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Large-Scale Transgenic Drosophila Resource Collections for Loss- and Gain-of-Function Studies. Genetics 2020; 214:755-767. [PMID: 32071193 DOI: 10.1534/genetics.119.302964] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/11/2020] [Indexed: 01/20/2023] Open
Abstract
The Transgenic RNAi Project (TRiP), a Drosophila melanogaster functional genomics platform at Harvard Medical School, was initiated in 2008 to generate and distribute a genome-scale collection of RNA interference (RNAi) fly stocks. To date, it has generated >15,000 RNAi fly stocks. As this covers most Drosophila genes, we have largely transitioned to development of new resources based on CRISPR technology. Here, we present an update on our libraries of publicly available RNAi and CRISPR fly stocks, and focus on the TRiP-CRISPR overexpression (TRiP-OE) and TRiP-CRISPR knockout (TRiP-KO) collections. TRiP-OE stocks express single guide RNAs targeting upstream of a gene transcription start site. Gene activation is triggered by coexpression of catalytically dead Cas9 fused to an activator domain, either VP64-p65-Rta or Synergistic Activation Mediator. TRiP-KO stocks express one or two single guide RNAs targeting the coding sequence of a gene or genes. Cutting is triggered by coexpression of Cas9, allowing for generation of indels in both germline and somatic tissue. To date, we have generated >5000 TRiP-OE or TRiP-KO stocks for the community. These resources provide versatile, transformative tools for gene activation, gene repression, and genome engineering.
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Okray Z, de Esch CEF, Van Esch H, Devriendt K, Claeys A, Yan J, Verbeeck J, Froyen G, Willemsen R, de Vrij FMS, Hassan BA. A novel fragile X syndrome mutation reveals a conserved role for the carboxy-terminus in FMRP localization and function. EMBO Mol Med 2015; 7:423-37. [PMID: 25693964 PMCID: PMC4403044 DOI: 10.15252/emmm.201404576] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Loss of function of the FMR1 gene leads to fragile X syndrome (FXS), the most common form of intellectual disability. The loss of FMR1 function is usually caused by epigenetic silencing of the FMR1 promoter leading to expansion and subsequent methylation of a CGG repeat in the 5′ untranslated region. Very few coding sequence variations have been experimentally characterized and shown to be causal to the disease. Here, we describe a novel FMR1 mutation and reveal an unexpected nuclear export function for the C-terminus of FMRP. We screened a cohort of patients with typical FXS symptoms who tested negative for CGG repeat expansion in the FMR1 locus. In one patient, we identified a guanine insertion in FMR1 exon 15. This mutation alters the open reading frame creating a short novel C-terminal sequence, followed by a stop codon. We find that this novel peptide encodes a functional nuclear localization signal (NLS) targeting the patient FMRP to the nucleolus in human cells. We also reveal an evolutionarily conserved nuclear export function associated with the endogenous C-terminus of FMRP. In vivo analyses in Drosophila demonstrate that a patient-mimetic mutation alters the localization and function of Dfmrp in neurons, leading to neomorphic neuronal phenotypes.
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Affiliation(s)
- Zeynep Okray
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium Program in Molecular and Developmental Genetics, Doctoral School of Biomedical Sciences, University of Leuven, Leuven, Belgium
| | - Celine E F de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hilde Van Esch
- Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Annelies Claeys
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Jiekun Yan
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Jelle Verbeeck
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Guy Froyen
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Femke M S de Vrij
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bassem A Hassan
- VIB Center for the Biology of Disease, VIB, Leuven, Belgium Center for Human Genetics, University of Leuven School of Medicine and University Hospitals Leuven, Leuven, Belgium Program in Molecular and Developmental Genetics, Doctoral School of Biomedical Sciences, University of Leuven, Leuven, Belgium
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Depner H, Lützkendorf J, Babkir HA, Sigrist SJ, Holt MG. Differential centrifugation-based biochemical fractionation of the Drosophila adult CNS. Nat Protoc 2014; 9:2796-808. [PMID: 25393777 DOI: 10.1038/nprot.2014.192] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Drosophila is widely used as a genetic model in questions of development, cellular function and disease. Genetic screens in flies have proven to be incredibly powerful in identifying crucial components for synapse formation and function, particularly in the case of the presynaptic release machinery. Although modern biochemical methods can identify individual proteins and lipids (and their binding partners), they have typically been excluded from use in Drosophila for technical reasons. To bridge this essential gap between genetics and biochemistry, we developed a fractionation method to isolate various parts of the synaptic machinery from Drosophila, thus allowing it to be studied in unprecedented biochemical detail. This is only possible because our protocol has unique advantages in terms of enriching and preserving endogenous protein complexes. The procedure involves decapitation of adult flies, homogenization and differential centrifugation of fly heads, which allow subsequent purification of presynaptic (and to a limited degree postsynaptic) components. It is designed to require only a rudimentary knowledge of biochemical fractionation, and it takes ∼3.5 h. The yield is typically 4 mg of synaptic membrane protein per gram of Drosophila heads.
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Affiliation(s)
- Harald Depner
- Institute for Biology - Genetics, Freie Universität Berlin, Berlin, Germany
| | - Janine Lützkendorf
- Institute for Biology - Genetics, Freie Universität Berlin, Berlin, Germany
| | - Husam A Babkir
- Institute for Biology - Genetics, Freie Universität Berlin, Berlin, Germany
| | - Stephan J Sigrist
- 1] Institute for Biology - Genetics, Freie Universität Berlin, Berlin, Germany. [2] NeuroCure Cluster of Excellence, Charité, Berlin, Germany
| | - Matthew G Holt
- Laboratory of Glia Biology, Vlaams Instituut voor Biotechnologie (VIB) Center for the Biology of Disease, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
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Muñoz-Soriano V, López-Domenech S, Paricio N. Why mammalian wound-healing researchers may wish to turn toDrosophilaas a model. Exp Dermatol 2014; 23:538-42. [DOI: 10.1111/exd.12472] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Verónica Muñoz-Soriano
- Departamento de Genética; Facultad CC Biológicas; Universidad de Valencia; Burjasot Spain
| | - Sandra López-Domenech
- Departamento de Genética; Facultad CC Biológicas; Universidad de Valencia; Burjasot Spain
| | - Nuria Paricio
- Departamento de Genética; Facultad CC Biológicas; Universidad de Valencia; Burjasot Spain
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Vandewalle J, Langen M, Zschaetzsch M, Nijhof B, Kramer JM, Brems H, Bauters M, Lauwers E, Srahna M, Marynen P, Verstreken P, Schenck A, Hassan BA, Froyen G. Ubiquitin ligase HUWE1 regulates axon branching through the Wnt/β-catenin pathway in a Drosophila model for intellectual disability. PLoS One 2013; 8:e81791. [PMID: 24303071 PMCID: PMC3841167 DOI: 10.1371/journal.pone.0081791] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 10/26/2013] [Indexed: 12/11/2022] Open
Abstract
We recently reported that duplication of the E3 ubiquitin ligase HUWE1 results in intellectual disability (ID) in male patients. However, the underlying molecular mechanism remains unknown. We used Drosophila melanogaster as a model to investigate the effect of increased HUWE1 levels on the developing nervous system. Similar to the observed levels in patients we overexpressed the HUWE1 mRNA about 2-fold in the fly. The development of the mushroom body and neuromuscular junctions were not altered, and basal neurotransmission was unaffected. These data are in agreement with normal learning and memory in the courtship conditioning paradigm. However, a disturbed branching phenotype at the axon terminals of the dorsal cluster neurons (DCN) was detected. Interestingly, overexpression of HUWE1 was found to decrease the protein levels of dishevelled (dsh) by 50%. As dsh as well as Fz2 mutant flies showed the same disturbed DCN branching phenotype, and the constitutive active homolog of β-catenin, armadillo, could partially rescue this phenotype, our data strongly suggest that increased dosage of HUWE1 compromises the Wnt/β-catenin pathway possibly by enhancing the degradation of dsh.
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Affiliation(s)
- Joke Vandewalle
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marion Langen
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Marlen Zschaetzsch
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Bonnie Nijhof
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour & Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jamie M. Kramer
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour & Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilde Brems
- Laboratory for Neurofibromatosis Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marijke Bauters
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Elsa Lauwers
- Laboratory of Neuronal Communication, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Mohammed Srahna
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Patrik Verstreken
- Laboratory of Neuronal Communication, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
| | - Annette Schenck
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Donders Institute for Brain, Cognition and Behaviour & Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bassem A. Hassan
- Laboratory of Neurogenetics, VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium
- * E-mail: (GF); (BAH)
| | - Guy Froyen
- Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, Belgium
- * E-mail: (GF); (BAH)
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