:
S19 > 0.5
Notes:
|
| Heat nociception (1) | CG31783
| ninaD | | 0 |
Developmentally lethal
| no |
ReferenceA genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene. Neely et al.,
2010
Worldwide, acute, and chronic pain affects 20% of the adult population and represents an enormous financial and emotional burden. Using genome-wide neuronal-specific RNAi knockdown in Drosophila, we report a global screen for an innate behavior and identify hundreds of genes implicated in heat nociception, including the α2δ family calcium channel subunit straightjacket (stj). Mice mutant for the stj ortholog CACNA2D3 (α2δ3) also exhibit impaired behavioral heat pain sensitivity. In addition, in humans, α2δ3 SNP variants associate with reduced sensitivity to acute noxious heat and chronic back pain. Functional imaging in α2δ3 mutant mice revealed impaired transmission of thermal pain-evoked signals from the thalamus to higher-order pain centers. Intriguingly, in α2δ3 mutant mice, thermal pain and tactile stimulation triggered strong cross-activation, or synesthesia, of brain regions involved in vision, olfaction, and hearing.
Screen detailsStable Id:
GR00135-A-1
Screen title:
Heat nociception (1)
Assay:
Noxious heat avoidance and viability
Method:
Fly count
Scope:
Genome-wide
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Organism
Biomodel:
elav-GAL4
Library:
VDRC, np
Reagent type:
UAS-IR construct
Score type:
Z-score
Cutoff:
> 1.65
Notes:
Additional information about secondary screens (geotactic, phototaxis, and temperature sensitivity)
|
| Fly viability and adult morphology |
| CG31783 | | sp |
none
| no |
ReferenceA genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Dietzl et al.,
2007
Forward genetic screens in model organisms have provided important insights into numerous aspects of development, physiology and pathology. With the availability of complete genome sequences and the introduction of RNA-mediated gene interference (RNAi), systematic reverse genetic screens are now also possible. Until now, such genome-wide RNAi screens have mostly been restricted to cultured cells and ubiquitous gene inactivation in Caenorhabditis elegans. This powerful approach has not yet been applied in a tissue-specific manner. Here we report the generation and validation of a genome-wide library of Drosophila melanogaster RNAi transgenes, enabling the conditional inactivation of gene function in specific tissues of the intact organism. Our RNAi transgenes consist of short gene fragments cloned as inverted repeats and expressed using the binary GAL4/UAS system. We generated 22,270 transgenic lines, covering 88% of the predicted protein-coding genes in the Drosophila genome. Molecular and phenotypic assays indicate that the majority of these transgenes are functional. Our transgenic RNAi library thus opens up the prospect of systematically analysing gene functions in any tissue and at any stage of the Drosophila lifespan.
Screen detailsStable Id:
GR00139-A
Screen title:
Fly viability and adult morphology
Assay:
Adult morphology and viability
Method:
Visual inspection
Scope:
Selected and random genes
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Organism
Biomodel:
Act5C-GAL4
Library:
Custom-made, Custom-made
Reagent type:
UAS-IR construct
Score type:
Phenotype strength
Cutoff:
np
Notes:
Additional information about secondary screens (MS1096-GAL4, ey-GAL4, GMR-GAL4 and pnr-GAL4)
|
| Lipid storage | FBgn0002939
| | | 2.35 |
none
| no |
ReferenceCOPI complex is a regulator of lipid homeostasis. Beller et al.,
2008
Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets.
Screen detailsStable Id:
GR00002-A-0
Screen title:
Lipid storage
Assay:
Lipid droplet staining
Method:
High content (microscopy)
Scope:
Screen type:
Cell-based
Species:
Drosophila melanogaster
Biosource:
Cell line
Biomodel:
Kc167
Library:
, DRSC
Reagent type:
dsRNA
Score type:
B-score
Cutoff:
2.0 / -1.7
Notes:
|
| Cell growth and viability (2) |
| | | 0 |
none
| no |
ReferenceGenome-wide RNAi analysis of growth and viability in Drosophila cells. Boutros et al.,
2004
A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale.
Screen detailsStable Id:
GR00031-A-2
Screen title:
Cell growth and viability (2)
Assay:
Cell number and viability
Method:
Luminescence
Scope:
Genome-wide
Screen type:
Cell-based
Species:
Drosophila melanogaster
Biosource:
Cell line
Biomodel:
S2R+
Library:
Custom-made, HFA
Reagent type:
dsRNA
Score type:
Z-score
Cutoff:
>= 3.0
Notes:
|
| Lipid storage | FBgn0002939
| | | 0 |
none
| no |
ReferenceCOPI complex is a regulator of lipid homeostasis. Beller et al.,
2008
Lipid droplets are ubiquitous triglyceride and sterol ester storage organelles required for energy storage homeostasis and biosynthesis. Although little is known about lipid droplet formation and regulation, it is clear that members of the PAT (perilipin, adipocyte differentiation related protein, tail interacting protein of 47 kDa) protein family coat the droplet surface and mediate interactions with lipases that remobilize the stored lipids. We identified key Drosophila candidate genes for lipid droplet regulation by RNA interference (RNAi) screening with an image segmentation-based optical read-out system, and show that these regulatory functions are conserved in the mouse. Those include the vesicle-mediated Coat Protein Complex I (COPI) transport complex, which is required for limiting lipid storage. We found that COPI components regulate the PAT protein composition at the lipid droplet surface, and promote the association of adipocyte triglyceride lipase (ATGL) with the lipid droplet surface to mediate lipolysis. Two compounds known to inhibit COPI function, Exo1 and Brefeldin A, phenocopy COPI knockdowns. Furthermore, RNAi inhibition of ATGL and simultaneous drug treatment indicate that COPI and ATGL function in the same pathway. These data indicate that the COPI complex is an evolutionarily conserved regulator of lipid homeostasis, and highlight an interaction between vesicle transport systems and lipid droplets.
Screen detailsStable Id:
GR00002-A-0
Screen title:
Lipid storage
Assay:
Lipid droplet staining
Method:
High content (microscopy)
Scope:
Screen type:
Cell-based
Species:
Drosophila melanogaster
Biosource:
Cell line
Biomodel:
Kc167
Library:
, DRSC
Reagent type:
dsRNA
Score type:
B-score
Cutoff:
2.0 / -1.7
Notes:
|
| Heart development and function (1) | CG31783
| | | 1 |
none
| no |
ReferenceA global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function. Neely et al.,
2010
Heart diseases are the most common causes of morbidity and death in humans. Using cardiac-specific RNAi-silencing in Drosophila, we knocked down 7061 evolutionarily conserved genes under conditions of stress. We present a first global roadmap of pathways potentially playing conserved roles in the cardiovascular system. One critical pathway identified was the CCR4-Not complex implicated in transcriptional and posttranscriptional regulatory mechanisms. Silencing of CCR4-Not components in adult Drosophila resulted in myofibrillar disarray and dilated cardiomyopathy. Heterozygous not3 knockout mice showed spontaneous impairment of cardiac contractility and increased susceptibility to heart failure. These heart defects were reversed via inhibition of HDACs, suggesting a mechanistic link to epigenetic chromatin remodeling. In humans, we show that a common NOT3 SNP correlates with altered cardiac QT intervals, a known cause of potentially lethal ventricular tachyarrhythmias. Thus, our functional genome-wide screen in Drosophila can identify candidates that directly translate into conserved mammalian genes involved in heart function.
Screen detailsStable Id:
GR00138-A-1
Screen title:
Heart development and function (1)
Assay:
Viability
Method:
Fly count
Scope:
Selected genes
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Tissue
Biomodel:
TinCΔ4 12a-Gal4
Library:
VDRC, np
Reagent type:
UAS-IR construct
Score type:
Developmental lethality
Cutoff:
<= 0.6666
Notes:
|
| Notch pathway regulation (4) | CG31783
| | | 0 |
none
| no |
ReferenceGenome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Mummery-Widmer et al.,
2009
Genome-wide RNA interference (RNAi) screens have identified near-complete sets of genes involved in cellular processes. However, this methodology has not yet been used to study complex developmental processes in a tissue-specific manner. Here we report the use of a library of Drosophila strains expressing inducible hairpin RNAi constructs to study the Notch signalling pathway during external sensory organ development. We assigned putative loss-of-function phenotypes to 21.2% of the protein-coding Drosophila genes. Using secondary assays, we identified 6 new genes involved in asymmetric cell division and 23 novel genes regulating the Notch signalling pathway. By integrating our phenotypic results with protein interaction data, we constructed a genome-wide, functionally validated interaction network governing Notch signalling and asymmetric cell division. We used clustering algorithms to identify nuclear import pathways and the COP9 signallosome as Notch regulators. Our results show that complex developmental processes can be analysed on a genome-wide level and provide a unique resource for functional annotation of the Drosophila genome.
Screen detailsStable Id:
GR00144-A-4
Screen title:
Notch pathway regulation (4)
Assay:
External sensory organ morphology and viability
Method:
Visual inspection
Scope:
Genome-wide
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Tissue
Biomodel:
pnr-GAL4
Library:
VDRC, np
Reagent type:
UAS-IR construct
Score type:
Phenotype strength
Cutoff:
np
Notes:
|
| Adiposity regulation (1) | FBgn0002939
| ninaD | | -0.36 |
none
| no |
ReferenceDrosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate. Pospisilik et al.,
2010
Over 1 billion people are estimated to be overweight, placing them at risk for diabetes, cardiovascular disease, and cancer. We performed a systems-level genetic dissection of adiposity regulation using genome-wide RNAi screening in adult Drosophila. As a follow-up, the resulting approximately 500 candidate obesity genes were functionally classified using muscle-, oenocyte-, fat-body-, and neuronal-specific knockdown in vivo and revealed hedgehog signaling as the top-scoring fat-body-specific pathway. To extrapolate these findings into mammals, we generated fat-specific hedgehog-activation mutant mice. Intriguingly, these mice displayed near total loss of white, but not brown, fat compartments. Mechanistically, activation of hedgehog signaling irreversibly blocked differentiation of white adipocytes through direct, coordinate modulation of early adipogenic factors. These findings identify a role for hedgehog signaling in white/brown adipocyte determination and link in vivo RNAi-based scanning of the Drosophila genome to regulation of adipocyte cell fate in mammals.
Screen detailsStable Id:
GR00190-A-1
Screen title:
Adiposity regulation (1)
Assay:
Total fly triglyceride expression
Method:
Colorimetric determination
Scope:
Genome-wide
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Organism
Biomodel:
Hsp70-GAL4;Tub-GAL80ts
Library:
VDRC, np
Reagent type:
UAS-IR construct
Score type:
Triglyceride change
Cutoff:
Z-score > 1.65 after 3 screening rounds
Notes:
Additional information about the primary screen
|
| Serratia marcescens infection (1) | CG31783
| ninaD | | 0.25 |
none
| no |
ReferenceGenome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Cronin et al.,
2009
Innate immunity represents the first line of defense in animals. We report a genome-wide in vivo Drosophila RNA interference screen to uncover genes involved in susceptibility or resistance to intestinal infection with the bacterium Serratia marcescens. We first employed whole-organism gene suppression, followed by tissue-specific silencing in gut epithelium or hemocytes to identify several hundred genes involved in intestinal antibacterial immunity. Among the pathways identified, we showed that the JAK-STAT signaling pathway controls host defense in the gut by regulating stem cell proliferation and thus epithelial cell homeostasis. Therefore, we revealed multiple genes involved in antibacterial defense and the regulation of innate immunity.
Screen detailsStable Id:
GR00142-A-1
Screen title:
Serratia marcescens infection (1)
Assay:
Heat shock and viability
Method:
Fly count
Scope:
Random genes
Screen type:
in vivo
Species:
Drosophila melanogaster
Biosource:
Organism
Biomodel:
HSP70-GAL4; TubGAL80ts
Library:
VDRC, np
Reagent type:
UAS-IR construct
Score type:
Days life time (LT50)
Cutoff:
< -1.5 SD OR > 2 SD
Notes:
|
| Cell growth and viability (1) |
| | | -1.2 |
none
| yes |
ReferenceGenome-wide RNAi analysis of growth and viability in Drosophila cells. Boutros et al.,
2004
A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale.
Screen detailsStable Id:
GR00031-A-1
Screen title:
Cell growth and viability (1)
Assay:
Cell number and viability
Method:
Luminescence
Scope:
Genome-wide
Screen type:
Cell-based
Species:
Drosophila melanogaster
Biosource:
Cell line
Biomodel:
Kc167
Library:
Custom-made, HFA
Reagent type:
dsRNA
Score type:
Z-score
Cutoff:
>= 3.0
Notes:
|
