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Misra S, Buehner NA, Singh A, Wolfner MF. Female factors modulate Sex Peptide's association with sperm in Drosophila melanogaster. BMC Biol 2022; 20:279. [PMID: 36514080 PMCID: PMC9749180 DOI: 10.1186/s12915-022-01465-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 11/15/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Male-derived seminal fluid proteins (SFPs) that enter female fruitflies during mating induce a myriad of physiological and behavioral changes, optimizing fertility of the mating pair. Some post-mating changes in female Drosophila melanogaster persist for ~10-14 days. Their long-term persistence is because the seminal protein that induces these particular changes, the Sex Peptide (SP), is retained long term in females by binding to sperm, with gradual release of its active domain from sperm. Several other "long-term response SFPs" (LTR-SFPs) "prime" the binding of SP to sperm. Whether female factors play a role in this process is unknown, though it is important to study both sexes for a comprehensive physiological understanding of SFP/sperm interactions and for consideration in models of sexual conflict. RESULTS We report here that sperm in male ejaculates bind SP more weakly than sperm that have entered females. Moreover, we show that the amount of SP, and other SFPs, bound to sperm increases with time and transit of individual seminal proteins within the female reproductive tract (FRT). Thus, female contributions are needed for maximal and appropriate binding of SP, and other SFPs, to sperm. Towards understanding the source of female molecular contributions, we ablated spermathecal secretory cells (SSCs) and/or parovaria (female accessory glands), which contribute secretory proteins to the FRT. We found no dramatic change in the initial levels of SP bound to sperm stored in mated females with ablated or defective SSCs and/or parovaria, indicating that female molecules that facilitate the binding of SP to sperm are not uniquely derived from SSCs and parovaria. However, we observed higher levels of SP (and sperm) retention long term in females whose SSCs and parovaria had been ablated, indicating secretions from these female tissues are necessary for the gradual release of Sex Peptide's active region from stored sperm. CONCLUSION This study reveals that the SP-sperm binding pathway is not entirely male-derived and that female contributions are needed to regulate the levels of SP associated with sperm stored in their storage sites.
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Affiliation(s)
- Snigdha Misra
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.,Present address: School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, UK, 248007, India
| | - Norene A Buehner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Akanksha Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.,Present address: Centre for Life Sciences, Mahindra University, Hyderabad, Telangana, 500043, India
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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López-Varea A, Vega-Cuesta P, Ruiz-Gómez A, Ostalé CM, Molnar C, Hevia CF, Martín M, Organista MF, de Celis J, Culí J, Esteban N, de Celis JF. Genome-wide phenotypic RNAi screen in the Drosophila wing: phenotypic description of functional classes. G3 (BETHESDA, MD.) 2021; 11:6380434. [PMID: 34599810 PMCID: PMC8664486 DOI: 10.1093/g3journal/jkab349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/23/2021] [Indexed: 01/01/2023]
Abstract
The Drosophila genome contains approximately 14,000 protein-coding genes encoding all the necessary information to sustain cellular physiology, tissue organization, organism development, and behavior. In this manuscript, we describe in some detail the phenotypes in the adult fly wing generated after knockdown of approximately 80% of Drosophila genes. We combined this phenotypic description with a comprehensive molecular classification of the Drosophila proteins into classes that summarize the main expected or known biochemical/functional aspect of each protein. This information, combined with mRNA expression levels and in situ expression patterns, provides a simplified atlas of the Drosophila genome, from housekeeping proteins to the components of the signaling pathways directing wing development, that might help to further understand the contribution of each gene group to wing formation.
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Affiliation(s)
- Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Vega-Cuesta
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ana Ruiz-Gómez
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Molnar
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain.,IRB Barcelona, Barcelona 08028, Spain
| | - Covadonga F Hevia
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mercedes Martín
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Maria F Organista
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jesus de Celis
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Joaquín Culí
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa," CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
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3
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López-Varea A, Ostalé CM, Vega-Cuesta P, Ruiz-Gómez A, Organista MF, Martín M, Hevia CF, Molnar C, de Celis J, Culi J, Esteban N, de Celis JF. Genome-wide Phenotypic RNAi Screen in the Drosophila Wing: Global Parameters. G3-GENES GENOMES GENETICS 2021; 11:6380435. [PMID: 34599819 PMCID: PMC8962446 DOI: 10.1093/g3journal/jkab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/27/2021] [Indexed: 11/17/2022]
Abstract
We have screened a collection of UAS-RNAi lines targeting 10,920 Drosophila protein-coding genes for phenotypes in the adult wing. We identified 3653 genes (33%) whose knockdown causes either larval/pupal lethality or a mutant phenotype affecting the formation of a normal wing. The most frequent phenotypes consist of changes in wing size, vein differentiation, and patterning, defects in the wing margin and in the apposition of the dorsal and ventral wing surfaces. We also defined 16 functional categories encompassing the most relevant aspect of each protein function and assigned each Drosophila gene to one of these functional groups. This allowed us to identify which mutant phenotypes are enriched within each functional group. Finally, we used previously published gene expression datasets to determine which genes are or are not expressed in the wing disc. Integrating expression, phenotypic and molecular information offers considerable precision to identify the relevant genes affecting wing formation and the biological processes regulated by them.
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Affiliation(s)
- Ana López-Varea
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina M Ostalé
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Patricia Vega-Cuesta
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Ana Ruiz-Gómez
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - María F Organista
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Mercedes Martín
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Covadonga F Hevia
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Molnar
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jesús de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Joaquim Culi
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Nuria Esteban
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jose F de Celis
- Centro de Biología Molecular "Severo Ochoa", CSIC and Universidad Autónoma de Madrid, Madrid 28049, Spain
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4
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Crittenden JR, Skoulakis EMC, Goldstein ES, Davis RL. Drosophila mef2 is essential for normal mushroom body and wing development. Biol Open 2018; 7:bio.035618. [PMID: 30115617 PMCID: PMC6176937 DOI: 10.1242/bio.035618] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MEF2 (myocyte enhancer factor 2) transcription factors are found in the brain and muscle of insects and vertebrates and are essential for the differentiation of multiple cell types. We show that in the fruit fly Drosophila, MEF2 is essential for the formation of mushroom bodies in the embryonic brain and for the normal development of wings in the adult. In embryos mutant for mef2, there is a striking reduction in the number of mushroom body neurons and their axon bundles are not detectable. The onset of MEF2 expression in neurons of the mushroom bodies coincides with their formation in the embryo and, in larvae, expression is restricted to post-mitotic neurons. In flies with a mef2 point mutation that disrupts nuclear localization, we find that MEF2 is restricted to a subset of Kenyon cells that project to the α/β, and γ axonal lobes of the mushroom bodies, but not to those forming the α’/β’ lobes. Summary:Drosophila mef2 expression is restricted to subsets of mushroom body neurons, from the time of their differentiation to adulthood, and is essential for mushroom body formation.
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Affiliation(s)
- Jill R Crittenden
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Efthimios M C Skoulakis
- Division of Neuroscience, Biomedical Sciences Research Centre 'Alexander Fleming', Vari, 16672, Greece
| | - Elliott S Goldstein
- School of Life Science, Cellular, Molecular and Bioscience Program, Arizona State University, Tempe, AZ, 85287, USA
| | - Ronald L Davis
- Department of Neuroscience, The Scripps Research Institute Florida, Jupiter, FL 33458, USA
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5
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Thuma L, Carter D, Weavers H, Martin P. Drosophila immune cells extravasate from vessels to wounds using Tre1 GPCR and Rho signaling. J Cell Biol 2018; 217:3045-3056. [PMID: 29941473 PMCID: PMC6122984 DOI: 10.1083/jcb.201801013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/04/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022] Open
Abstract
In contrast to vertebrates, adult Drosophila melanogaster have an open cardiovascular system. However, Thuma et al. find that in late pupation, hemolymph flows through Drosophila wing veins, providing a unique genetic and live-imaging opportunity to investigate the mechanisms driving immune cell extravasation from vessels to wounds and reveal new roles for Tre1 and Rho signaling in this process. Inflammation is pivotal to fight infection, clear debris, and orchestrate repair of injured tissues. Although Drosophila melanogaster have proven invaluable for studying extravascular recruitment of innate immune cells (hemocytes) to wounds, they have been somewhat neglected as viable models to investigate a key rate-limiting component of inflammation—that of immune cell extravasation across vessel walls—due to their open circulation. We have now identified a period during pupal development when wing hearts pulse hemolymph, including circulating hemocytes, through developing wing veins. Wounding near these vessels triggers local immune cell extravasation, enabling live imaging and correlative light-electron microscopy of these events in vivo. We show that RNAi knockdown of immune cell integrin blocks diapedesis, just as in vertebrates, and we uncover a novel role for Rho-like signaling through the GPCR Tre1, a gene previously implicated in the trans-epithelial migration of germ cells. We believe this new Drosophila model complements current murine models and provides new mechanistic insight into immune cell extravasation.
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Affiliation(s)
- Leila Thuma
- Department of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, UK
| | - Deborah Carter
- Department of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, UK
| | - Helen Weavers
- School of Cellular and Molecular Medicine, Biomedical Sciences, University of Bristol, Bristol, UK .,School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, UK
| | - Paul Martin
- Department of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, UK .,School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, UK.,School of Medicine, Cardiff University, Cardiff, UK
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6
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Calpena E, López Del Amo V, Chakraborty M, Llamusí B, Artero R, Espinós C, Galindo MI. The Drosophila junctophilin gene is functionally equivalent to its four mammalian counterparts and is a modifier of a Huntingtin poly-Q expansion and the Notch pathway. Dis Model Mech 2018; 11:dmm.029082. [PMID: 29208631 PMCID: PMC5818072 DOI: 10.1242/dmm.029082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 11/08/2017] [Indexed: 12/13/2022] Open
Abstract
Members of the Junctophilin (JPH) protein family have emerged as key actors in all excitable cells, with crucial implications for human pathophysiology. In mammals, this family consists of four members (JPH1-JPH4) that are differentially expressed throughout excitable cells. The analysis of knockout mice lacking JPH subtypes has demonstrated their essential contribution to physiological functions in skeletal and cardiac muscles and in neurons. Moreover, mutations in the human JPH2 gene are associated with hypertrophic and dilated cardiomyopathies; mutations in JPH3 are responsible for the neurodegenerative Huntington's disease-like-2 (HDL2), whereas JPH1 acts as a genetic modifier in Charcot–Marie–Tooth 2K peripheral neuropathy. Drosophila melanogaster has a single junctophilin (jp) gene, as is the case in all invertebrates, which might retain equivalent functions of the four homologous JPH genes present in mammalian genomes. Therefore, owing to the lack of putatively redundant genes, a jpDrosophila model could provide an excellent platform to model the Junctophilin-related diseases, to discover the ancestral functions of the JPH proteins and to reveal new pathways. By up- and downregulation of Jp in a tissue-specific manner in Drosophila, we show that altering its levels of expression produces a phenotypic spectrum characterized by muscular deficits, dilated cardiomyopathy and neuronal alterations. Importantly, our study has demonstrated that Jp modifies the neuronal degeneration in a Drosophila model of Huntington's disease, and it has allowed us to uncover an unsuspected functional relationship with the Notch pathway. Therefore, this Drosophila model has revealed new aspects of Junctophilin function that can be relevant for the disease mechanisms of their human counterparts. Summary: This work reveals that the Drosophila Junctophilin protein has similar functions to its mammalian homologues and uncovers new interactions of potential biomedical interest with Huntingtin and Notch signalling.
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Affiliation(s)
- Eduardo Calpena
- Program in Molecular Mechanisms of Disease, Centro de Investigación Príncipe Felipe (CIPF), c/ Eduardo Primo Yúfera no. 3, 46012 Valencia, Spain
| | - Víctor López Del Amo
- Program in Molecular Mechanisms of Disease, Centro de Investigación Príncipe Felipe (CIPF), c/ Eduardo Primo Yúfera no. 3, 46012 Valencia, Spain
| | - Mouli Chakraborty
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain.,Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, c/ Dr Moliner 50, 46100 Burjasot, Spain
| | - Beatriz Llamusí
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain.,Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, c/ Dr Moliner 50, 46100 Burjasot, Spain
| | - Rubén Artero
- Translational Genomics Group, Incliva Health Research Institute, Avda. Menendez Pelayo 4 acc 46010, Valencia, Spain.,Department of Genetics and Estructura de Recerca Interdisciplinar en Biotecnologia i Biomedicina (ERI BIOTECMED), Universitat de València, c/ Dr Moliner 50, 46100 Burjasot, Spain
| | - Carmen Espinós
- Program in Molecular Mechanisms of Disease, Centro de Investigación Príncipe Felipe (CIPF), c/ Eduardo Primo Yúfera no. 3, 46012 Valencia, Spain.,UPV-CIPF Joint Unit Disease Mechanisms and Nanomedicine, 46012 Valencia, Spain
| | - Máximo I Galindo
- Program in Molecular Mechanisms of Disease, Centro de Investigación Príncipe Felipe (CIPF), c/ Eduardo Primo Yúfera no. 3, 46012 Valencia, Spain .,UPV-CIPF Joint Unit Disease Mechanisms and Nanomedicine, 46012 Valencia, Spain.,Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
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7
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Hodges C, Kirkland JG, Crabtree GR. The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026930. [PMID: 27413115 DOI: 10.1101/cshperspect.a026930] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During the last decade, a host of epigenetic mechanisms were found to contribute to cancer and other human diseases. Several genomic studies have revealed that ∼20% of malignancies have alterations of the subunits of polymorphic BRG-/BRM-associated factor (BAF) and Polybromo-associated BAF (PBAF) complexes, making them among the most frequently mutated complexes in cancer. Recurrent mutations arise in genes encoding several BAF/PBAF subunits, including ARID1A, ARID2, PBRM1, SMARCA4, and SMARCB1 These subunits share some degree of conservation with subunits from related adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in model organisms, in which a large body of work provides insight into their roles in cancer. Here, we review the roles of BAF- and PBAF-like complexes in these organisms, and relate these findings to recent discoveries in cancer epigenomics. We review several roles of BAF and PBAF complexes in cancer, including transcriptional regulation, DNA repair, and regulation of chromatin architecture and topology. More recent results highlight the need for new techniques to study these complexes.
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Affiliation(s)
- Courtney Hodges
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Jacob G Kirkland
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
| | - Gerald R Crabtree
- Departments of Pathology, Developmental Biology, and Genetics, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305
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8
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Accumulation of Laminin Monomers in Drosophila Glia Leads to Glial Endoplasmic Reticulum Stress and Disrupted Larval Locomotion. J Neurosci 2016; 36:1151-64. [PMID: 26818504 DOI: 10.1523/jneurosci.1797-15.2016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED The nervous system is surrounded by an extracellular matrix composed of large glycoproteins, including perlecan, collagens, and laminins. Glial cells in many organisms secrete laminin, a large heterotrimeric protein consisting of an α, β, and γ subunit. Prior studies have found that loss of laminin subunits from vertebrate Schwann cells causes loss of myelination and neuropathies, results attributed to loss of laminin-receptor signaling. We demonstrate that loss of the laminin γ subunit (LanB2) in the peripheral glia of Drosophila melanogaster results in the disruption of glial morphology due to disruption of laminin secretion. Specifically, knockdown of LanB2 in peripheral glia results in accumulation of the β subunit (LanB1), leading to distended endoplasmic reticulum (ER), ER stress, and glial swelling. The physiological consequences of disruption of laminin secretion in glia included decreased larval locomotion and ultimately lethality. Loss of the γ subunit from wrapping glia resulted in a disruption in the glial ensheathment of axons but surprisingly did not affect animal locomotion. We found that Tango1, a protein thought to exclusively mediate collagen secretion, is also important for laminin secretion in glia via a collagen-independent mechanism. However loss of secretion of the laminin trimer does not disrupt animal locomotion. Rather, it is the loss of one subunit that leads to deleterious consequences through the accumulation of the remaining subunits. SIGNIFICANCE STATEMENT This research presents a new perspective on how mutations in the extracellular matrix protein laminin cause severe consequences in glial wrapping and function. Glial-specific loss of the β or γ laminin subunit disrupted glia morphology and led to ER expansion and stress due to retention of other subunits. The retention of the unpaired laminin subunit was key to the glial disruption as loss of Tango1 blocked secretion of the complete laminin trimer but did not lead to glial or locomotion defects. The effects were observed in the perineurial glia that envelope the peripheral and central nervous systems, providing evidence for the importance of this class of glia in supporting nervous system function.
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9
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Venken KJT, Sarrion-Perdigones A, Vandeventer PJ, Abel NS, Christiansen AE, Hoffman KL. Genome engineering: Drosophila melanogaster and beyond. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 5:233-67. [PMID: 26447401 DOI: 10.1002/wdev.214] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 08/03/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
A central challenge in investigating biological phenomena is the development of techniques to modify genomic DNA with nucleotide precision that can be transmitted through the germ line. Recent years have brought a boon in these technologies, now collectively known as genome engineering. Defined genomic manipulations at the nucleotide level enable a variety of reverse engineering paradigms, providing new opportunities to interrogate diverse biological functions. These genetic modifications include controlled removal, insertion, and substitution of genetic fragments, both small and large. Small fragments up to a few kilobases (e.g., single nucleotide mutations, small deletions, or gene tagging at single or multiple gene loci) to large fragments up to megabase resolution can be manipulated at single loci to create deletions, duplications, inversions, or translocations of substantial sections of whole chromosome arms. A specialized substitution of chromosomal portions that presumably are functionally orthologous between different organisms through syntenic replacement, can provide proof of evolutionary conservation between regulatory sequences. Large transgenes containing endogenous or synthetic DNA can be integrated at defined genomic locations, permitting an alternative proof of evolutionary conservation, and sophisticated transgenes can be used to interrogate biological phenomena. Precision engineering can additionally be used to manipulate the genomes of organelles (e.g., mitochondria). Novel genome engineering paradigms are often accelerated in existing, easily genetically tractable model organisms, primarily because these paradigms can be integrated in a rigorous, existing technology foundation. The Drosophila melanogaster fly model is ideal for these types of studies. Due to its small genome size, having just four chromosomes, the vast amount of cutting-edge genetic technologies, and its short life-cycle and inexpensive maintenance requirements, the fly is exceptionally amenable to complex genetic analysis using advanced genome engineering. Thus, highly sophisticated methods developed in the fly model can be used in nearly any sequenced organism. Here, we summarize different ways to perform precise inheritable genome engineering using integrases, recombinases, and DNA nucleases in the D. melanogaster. For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Koen J T Venken
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, USA
| | | | - Paul J Vandeventer
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Nicholas S Abel
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Audrey E Christiansen
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
| | - Kristi L Hoffman
- Department of Biochemistry and Molecular Biology, Verna and Marrs McLean, Houston, TX, USA
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10
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Schleede J, Blair SS. The Gyc76C Receptor Guanylyl Cyclase and the Foraging cGMP-Dependent Kinase Regulate Extracellular Matrix Organization and BMP Signaling in the Developing Wing of Drosophila melanogaster. PLoS Genet 2015; 11:e1005576. [PMID: 26440503 PMCID: PMC4595086 DOI: 10.1371/journal.pgen.1005576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 09/16/2015] [Indexed: 12/30/2022] Open
Abstract
The developing crossveins of the wing of Drosophila melanogaster are specified by long-range BMP signaling and are especially sensitive to loss of extracellular modulators of BMP signaling such as the Chordin homolog Short gastrulation (Sog). However, the role of the extracellular matrix in BMP signaling and Sog activity in the crossveins has been poorly explored. Using a genetic mosaic screen for mutations that disrupt BMP signaling and posterior crossvein development, we identify Gyc76C, a member of the receptor guanylyl cyclase family that includes mammalian natriuretic peptide receptors. We show that Gyc76C and the soluble cGMP-dependent kinase Foraging, likely linked by cGMP, are necessary for normal refinement and maintenance of long-range BMP signaling in the posterior crossvein. This does not occur through cell-autonomous crosstalk between cGMP and BMP signal transduction, but likely through altered extracellular activity of Sog. We identify a novel pathway leading from Gyc76C to the organization of the wing extracellular matrix by matrix metalloproteinases, and show that both the extracellular matrix and BMP signaling effects are largely mediated by changes in the activity of matrix metalloproteinases. We discuss parallels and differences between this pathway and other examples of cGMP activity in both Drosophila melanogaster and mammalian cells and tissues. Signaling between cells regulates many processes, including the choices cells make between different fates during development and regeneration, and misregulation of such signaling underlies many human pathologies. To understand how such signals control developmental decisions, it is necessary to elucidate both how cells regulate and respond to different levels of signaling, and how different types of signals combine and regulate each other. We have used genetic screening in the fruitfly Drosophila melanogaster to identify mutations that reduce or eliminate signals carried by Bone Morphogenetic Proteins (BMPs), and show that BMP signaling is sensitive Gyc76C, a peptide receptor that stimulates the production of cGMP in cells. We identify downstream intracellular effectors of this cGMP activity, but provide evidence that the effects on the BMP pathway are not mediated at the intracellular level, but rather through cGMP’s effects upon the extracellular matrix and matrix-remodeling proteinases, which in turn affects the activity of extracellular BMP-binding proteins. We discuss differences and parallels with other examples of cGMP activity in Drosophila melanogaster and mammals.
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Affiliation(s)
- Justin Schleede
- Department of Zoology, University of Wisconsin, Madison, Wisconsin, United States of America
- Genetics Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Seth S. Blair
- Department of Zoology, University of Wisconsin, Madison, Wisconsin, United States of America
- * E-mail:
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11
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Signaling by the engulfment receptor draper: a screen in Drosophila melanogaster implicates cytoskeletal regulators, Jun N-terminal Kinase, and Yorkie. Genetics 2014; 199:117-34. [PMID: 25395664 DOI: 10.1534/genetics.114.172544] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Draper, the Drosophila melanogaster homolog of the Ced-1 protein of Caenorhabditis elegans, is a cell-surface receptor required for the recognition and engulfment of apoptotic cells, glial clearance of axon fragments and dendritic pruning, and salivary gland autophagy. To further elucidate mechanisms of Draper signaling, we screened chromosomal deficiencies to identify loci that dominantly modify the phenotype of overexpression of Draper isoform II (suppressed differentiation of the posterior crossvein in the wing). We found evidence for 43 genetic modifiers of Draper II. Twenty-four of the 37 suppressor loci and 3 of the 6 enhancer loci were identified. An additional 5 suppressors and 2 enhancers were identified among mutations in functionally related genes. These studies reveal positive contributions to Drpr signaling for the Jun N-terminal Kinase pathway, supported by genetic interactions with hemipterous, basket, jun, and puckered, and for cytoskeleton regulation as indicated by genetic interactions with rac1, rac2, RhoA, myoblast city, Wiskcott-Aldrich syndrome protein, and the formin CG32138, and for yorkie and expanded. These findings indicate that Jun N-terminal Kinase activation and cytoskeletal remodeling collaborate in Draper signaling. Relationships between Draper signaling and Decapentaplegic signaling, insulin signaling, Salvador/Warts/Hippo signaling, apical-basal cell polarity, and cellular responses to mechanical forces are also discussed.
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Venken KJT, Bellen HJ. Chemical mutagens, transposons, and transgenes to interrogate gene function in Drosophila melanogaster. Methods 2014; 68:15-28. [PMID: 24583113 DOI: 10.1016/j.ymeth.2014.02.025] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/17/2014] [Accepted: 02/19/2014] [Indexed: 12/22/2022] Open
Abstract
The study of genetics, genes, and chromosomal inheritance was initiated by Thomas Morgan in 1910, when the first visible mutations were identified in fruit flies. The field expanded upon the work initiated by Herman Muller in 1926 when he used X-rays to develop the first balancer chromosomes. Today, balancers are still invaluable to maintain mutations and transgenes but the arsenal of tools has expanded vastly and numerous new methods have been developed, many relying on the availability of the genome sequence and transposable elements. Forward genetic screens based on chemical mutagenesis or transposable elements have resulted in the unbiased identification of many novel players involved in processes probed by specific phenotypic assays. Reverse genetic approaches have relied on the availability of a carefully selected set of transposon insertions spread throughout the genome to allow the manipulation of the region in the vicinity of each insertion. Lastly, the ability to transform Drosophila with single copy transgenes using transposons or site-specific integration using the ΦC31 integrase has allowed numerous manipulations, including the ability to create and integrate genomic rescue constructs, generate duplications, RNAi knock-out technology, binary expression systems like the GAL4/UAS system as well as other methods. Here, we will discuss the most useful methodologies to interrogate the fruit fly genome in vivo focusing on chemical mutagenesis, transposons and transgenes. Genome engineering approaches based on nucleases and RNAi technology are discussed in following chapters.
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Affiliation(s)
- Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Program in Developmental Biology, Baylor College of Medicine, TX 77030, United States.
| | - Hugo J Bellen
- Program in Developmental Biology, Departments of Molecular and Human Genetics, Department of Neuroscience, Howard Hughes Medical Institute, Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, United States.
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13
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Molnar C, de Celis JF. Tay bridge is a negative regulator of EGFR signalling and interacts with Erk and Mkp3 in the Drosophila melanogaster wing. PLoS Genet 2013; 9:e1003982. [PMID: 24348264 PMCID: PMC3861119 DOI: 10.1371/journal.pgen.1003982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 10/14/2013] [Indexed: 11/18/2022] Open
Abstract
The regulation of Extracellular regulated kinase (Erk) activity is a key aspect of signalling by pathways activated by extracellular ligands acting through tyrosine kinase transmembrane receptors. In this process, participate proteins with kinase activity that phosphorylate and activate Erk, as well as different phosphatases that inactivate Erk by de-phosphorylation. The state of Erk phosphorylation affects not only its activity, but also its subcellular localization, defining the repertoire of Erk target proteins, and consequently, the cellular response to Erk. In this work, we characterise Tay bridge as a novel component of the EGFR/Erk signalling pathway. Tay bridge is a large nuclear protein with a domain of homology with human AUTS2, and was previously identified due to the neuronal phenotypes displayed by loss-of-function mutations. We show that Tay bridge antagonizes EGFR signalling in the Drosophila melanogaster wing disc and other tissues, and that the protein interacts with both Erk and Mkp3. We suggest that Tay bridge constitutes a novel element involved in the regulation of Erk activity, acting as a nuclear docking for Erk that retains this protein in an inactive form in the nucleus. Extracellular regulated kinases (Erk) mediate signalling by pathways activated by tyrosine kinase transmembrane receptors. The level of activated Erk depends on a highly regulated balance between cytoplasmic kinases and nuclear/cytoplasmic phosphatases, which determine the state of Erk phosphorylation. This affects Erk activity and its subcellular localization, defining the repertoire of Erk targets, and consequently, the cellular response to Erk. In this work, we use a genetic approach to characterise the gene tay bridge as a novel component of the EGFR/Erk signalling pathway. Tay bridge has a domain of homology with human AUTS2, and was previously identified due to the neuronal phenotypes displayed by loss-of-function mutations. We show that Tay bridge antagonizes EGFR signalling in the Drosophila melanogaster wing disc and other tissues, and that the protein interacts with both Erk and Mkp3. We suggest that Tay bridge constitutes a novel element involved in the regulation of Erk activity, acting as a nuclear docking for Erk that retains this protein in an inactive form in the nucleus. These results could provide important insights into the clinical consequences of AUTS2 mutations in humans, which are related to behavioural perturbations including autism, mental retardation, Attention Deficit Hyperactivity Disorder and alcohol drinking behaviour.
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Affiliation(s)
- Cristina Molnar
- Centro de Biología Molecular “Severo Ochoa,” CSIC and Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose F. de Celis
- Centro de Biología Molecular “Severo Ochoa,” CSIC and Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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14
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Cipressa F, Cenci G. Effete, an E2 ubiquitin-conjugating enzyme with multiple roles in Drosophila development and chromatin organization. Fly (Austin) 2013; 7:256-62. [PMID: 24088712 DOI: 10.4161/fly.26567] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The Drosophila effete gene encodes an extremely conserved class I E2 ubiquitin-conjugating enzyme. Growing evidence indicates that Eff is involved in many cellular processes including eye development, maintenance of female germline stem cells, and regulation of apoptosis. Eff is also a major component of Drosophila chromatin and it is particularly enriched in chromatin with repressive properties. In addition, Eff is required for telomere protection and to prevent telomere fusion. Consistent with its multiple roles in chromatin maintenance, Eff is also one of the rare factors that modulate both telomere-induced and heterochromatin-induced position effect variegation.
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Affiliation(s)
- Francesca Cipressa
- Dipartimento di Biologia e Biotecnologie "C. Darwin"; SAPIENZA Università di Roma; Roma, Italy
| | - Giovanni Cenci
- Dipartimento di Biologia e Biotecnologie "C. Darwin"; SAPIENZA Università di Roma; Roma, Italy
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15
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Swaminathan A, Barnes VL, Fox S, Gammouh S, Pile LA. Identification of genetic suppressors of the Sin3A knockdown wing phenotype. PLoS One 2012; 7:e49563. [PMID: 23166712 PMCID: PMC3499482 DOI: 10.1371/journal.pone.0049563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
The role of the Sin3A transcriptional corepressor in regulating the cell cycle is established in various metazoans. Little is known, however, about the signaling pathways that trigger or are triggered by Sin3A function. To discover genes that work in similar or opposing pathways to Sin3A during development, we have performed an unbiased screen of deficiencies of the Drosophila third chromosome. Additionally, we have performed a targeted loss of function screen to identify cell cycle genes that genetically interact with Sin3A. We have identified genes that encode proteins involved in regulation of gene expression, signaling pathways and cell cycle that can suppress the curved wing phenotype caused by the knockdown of Sin3A. These data indicate that Sin3A function is quite diverse and impacts a wide variety of cellular processes.
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Affiliation(s)
- Aishwarya Swaminathan
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Valerie L. Barnes
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Stephanie Fox
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Sarah Gammouh
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Lori A. Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
- * E-mail:
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16
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Molnar C, Casado M, López-Varea A, Cruz C, de Celis JF. Genetic annotation of gain-of-function screens using RNA interference and in situ hybridization of candidate genes in the Drosophila wing. Genetics 2012; 192:741-52. [PMID: 22798488 PMCID: PMC3454894 DOI: 10.1534/genetics.112.143537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 07/07/2012] [Indexed: 11/18/2022] Open
Abstract
Gain-of-function screens in Drosophila are an effective method with which to identify genes that affect the development of particular structures or cell types. It has been found that a fraction of 2-10% of the genes tested, depending on the particularities of the screen, results in a discernible phenotype when overexpressed. However, it is not clear to what extent a gain-of-function phenotype generated by overexpression is informative about the normal function of the gene. Thus, very few reports attempt to correlate the loss- and overexpression phenotype for collections of genes identified in gain-of-function screens. In this work we use RNA interference and in situ hybridization to annotate a collection of 123 P-GS insertions that in combination with different Gal4 drivers affect the size and/or patterning of the wing. We identify the gene causing the overexpression phenotype by expressing, in a background of overexpression, RNA interference for the genes affected by each P-GS insertion. Then, we compare the loss and gain-of-function phenotypes obtained for each gene and relate them to its expression pattern in the wing disc. We find that 52% of genes identified by their overexpression phenotype are required during normal development. However, only in 9% of the cases analyzed was there some complementarity between the gain- and loss-of-function phenotype, suggesting that, in general, the overexpression phenotypes would not be indicative of the normal requirements of the gene.
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Affiliation(s)
- Cristina Molnar
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autónoma de Madrid and CSIC, Madrid 28049, Spain
| | - Mar Casado
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autónoma de Madrid and CSIC, Madrid 28049, Spain
| | - Ana López-Varea
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autónoma de Madrid and CSIC, Madrid 28049, Spain
| | | | - Jose F. de Celis
- Centro de Biología Molecular “Severo Ochoa,” Universidad Autónoma de Madrid and CSIC, Madrid 28049, Spain
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17
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Butchar JP, Cain D, Manivannan SN, McCue AD, Bonanno L, Halula S, Truesdell S, Austin CL, Jacobsen TL, Simcox A. New negative feedback regulators of Egfr signaling in Drosophila. Genetics 2012; 191:1213-26. [PMID: 22595244 PMCID: PMC3416002 DOI: 10.1534/genetics.112.141093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/07/2012] [Indexed: 12/18/2022] Open
Abstract
The highly conserved epidermal growth factor receptor (Egfr) pathway is required in all animals for normal development and homeostasis; consequently, aberrant Egfr signaling is implicated in a number of diseases. Genetic analysis of Drosophila melanogaster Egfr has contributed significantly to understanding this conserved pathway and led to the discovery of new components and targets. Here we used microarray analysis of third instar wing discs, in which Egfr signaling was perturbed, to identify new Egfr-responsive genes. Upregulated transcripts included five known targets, suggesting the approach was valid. We investigated the function of 29 previously uncharacterized genes, which had pronounced responses. The Egfr pathway is important for wing-vein patterning and using reverse genetic analysis we identified five genes that showed venation defects. Three of these genes are expressed in vein primordia and all showed transcriptional changes in response to altered Egfr activity consistent with being targets of the pathway. Genetic interactions with Egfr further linked two of the genes, Sulfated (Sulf1), an endosulfatase gene, and CG4096, an A Disintegrin And Metalloproteinase with ThromboSpondin motifs (ADAMTS) gene, to the pathway. Sulf1 showed a strong genetic interaction with the neuregulin-like ligand vein (vn) and may influence binding of Vn to heparan-sulfated proteoglycans (HSPGs). How Drosophila Egfr activity is modulated by CG4096 is unknown, but interestingly vertebrate EGF ligands are regulated by a related ADAMTS protein. We suggest Sulf1 and CG4096 are negative feedback regulators of Egfr signaling that function in the extracellular space to influence ligand activity.
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Affiliation(s)
- Jonathan P. Butchar
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Donna Cain
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | | | - Andrea D. McCue
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Liana Bonanno
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Sarah Halula
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Sharon Truesdell
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Christina L. Austin
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Thomas L. Jacobsen
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Amanda Simcox
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
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18
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Choo SW, White R, Russell S. Genome-wide analysis of the binding of the Hox protein Ultrabithorax and the Hox cofactor Homothorax in Drosophila. PLoS One 2011; 6:e14778. [PMID: 21483667 PMCID: PMC3071696 DOI: 10.1371/journal.pone.0014778] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 02/15/2011] [Indexed: 12/15/2022] Open
Abstract
Hox genes encode a family of transcription factors that are key developmental regulators with a highly conserved role in specifying segmental diversity along the metazoan body axis. Although they have been shown to regulate a wide variety of downstream processes, direct transcriptional targets have been difficult to identify and this has been a major obstacle to our understanding of Hox gene function. We report the identification of genome-wide binding sites for the Hox protein Ultrabithorax (Ubx) using a YFP-tagged Drosophila protein-trap line together with chromatin immunoprecipitation and microarray analysis. We identify 1,147 genes bound by Ubx at high confidence in chromatin from the haltere imaginal disc, a prominent site of Ubx function where it specifies haltere versus wing development. The functional relevance of these genes is supported by their overlap with genes differentially expressed between wing and haltere imaginal discs. The Ubx-bound gene set is highly enriched in genes involved in developmental processes and contains both high-level regulators as well as genes involved in more basic cellular functions. Several signalling pathways are highly enriched in the Ubx target gene set and our analysis supports the view that Hox genes regulate many levels of developmental pathways and have targets distributed throughout the gene network. We also performed genome-wide analysis of the binding sites for the Hox cofactor Homothorax (Hth), revealing a striking similarity with the Ubx binding profile. We suggest that these binding profiles may be strongly influenced by chromatin accessibility and provide evidence of a link between Ubx/Hth binding and chromatin state at genes regulated by Polycomb silencing. Overall, we define a set of direct Ubx targets in the haltere imaginal disc and suggest that chromatin accessibility has important implications for Hox target selection and for transcription factor binding in general.
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Affiliation(s)
- Siew Woh Choo
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Robert White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
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19
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Li J, Fang Y, Zhang L, Begna D. Honeybee (Apis mellifera ligustica) drone embryo proteomes. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:372-384. [PMID: 21172355 DOI: 10.1016/j.jinsphys.2010.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/09/2010] [Accepted: 12/10/2010] [Indexed: 05/30/2023]
Abstract
Little attention has been paid to the drone honeybee (Apis mellifera ligustica) which is a haploid individual carrying only the set of alleles that it inherits from its mother. Molecular mechanisms underlying drone embryogenesis are poorly understood. This study evaluated protein expression profiles of drone embryogenesis at embryonic ages of 24, 48 and 72h. More than 100 reproducible proteins were analyzed by mass spectrometry on 2D electrophoresis gels. Sixty-two proteins were significantly changed at the selected three experimental age points. Expression of the metabolic energy requirement-related protein peaked at the embryonic age of 48h, whereas development and metabolizing amino acid-related proteins expressed optimally at 72h. Cytoskeleton, protein folding and antioxidant-related proteins were highly expressed at 48 and 72h. Protein networks of the identified proteins were constructed and protein expressions were validated at the transcription level. This first proteomic study of drone embryogenesis in the honeybee may provide geneticists an exact timetable and candidate protein outline for further manipulations of drone stem cells.
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Affiliation(s)
- Jianke Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Science/Key Laboratory of Pollinating Insect Biology, 1# Beigou, Xiangshan, Haidian District, Beijing, China.
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20
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Hox gene Ultrabithorax regulates distinct sets of target genes at successive stages of Drosophila haltere morphogenesis. Proc Natl Acad Sci U S A 2011; 108:2855-60. [PMID: 21282633 DOI: 10.1073/pnas.1015077108] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hox genes encode highly conserved transcription factors that regionalize the animal body axis by controlling complex developmental processes. Although they are known to operate in multiple cell types and at different stages, we are still missing the batteries of genes targeted by any one Hox gene over the course of a single developmental process to achieve a particular cell and organ morphology. The transformation of wings into halteres by the Hox gene Ultrabithorax (Ubx) in Drosophila melanogaster presents an excellent model system to study the Hox control of transcriptional networks during successive stages of appendage morphogenesis and cell differentiation. We have used an inducible misexpression system to switch on Ubx in the wing epithelium at successive stages during metamorphosis--in the larva, prepupa, and pupa. We have then used extensive microarray expression profiling and quantitative RT-PCR to identify the primary transcriptional responses to Ubx. We find that Ubx targets range from regulatory genes like transcription factors and signaling components to terminal differentiation genes affecting a broad repertoire of cell behaviors and metabolic reactions. Ubx up- and down-regulates hundreds of downstream genes at each stage, mostly in a subtle manner. Strikingly, our analysis reveals that Ubx target genes are largely distinct at different stages of appendage morphogenesis, suggesting extensive interactions between Hox genes and hormone-controlled regulatory networks to orchestrate complex genetic programs during metamorphosis.
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21
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Olguín P, Glavic A, Mlodzik M. Intertissue mechanical stress affects Frizzled-mediated planar cell polarity in the Drosophila notum epidermis. Curr Biol 2011; 21:236-42. [PMID: 21276726 DOI: 10.1016/j.cub.2011.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 11/09/2010] [Accepted: 12/31/2010] [Indexed: 10/18/2022]
Abstract
Frizzled/planar cell polarity (Fz/PCP) signaling controls the orientation of sensory bristles and cellular hairs (trichomes) along the anteroposterior axis of the Drosophila thorax (notum). A subset of the trichome-producing notum cells differentiate as "tendon cells," serving as attachment sites for the indirect flight muscles (IFMs) to the exoskeleton. Through the analysis of chascon (chas), a gene identified by its ability to disrupt Fz/PCP signaling under overexpression conditions, and jitterbug (jbug)/filamin, we show that maintenance of anteroposterior planar polarization requires the notum epithelia to balance mechanical stress generated by the attachment of the IFMs. chas is expressed in notum tendon cells, and its loss of function disturbs cellular orientation at and near the regions where IFMs attach to the epidermis. This effect is independent of the Fz/PCP and fat/dachsous systems. The chas phenotype arises during normal shortening of the IFMs and is suppressed by genetic ablation of the IFMs. chas acts through jbug/filamin and cooperates with MyosinII to modulate the mechanoresponse of notum tendon cells. These observations support the notion that the ability of epithelia to respond to mechanical stress generated by one or more interactions with other tissues during development and organogenesis influences the maintenance of its shape and PCP features.
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Affiliation(s)
- Patricio Olguín
- Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029, USA
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22
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Resnik-Docampo M, de Celis JF. MAP4K3 is a component of the TORC1 signalling complex that modulates cell growth and viability in Drosophila melanogaster. PLoS One 2011; 6:e14528. [PMID: 21267071 PMCID: PMC3022576 DOI: 10.1371/journal.pone.0014528] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 12/17/2010] [Indexed: 12/03/2022] Open
Abstract
Background MAP4K3 is a conserved Ser/Thr kinase that has being found in connection with several signalling pathways, including the Imd, EGFR, TORC1 and JNK modules, in different organisms and experimental assays. We have analyzed the consequences of changing the levels of MAP4K3 expression in the development of the Drosophila wing, a convenient model system to characterize gene function during epithelial development. Methodology and Principal Findings Using loss-of-function mutants and over-expression conditions we find that MAP4K3 activity affects cell growth and viability in the Drosophila wing. These requirements are related to the modulation of the TORC1 and JNK signalling pathways, and are best detected when the larvae grow in a medium with low protein concentration (TORC1) or are exposed to irradiation (JNK). We also show that MAP4K3 display strong genetic interactions with different components of the InR/Tor signalling pathway, and can interact directly with the GTPases RagA and RagC and with the multi-domain kinase Tor. Conclusions and Significance We suggest that MAP4K3 has two independent functions during wing development, one related to the activation of the JNK pathway in response to stress and other in the assembling or activation of the TORC1 complex, being critical to modulate cellular responses to changes in nutrient availability.
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Affiliation(s)
- Martín Resnik-Docampo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose F. de Celis
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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23
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Enderle D, Beisel C, Stadler MB, Gerstung M, Athri P, Paro R. Polycomb preferentially targets stalled promoters of coding and noncoding transcripts. Genome Res 2010; 21:216-26. [PMID: 21177970 DOI: 10.1101/gr.114348.110] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Polycomb group (PcG) and Trithorax group (TrxG) of proteins are required for stable and heritable maintenance of repressed and active gene expression states. Their antagonistic function on gene control, repression for PcG and activity for TrxG, is mediated by binding to chromatin and subsequent epigenetic modification of target loci. Despite our broad knowledge about composition and enzymatic activities of the protein complexes involved, our understanding still lacks important mechanistic detail and a comprehensive view on target genes. In this study we use an extensive data set of ChIP-seq, RNA-seq, and genome-wide detection of transcription start sites (TSSs) to identify and analyze thousands of binding sites for the PcG proteins and Trithorax from a Drosophila S2 cell line. In addition of finding a preference for stalled promoter regions of annotated genes, we uncover many intergenic PcG binding sites coinciding with nonannotated TSSs. Interestingly, this set includes previously unknown promoters for primary transcripts of microRNA genes, thereby expanding the scope of Polycomb control to noncoding RNAs essential for development, apoptosis, and growth.
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Affiliation(s)
- Daniel Enderle
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
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24
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Terriente-Félix A, Molnar C, Gómez-Skarmeta JL, de Celis JF. A conserved function of the chromatin ATPase Kismet in the regulation of hedgehog expression. Dev Biol 2010; 350:382-92. [PMID: 21146514 DOI: 10.1016/j.ydbio.2010.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/24/2010] [Accepted: 12/01/2010] [Indexed: 12/31/2022]
Abstract
The development of the Drosophila melanogaster wing depends on its subdivision into anterior and posterior compartments, which constitute two independent cell lineages since their origin in the embryonic ectoderm. The anterior-posterior compartment boundary is the place where signaling by the Hedgehog pathway takes place, and this requires pathway activation in anterior cells by ligand expressed exclusively in posterior cells. Several mechanisms ensure the confinement of hedgehog expression to posterior cells, including repression by Cubitus interruptus, the co-repressor Groucho and Master of thick veins. In this work we identified Kismet, a chromodomain-containing protein of the SNF2-like family of ATPases, as a novel component of the hedgehog transcriptional repression mechanism in anterior compartment cells. In kismet mutants, hedgehog is ectopically expressed in a domain of anterior cells close to the anterior-posterior compartment boundary, causing inappropriate activation of the pathway and changes in the development of the central region of the wing. The contribution of Kismet to the silencing of hedgehog expression is limited to anterior cells with low levels of the repressor form of Cubitus interruptus. We also show that knockdown of CHD8, the kismet homolog in Xenopus tropicalis, is also associated with ectopic sonic hedgehog expression and up-regulation of one of its target genes in the eye, Pax2, indicating the evolutionary conservation of Kismet/CHD8 function in negatively controlling hedgehog expression.
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Affiliation(s)
- Ana Terriente-Félix
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid Cantoblanco, Madrid, Spain
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25
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Bap170, a subunit of the Drosophila PBAP chromatin remodeling complex, negatively regulates the EGFR signaling. Genetics 2010; 186:167-81. [PMID: 20551433 DOI: 10.1534/genetics.110.118695] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BAP and PBAP constitute the two different forms of the Drosophila melanogaster Brahma chromatin remodelers. A common multisubunit core, containing the Brahma ATPase, can associate either with Osa to form the BAP complex or with Bap170, Bap180, and Sayp to constitute the PBAP complex. Although required for many biological processes, recent genetic analyses revealed that one role of the BAP complex during Drosophila wing development is the proper regulation of EGFR target genes. Here, we show that Bap170, a distinctive subunit of the PBAP complex, participates instead in the negative regulation of EGFR signaling. In adults, loss of Bap170 generates phenotypes similar to the defects induced by hyperactivation of the EGFR pathway, such as overrecruitment of cone and photoreceptor cells and formation extra veins. In genetic interactions, bap170 mutations suppress the loss of veins and photoreceptors caused by mutations affecting the activity of the EGFR pathway. Our results suggest a dual requirement of the PBAP complex: for transcriptional repression of rhomboid and for efficient expression of argos. Interestingly, genetic evidence also indicates that Bap170-mediated repression of rho is inhibited by EGFR signaling, suggesting a scenario of mutual antagonism between EGFR signaling and PBAP function.
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Targeted gain-of-function screening in Drosophila using GAL4-UAS and random transposon insertions. Genet Res (Camb) 2009; 91:243-58. [PMID: 19640320 DOI: 10.1017/s0016672309990152] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Alterations in the activity level or temporal expression of key signalling genes elicit profound patterning effects during development. Consequently, gain-of-function genetic schemes that overexpress or misexpress such loci can identify novel candidates for functions essential for a developmental process. GAL4-Upstream Activating Sequence (UAS)-targeted regulation of gene expression in Drosophila has allowed rapid analyses of coding sequences for potential roles in specific tissues at particular developmental stages. GAL4 has also been combined with randomly mobilized transposons capable of UAS-directed misexpression or overexpression of flanking sequences. This combination has produced a genetic screening system that can uncover novel loci refractory to standard loss of function genetic approaches, such as redundant genes. Available libraries of strains with sequenced insertion sites can allow direct correlation of phenotypes to genetic function. These techniques have also been applied to genetic interaction screening, where a GAL4 driver and UAS-regulated insertion collection are combined with an extant mutant genotype. In this article, we summarize studies that have utilized GAL4-UAS overexpression or misexpression of random loci to screen for candidates involved in specific developmental processes.
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A gain-of-function screen identifying genes required for growth and pattern formation of the Drosophila melanogaster wing. Genetics 2009; 183:1005-26. [PMID: 19737745 DOI: 10.1534/genetics.109.107748] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The Drosophila melanogaster wing is a model system for analyzing the genetic control of organ size, shape, and pattern formation. The formation of the wing involves a variety of processes, such as cell growth, proliferation, pattern formation, and differentiation. These developmental processes are under genetic control, and many genes participating in specific aspects of wing development have already being characterized. In this work, we aim to identify novel genes regulating wing growth and patterning. To this end, we have carried out a gain-of-function screen generating novel P-UAS (upstream activating sequences) insertions allowing forced gene expression. We produced 3,340 novel P-UAS insertions and isolated 300 that cause a variety of wing phenotypes in combination with a Gal4 driver expressed exclusively in the central domain of the presumptive wing blade. The mapping of these P-UAS insertion sites allowed us to identify the gene that causes the gain-of-function phenotypes. We show that a fraction of these phenotypes are related to the induction of cell death in the domain of ectopic gene expression. Finally, we present a preliminary characterization of a gene identified in the screen, the function of which is required for the development of the L5 longitudinal vein.
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Cliffe ST, Kramer JM, Hussain K, Robben JH, de Jong EK, de Brouwer AP, Nibbeling E, Kamsteeg EJ, Wong M, Prendiville J, James C, Padidela R, Becknell C, van Bokhoven H, Deen PMT, Hennekam RCM, Lindeman R, Schenck A, Roscioli T, Buckley MF. SLC29A3 gene is mutated in pigmented hypertrichosis with insulin-dependent diabetes mellitus syndrome and interacts with the insulin signaling pathway. Hum Mol Genet 2009; 18:2257-65. [PMID: 19336477 DOI: 10.1093/hmg/ddp161] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pigmented hypertrichotic dermatosis with insulin-dependent diabetes (PHID) syndrome is a recently described autosomal recessive disorder associated with predominantly antibody negative, insulin-dependent diabetes mellitus. In order to identify the genetic basis of PHID and study its relationship with glucose metabolism, we performed homozygosity mapping in five unrelated families followed by candidate gene sequencing. Five loss-of-function mutations were identified in the SLC29A3 gene which encodes a member of a highly conserved protein family that transports nucleosides, nucleobases and nucleoside analogue drugs, hENT3. We show that PHID is allelic with a related syndrome without diabetes mellitus, H syndrome. The interaction of SLC29A3 with insulin signaling pathways was then studied using an established model in Drosophila melanogaster. Ubiquitous knockdown of the Drosophila ortholog of hENT3, dENT1 is lethal under stringent conditions; whereas milder knockdown induced scutellar bristle phenotypes similar to those previously reported in the knockdown of the Drosophila ortholog of the Islet gene. A cellular growth assay showed a reduction of cell size/number which could be rescued or enhanced by manipulation of the Drosophila insulin receptor and its downstream signaling effectors, dPI3K and dAkt. In summary, inactivating mutations in SLC29A3 cause a syndromic form of insulin-dependent diabetes in humans and in Drosophila profoundly affect cell size/number through interactions with the insulin signaling pathway. These data suggest that further investigation of the role of SLC29A3 in glucose metabolism is a priority for diabetes research.
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Affiliation(s)
- Simon T Cliffe
- Department of Haematology and Genetics, South Eastern Area Laboratory Services, Sydney, NSW 2031, Australia
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Terriente-Félix A, de Celis JF. Osa, a subunit of the BAP chromatin-remodelling complex, participates in the regulation of gene expression in response to EGFR signalling in the Drosophila wing. Dev Biol 2009; 329:350-61. [PMID: 19306864 DOI: 10.1016/j.ydbio.2009.03.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 03/05/2009] [Accepted: 03/12/2009] [Indexed: 01/27/2023]
Abstract
Gene expression is regulated in part by protein complexes containing ATP-dependent chromatin-remodelling factors of the SWI/SNF family. In Drosophila there is only one SWI/SNF protein, named Brahma, which forms the catalytic subunit of two complexes composed of different proteins. The protein Osa defines the BAP complex, and the proteins Polybromo and Bap170 are only present in the complex named PBAP. In this work we have analysed the functional requirements of Osa during Drosophila wing development, and found that osa is needed for cell growth and survival in the wing imaginal disc, and for the correct patterning of sensory organs, veins and the wing margin. Other members of the BAP complex, such as Snr1, Bap55, Mor and Brm, also share these functions of Osa. We focused on the requirement of Osa during the formation of the wing veins. Genetic interactions between osa alleles and mutations affecting the activity of the EGFR pathway suggest that one aspect of Osa is intimately related to the response to EGFR activity. Thus, loss of osa and EGFR signalling results in similar wing vein phenotypes, and osa alleles enhance the loss of veins caused by reduced EGFR activity. In addition, Osa is required for the expression of several targets of EGFR signalling, such as Delta, rhomboid and argos. We suggest that one role of Osa and Brm in the wing is to establish a chromatin environment in the regulatory regions of EGFR target genes, making them available for both activators and repressors and facilitating transcription in response to EGFR signalling.
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Affiliation(s)
- Ana Terriente-Félix
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
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A gain-of-function screen in zebrafish identifies a guanylate cyclase with a role in neuronal degeneration. Mol Genet Genomics 2009; 281:551-63. [PMID: 19221799 DOI: 10.1007/s00438-009-0428-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 01/22/2009] [Indexed: 01/04/2023]
Abstract
Manipulation of gene expression is one of the most informative ways to study gene function. Genetic screens have been an informative method to identify genes involved in developmental processes. In the zebrafish, loss-of-function screens have been the primary approach for these studies. We sought to complement loss-of-function screens using an unbiased approach to overexpress genes with a Gal4-UAS based system, similar to the gain-of-function screens in Drosophila. Using MMLV as a mutagenic vector, a cassette containing a UAS promoter was readily inserted in the genome, often at the 5' end of genes, allowing Gal4-dependent overexpression. We confirmed that genes downstream of the viral insertions were overexpressed in a Gal4-VP16 dependent manner. We further demonstrate that misexpression of one such downstream gene gucy2F, a membrane-bound guanylate cyclase, throughout the nervous system results in multiple defects including a loss of forebrain neurons. This suggests proper control of cGMP production is important in neuronal survival. From this study, we propose that this gain-of-function approach can be applied to large-scale genetic screens in a vertebrate model organism and may reveal previously unknown gene function.
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A targeted gain-of-function screen identifies genes affecting salivary gland morphogenesis/tubulogenesis in Drosophila. Genetics 2008; 181:543-65. [PMID: 19064711 DOI: 10.1534/genetics.108.094052] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During development individual cells in tissues undergo complex cell-shape changes to drive the morphogenetic movements required to form tissues. Cell shape is determined by the cytoskeleton and cell-shape changes critically depend on a tight spatial and temporal control of cytoskeletal behavior. We have used the formation of the salivary glands in the Drosophila embryo, a process of tubulogenesis, as an assay for identifying factors that impinge on cell shape and the cytoskeleton. To this end we have performed a gain-of-function screen in the salivary glands, using a collection of fly lines carrying EP-element insertions that allow the overexpression of downstream-located genes using the UAS-Gal4 system. We used a salivary-gland-specific fork head-Gal4 line to restrict expression to the salivary glands, in combination with reporters of cell shape and the cytoskeleton. We identified a number of genes known to affect salivary gland formation, confirming the effectiveness of the screen. In addition, we found many genes not implicated previously in this process, some having known functions in other tissues. We report the initial characterization of a subset of genes, including chickadee, rhomboid1, egalitarian, bitesize, and capricious, through comparison of gain- and loss-of-function phenotypes.
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Glavic A, Molnar C, Cotoras D, de Celis JF. Drosophila Axud1 is involved in the control of proliferation and displays pro-apoptotic activity. Mech Dev 2008; 126:184-97. [PMID: 19084594 DOI: 10.1016/j.mod.2008.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Revised: 11/18/2008] [Accepted: 11/19/2008] [Indexed: 11/29/2022]
Abstract
Cell division rates and apoptosis sculpt the growing organs, and its regulation implements the developmental programmes that define organ size and shape. The balance between oncogenes and tumour suppressors modulate the cell cycle and the apoptotic machinery to achieve this goal, promoting and restricting proliferation or, in certain conditions, inducing the apoptotic programme. Analysis of human cancer cells with mutation in AXIN gene has uncovered the potential function of AXUD1 as a tumour suppressor. It has been described that Human AXUD1 is a nuclear protein. We find that a DAxud1-GFP fusion protein is localised to the nucleus during interphase, where it accumulates associated to the nuclear envelope, but becomes distributed in a diffused pattern in the nucleus of mitotic cells. We have analysed the function of the Drosophila AXUD1 homologue, and find that DAxud1 behaves as a tumour suppressor that regulates the proliferation rhythm of imaginal cells. Knocking down the activity of DAxud1 enhances the proliferation of these cells, causing in addition a reduction in cell size. Conversely, the increase in DAxud1 expression impedes cell cycle progression at mitosis through disturbance of Cdk1 activity, and induces the apoptosis of these cells in a JNK-dependent manner.
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Affiliation(s)
- Alvaro Glavic
- Millennium Nucleus Center for Genomics of the Cell, Department of Biology, Faculty of Sciences, University of Chile, Las Palmeras 3425, Santiago, Chile.
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Jao LE, Maddison L, Chen W, Burgess SM. Using retroviruses as a mutagenesis tool to explore the zebrafish genome. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:427-43. [PMID: 18977782 DOI: 10.1093/bfgp/eln038] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We review different uses of the retroviral mutagenesis technology as the tool to manipulate the zebrafish genome. In addition to serving as a mutagen in a phenotype-driven forward mutagenesis screen as it was originally adapted for, retroviral insertional mutagenesis can also be exploited in reverse genetic approaches, delivering enhancer- and gene-trap vectors for the purpose of examining gene expression patterns and mutagenesis, making sensitized mutants amenable for chemical and genetic modifier screens, and producing gain-of-function mutations by epigenetically overexpressing the retroviral-inserted genes. From a technology point of view, we also summarize the recent advances in the high-throughput cloning of retroviral integration sites, a pivotal step toward identifying mutations. Lastly, we point to some potential directions that retroviral mutagenesis might take from the lessons of studying other model organisms.
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Affiliation(s)
- Li-En Jao
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Eid JP, Arias AM, Robertson H, Hime GR, Dziadek M. The Drosophila STIM1 orthologue, dSTIM, has roles in cell fate specification and tissue patterning. BMC DEVELOPMENTAL BIOLOGY 2008; 8:104. [PMID: 18950512 PMCID: PMC2584103 DOI: 10.1186/1471-213x-8-104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Accepted: 10/24/2008] [Indexed: 11/16/2022]
Abstract
Background Mammalian STIM1 and STIM2 and the single Drosophila homologue dSTIM have been identified as key regulators of store-operated Ca2+ entry in cells. STIM proteins function both as molecular sensors of Ca2+concentration in the endoplasmic reticulum (ER) and the molecular triggers that activate SOC channels in the plasma membrane. Ca2+ is a crucial intracellular messenger utilised in many cellular processes, and regulators of Ca2+ homeostasis in the ER and cytosol are likely to play important roles in developmental processes. STIM protein expression is altered in several tumour types but the role of these proteins in developmental signalling pathways has not been thoroughly examined. Results We have investigated the expression and developmental function of dSTIM in Drosophila and shown that dSTIM is widely expressed in embryonic and larval tissues. Using the UAS-Gal4 induction system, we have expressed full-length dSTIM protein and a dsRNAi construct in different tissues. We demonstrate an essential role for dSTIM in larval development and survival, and a tissue-specific role in specification of mechanosensory bristles in the notum and specification of wing vein thickness. Conclusion Our studies show that dSTIM regulates growth and patterning of imaginal discs and indicate potential interactions with the Notch and Wingless signaling pathways. These interactions may be relevant to studies implicating STIM family proteins in tumorigenesis.
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Affiliation(s)
- Jean-Pierre Eid
- Department of Anatomy and Cell Biology, University of Melbourne, Victoria 3010, Australia.
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Abstract
Over the past decade the adoption and refinement of the GAL4 system by the Drosophila field has resulted in a wide array of tools with which the researcher can drive transgene expression in a precise spatiotemporal pattern. The GAL4 system relies on two components: (1) GAL4, a transcriptional activator from yeast, which is expressed in a tissue-specific manner and (2) a transgene under the control of the upstream activation sequence that is bound by GAL4 (UASG). The two components are brought together in a simple genetic cross. In the progeny of the cross, the transgene is only transcribed in those cells or tissues expressing the GAL4 protein. Recent modifications of the GAL4 system have improved the control of both the initiation and the spatial restriction of transgene expression. Here we describe the GAL4 system highlighting the properties that make it a powerful tool for the analysis of gene function in Drosophila and higher organisms.
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Affiliation(s)
- David A Elliott
- Wellcome Trust/Cancer Research UK Gurdon Institute, and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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Barrio R, López-Varea A, Casado M, de Celis JF. Characterization of dSnoN and its relationship to Decapentaplegic signaling in Drosophila. Dev Biol 2007; 306:66-81. [PMID: 17434471 DOI: 10.1016/j.ydbio.2007.02.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 02/26/2007] [Accepted: 02/28/2007] [Indexed: 12/13/2022]
Abstract
Vertebrate members of the ski/snoN family of proto-oncogenes antagonize TGFbeta and BMP signaling in a variety of experimental situations. This activity of Ski/SnoN proteins is related to their ability to interact with Smads, the proteins acting as key mediators of the transcriptional response to the TGFbeta superfamily members. However, despite extensive efforts to identify the physiological roles of the Ski/SnoN proteins, it is not yet clear whether they participate in regulating Activin and/or BMP signaling during normal development. It is therefore crucial to examine their roles in vivo mostly because of the large number of known Ski/SnoN-interacting proteins and the association between the up-regulation of these genes and cancer progression. Here we characterize the Drosophila homolog to vertebrate ski and snoN genes. The Drosophila dSnoN protein retains the ability of its vertebrate counterparts to antagonize BMP signaling in vivo and in cultured cells. dSnoN does not interfere with Mad phosphorylation but it interacts genetically with Mad, Medea and dSmad2. Mutations in either the Smad2-3 or Smad4 putative binding sites of dSnoN prevent the antagonism of dSnoN towards Dpp signaling, although homozygous flies for these mutations or for a genetic deficiency of the locus are viable and have wings of normal size and pattern.
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Affiliation(s)
- Rosa Barrio
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
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