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Bhat G, Li K, Locke G, Theodorou M, Kilambi K, Hori K, Ho D, Obar R, Williams L, Parzen H, Dephoure N, Braun C, Muskavitch M, Celniker SE, Gygi S, Artavanis-Tsakonas S. Next-generation Drosophila protein interactome map and its functional implications. Dev Cell 2024; 59:2506-2517.e6. [PMID: 38944040 DOI: 10.1016/j.devcel.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 01/27/2024] [Accepted: 06/05/2024] [Indexed: 07/01/2024]
Abstract
We describe a next-generation Drosophila protein interaction map-"DPIM2"-established from affinity purification-mass spectrometry of 5,805 baits, covering the largest fraction of the Drosophila proteome. The network contains 32,668 interactions among 3,644 proteins, organized into 632 clusters representing putative functional modules. Our analysis expands the pool of known protein interactions in Drosophila, provides annotation for poorly studied genes, and postulates previously undescribed protein interaction relationships. The predictive power and functional relevance of this network are probed through the lens of the Notch signaling pathway, and we find that newly identified members of complexes that include known Notch modifiers can also modulate Notch signaling. DPIM2 allows direct comparisons with a recently published human protein interaction network, defining the existence of functional interactions conserved across species. Thus, DPIM2 defines a valuable resource for predicting protein co-complex memberships and functional associations as well as generates functional hypotheses regarding specific protein interactions.
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Affiliation(s)
- Guruharsha Bhat
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Biogen, 225 Binney St, Cambridge, MA 02142, USA
| | - Kejie Li
- Biogen, 225 Binney St, Cambridge, MA 02142, USA; Triveni Bio, Watertown, MA, USA
| | - George Locke
- Biogen, 225 Binney St, Cambridge, MA 02142, USA; Senda Biosciences, Cambridge, MA, USA
| | - Marina Theodorou
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Biogen, 225 Binney St, Cambridge, MA 02142, USA; Nereid Therpaeutics, Boston, MA 02210, USA
| | - Krishna Kilambi
- Biogen, 225 Binney St, Cambridge, MA 02142, USA; Pfizer, Cambridge, MA, USA
| | - Kazuya Hori
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; University of Fukui, Fukui, Japan
| | - Diana Ho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Robert Obar
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Leah Williams
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Hannah Parzen
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Craig Braun
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Marc Muskavitch
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
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Ning P, Zheng Z, Aweya JJ, Yao D, Li S, Ma H, Wang F, Zhang Y. Litopenaeus vannamei notch affects lipopolysaccharides induced reactive oxygen species. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:74-82. [PMID: 29155012 DOI: 10.1016/j.dci.2017.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Notch signaling pathway was originally discovered in the development stage of drosophila but has recently been found to play essential roles in innate immunity. Most previous studies on Notch have focused on mammals, whereas, in this study, we employed the shrimp Litopenaeus vannamei as a model to study the functions of Notch in invertebrate innate immune system. Our results showed that LvNotch was highly expressed in hemocytes and could be strongly induced by lipopolysaccharides (LPS) injection. Small interfering RNA (siRNA)-mediated knockdown of LvNotch could significantly increase LPS induced L. vannamei mortality, which might be due to the fact that LPS induced ROS was greatly enhanced in LvNotch knockdown shrimps. Further, quantitative polymerase chain reaction (qPCR) analysis revealed that LvNotch could affect the expression of multiple genes, including dorsal, relish, anti-lipopolysaccharide factor 1 (ALF1), ALF3 and NADH dehydrogenases which were upregulated, and Hypoxia-inducible factor (HIF, α/β) which were downregulated in LPS treated shrimps. In summary, LvNotch is important in the control of inflammation-induced ROS production in shrimp.
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Affiliation(s)
- Pei Ning
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Zhihong Zheng
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Jude Juventus Aweya
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Defu Yao
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Shengkang Li
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Hongyu Ma
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China
| | - Fan Wang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
| | - Yueling Zhang
- Department of Biology and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, China.
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Salazar JL, Yamamoto S. Integration of Drosophila and Human Genetics to Understand Notch Signaling Related Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:141-185. [PMID: 30030826 PMCID: PMC6233323 DOI: 10.1007/978-3-319-89512-3_8] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Notch signaling research dates back to more than one hundred years, beginning with the identification of the Notch mutant in the fruit fly Drosophila melanogaster. Since then, research on Notch and related genes in flies has laid the foundation of what we now know as the Notch signaling pathway. In the 1990s, basic biological and biochemical studies of Notch signaling components in mammalian systems, as well as identification of rare mutations in Notch signaling pathway genes in human patients with rare Mendelian diseases or cancer, increased the significance of this pathway in human biology and medicine. In the 21st century, Drosophila and other genetic model organisms continue to play a leading role in understanding basic Notch biology. Furthermore, these model organisms can be used in a translational manner to study underlying mechanisms of Notch-related human diseases and to investigate the function of novel disease associated genes and variants. In this chapter, we first briefly review the major contributions of Drosophila to Notch signaling research, discussing the similarities and differences between the fly and human pathways. Next, we introduce several biological contexts in Drosophila in which Notch signaling has been extensively characterized. Finally, we discuss a number of genetic diseases caused by mutations in genes in the Notch signaling pathway in humans and we expand on how Drosophila can be used to study rare genetic variants associated with these and novel disorders. By combining modern genomics and state-of-the art technologies, Drosophila research is continuing to reveal exciting biology that sheds light onto mechanisms of disease.
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Affiliation(s)
- Jose L Salazar
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX, USA.
- Program in Developmental Biology, BCM, Houston, TX, USA.
- Department of Neuroscience, BCM, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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The Notch Interactome: Complexity in Signaling Circuitry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1066:125-140. [PMID: 30030825 DOI: 10.1007/978-3-319-89512-3_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Notch pathway controls a very broad spectrum of cell fates in metazoans during development, influencing proliferation, differentiation and cell death. Given its central role in normal development and homeostasis, misregulation of Notch signals can lead to various disorders including cancer. How the Notch pathway mediates such pleiotropic and differential effects is of fundamental importance. It is becoming increasingly clear through a number of large-scale genetic and proteomic studies that Notch interacts with a staggeringly large number of other genes and pathways in a context-dependent, complex, and highly regulated network, which determines the ultimate biological outcome. How best to interpret and analyze the continuously increasing wealth of data on Notch interactors remains a challenge. Here we review the current state of genetic and proteomic data related to the Notch interactome.
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Mašek J, Andersson ER. The developmental biology of genetic Notch disorders. Development 2017; 144:1743-1763. [PMID: 28512196 DOI: 10.1242/dev.148007] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Notch signaling regulates a vast array of crucial developmental processes. It is therefore not surprising that mutations in genes encoding Notch receptors or ligands lead to a variety of congenital disorders in humans. For example, loss of function of Notch results in Adams-Oliver syndrome, Alagille syndrome, spondylocostal dysostosis and congenital heart disorders, while Notch gain of function results in Hajdu-Cheney syndrome, serpentine fibula polycystic kidney syndrome, infantile myofibromatosis and lateral meningocele syndrome. Furthermore, structure-abrogating mutations in NOTCH3 result in CADASIL. Here, we discuss these human congenital disorders in the context of known roles for Notch signaling during development. Drawing on recent analyses by the exome aggregation consortium (EXAC) and on recent studies of Notch signaling in model organisms, we further highlight additional Notch receptors or ligands that are likely to be involved in human genetic diseases.
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Affiliation(s)
- Jan Mašek
- Karolinska Institutet, Huddinge 14183, Sweden
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A large-scale in vivo RNAi screen to identify genes involved in Notch-mediated follicle cell differentiation and cell cycle switches. Sci Rep 2015. [PMID: 26205122 PMCID: PMC4513280 DOI: 10.1038/srep12328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During Drosophila oogenesis, follicle cells sequentially undergo three distinct cell-cycle programs: the mitotic cycle, endocycle, and gene amplification. Notch signaling plays a central role in regulating follicle-cell differentiation and cell-cycle switches; its activation is essential for the mitotic cycle/endocycle (M/E) switch. Cut, a linker between Notch signaling and cell-cycle regulators, is specifically downregulated by Notch during the endocycle stage. To determine how signaling pathways coordinate during the M/E switch and to identify novel genes involved in follicle cell differentiation, we performed an in vivo RNAi screen through induced knockdown of gene expression and examination of Cut expression in follicle cells. We screened 2205 RNAi lines and found 33 genes regulating Cut expression during the M/E switch. These genes were confirmed with the staining of two other Notch signaling downstream factors, Hindsight and Broad, and validated with multiple independent RNAi lines. We applied gene ontology software to find enriched biological meaning and compared our results with other publications to find conserved genes across tissues. Specifically, we found earlier endocycle entry in anterior follicle cells than those in the posterior, identified that the insulin-PI3K pathway participates in the precise M/E switch, and suggested Nejire as a cofactor of Notch signaling during oogenesis.
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8
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Yu Z, Liu J, Deng WM, Jiao R. Histone chaperone CAF-1: essential roles in multi-cellular organism development. Cell Mol Life Sci 2015; 72:327-37. [PMID: 25292338 PMCID: PMC11114026 DOI: 10.1007/s00018-014-1748-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/16/2014] [Accepted: 09/29/2014] [Indexed: 01/01/2023]
Abstract
More and more studies have shown chromatin remodelers and histone modifiers play essential roles in regulating developmental patterns by organizing specific chromosomal architecture to establish programmed transcriptional profiles, with implications that histone chaperones execute a coordinating role in these processes. Chromatin assembly factor-1 (CAF-1), an evolutionarily conserved three-subunit protein complex, was identified as a histone chaperone coupled with DNA replication and repair in cultured mammalian cells and yeasts. Interestingly, recent findings indicate CAF-1 may have important regulatory roles during development by interacting with specific transcription factors and epigenetic regulators. In this review, we focus on the essential roles of CAF-1 in regulating heterochromatin organization, asymmetric cell division, and specific signal transduction through epigenetic modulations of the chromatin. In the end, we aim at providing a current image of facets of CAF-1 as a histone chaperone to orchestrate cell proliferation and differentiation during multi-cellular organism development.
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Affiliation(s)
- Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Jiyong Liu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295 USA
| | - Renjie Jiao
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100080 China
- Guangzhou Hoffmann Institute of Immunology, School of Basic Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou, 510182 China
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Zacharioudaki E, Bray SJ. Tools and methods for studying Notch signaling in Drosophila melanogaster. Methods 2014; 68:173-82. [PMID: 24704358 PMCID: PMC4059942 DOI: 10.1016/j.ymeth.2014.03.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/23/2014] [Accepted: 03/25/2014] [Indexed: 01/08/2023] Open
Abstract
Notch signaling involves a highly conserved pathway that mediates communication between neighboring cells. Activation of Notch by its ligands, results in the release of the Notch intracellular domain (NICD), which enters the nucleus and regulates transcription. This pathway has been implicated in many developmental decisions and diseases (including cancers) over the past decades. The simplicity of the Notch pathway in Drosophila melanogaster, in combination with the availability of powerful genetics, make this an attractive model for studying fundamental principles of Notch regulation and function. In this article we present some of the established and emerging tools that are available to monitor and manipulate the Notch pathway in Drosophila and discuss their strengths and weaknesses.
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Affiliation(s)
- Evanthia Zacharioudaki
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Sarah J Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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Yu Z, Wu H, Chen H, Wang R, Liang X, Liu J, Li C, Deng WM, Jiao R. CAF-1 promotes Notch signaling through epigenetic control of target gene expression during Drosophila development. Development 2013; 140:3635-44. [PMID: 23942516 DOI: 10.1242/dev.094599] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The histone chaperone CAF-1 is known for its role in DNA replication-coupled histone deposition. However, loss of function causes lethality only in higher multicellular organisms such as mice and flies, but not in unicellular organisms such as yeasts, suggesting that CAF-1 has other important functions than histone deposition during animal development. Emerging evidence indicates that CAF-1 also has a role in higher order chromatin organization and heterochromatin-mediated gene expression; it remains unclear whether CAF-1 has a role in specific signaling cascades to promote gene expression during development. Here, we report that knockdown of one of the subunits of Drosophila CAF-1, dCAF-1-p105 (Caf1-105), results in phenotypes that resemble those of, and are augmented synergistically by, mutations of Notch positive regulatory pathway components. Depletion of dCAF-1-p105 leads to abrogation of cut expression and to downregulation of other Notch target genes in wing imaginal discs. dCAF-1-p105 is associated with Suppressor of Hairless [Su(H)] and regulates its binding to the enhancer region of E(spl)mβ. The association of dCAF-1-p105 with Su(H) on chromatin establishes an active local chromatin status for transcription by maintaining a high level of histone H4 acetylation. In response to induced Notch activation, dCAF-1 associates with the Notch intracellular domain to activate the expression of Notch target genes in cultured S2 cells, manifesting the role of dCAF-1 in Notch signaling. Together, our results reveal a novel epigenetic function of dCAF-1 in promoting Notch pathway activity that regulates normal Drosophila development.
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Affiliation(s)
- Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, The Chinese Academy of Sciences, Datun Road 15, Beijing, China
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Le Bouteiller M, Souilhol C, Beck-Cormier S, Stedman A, Burlen-Defranoux O, Vandormael-Pournin S, Bernex F, Cumano A, Cohen-Tannoudji M. Notchless-dependent ribosome synthesis is required for the maintenance of adult hematopoietic stem cells. ACTA ACUST UNITED AC 2013; 210:2351-69. [PMID: 24062412 PMCID: PMC3804936 DOI: 10.1084/jem.20122019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Conditional deletion of Notchless leads to rapid deletion and exhaustion of HSCs and early progenitor cells, whereas committed progenitor cells survive as a result of differences in ribosomal biogenesis. Blood cell production relies on the coordinated activities of hematopoietic stem cells (HSCs) and multipotent and lineage-restricted progenitors. Here, we identify Notchless (Nle) as a critical factor for HSC maintenance under both homeostatic and cytopenic conditions. Nle deficiency leads to a rapid and drastic exhaustion of HSCs and immature progenitors and failure to maintain quiescence in HSCs. In contrast, Nle is dispensable for cycling-restricted progenitors and differentiated cells. In yeast, Nle/Rsa4 is essential for ribosome biogenesis, and we show that its role in pre-60S subunit maturation has been conserved in the mouse. Despite its implication in this basal cellular process, Nle deletion affects ribosome biogenesis only in HSCs and immature progenitors. Ribosome biogenesis defects are accompanied by p53 activation, which causes their rapid exhaustion. Collectively, our findings establish an essential role for Nle in HSC and immature progenitor functions and uncover previously unsuspected differences in ribosome biogenesis that distinguish stem cells from restricted progenitor populations.
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Affiliation(s)
- Marie Le Bouteiller
- Institut Pasteur, Unité de Génétique Fonctionnelle de la Souris, Département de Biologie du Développement et Cellules Souches, F-75015 Paris, France
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12
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Identification of genes underlying hypoxia tolerance in Drosophila by a P-element screen. G3-GENES GENOMES GENETICS 2012; 2:1169-78. [PMID: 23050227 PMCID: PMC3464109 DOI: 10.1534/g3.112.003681] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 07/23/2012] [Indexed: 01/17/2023]
Abstract
Hypoxia occurs in physiologic conditions (e.g. high altitude) or during pathologic states (e.g. ischemia). Our research is focused on understanding the molecular mechanisms that lead to adaptation and survival or injury to hypoxic stress using Drosophila as a model system. To identify genes involved in hypoxia tolerance, we screened the P-SUP P-element insertion lines available for all the chromosomes of Drosophila. We screened for the eclosion rates of embryos developing under 5% O(2) condition and the number of adult flies surviving one week after eclosion in the same hypoxic environment. Out of 2187 lines (covering ~1870 genes) screened, 44 P-element lines representing 44 individual genes had significantly higher eclosion rates (i.e. >70%) than those of the controls (i.e. ~7-8%) under hypoxia. The molecular function of these candidate genes ranged from cell cycle regulation, DNA or protein binding, GTP binding activity, and transcriptional regulators. In addition, based on pathway analysis, we found these genes are involved in multiple pathways, such as Notch, Wnt, Jnk, and Hedgehog. Particularly, we found that 20 out of the 44 candidate genes are linked to Notch signaling pathway, strongly suggesting that this pathway is essential for hypoxia tolerance in flies. By employing the UAS/RNAi-Gal4 system, we discovered that genes such as osa (linked to Wnt and Notch pathways) and lqf (Notch regulator) play an important role in survival and development under hypoxia in Drosophila. Based on these results and our previous studies, we conclude that hypoxia tolerance is a polygenic trait including the Notch pathway.
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Fisher KH, Wright VM, Taylor A, Zeidler MP, Brown S. Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway. BMC Genomics 2012; 13:506. [PMID: 23006893 PMCID: PMC3526451 DOI: 10.1186/1471-2164-13-506] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 09/12/2012] [Indexed: 12/01/2022] Open
Abstract
Background Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated. Results Here we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols. Conclusions Our work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens.
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Affiliation(s)
- Katherine H Fisher
- The MRC Centre for Developmental and Biomedical Genetics and The Department of Biomedical Science, University of Sheffield, Firth Court,Western Bank, Sheffield S10 2TN, UK
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Guruharsha KG, Kankel MW, Artavanis-Tsakonas S. The Notch signalling system: recent insights into the complexity of a conserved pathway. Nat Rev Genet 2012; 13:654-66. [PMID: 22868267 DOI: 10.1038/nrg3272] [Citation(s) in RCA: 529] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Notch signalling links the fate of one cell to that of an immediate neighbour and consequently controls differentiation, proliferation and apoptotic events in multiple metazoan tissues. Perturbations in this pathway activity have been linked to several human genetic disorders and cancers. Recent genome-scale studies in Drosophila melanogaster have revealed an extraordinarily complex network of genes that can affect Notch activity. This highly interconnected network contrasts our traditional view of the Notch pathway as a simple linear sequence of events. Although we now have an unprecedented insight into the way in which such a fundamental signalling mechanism is controlled by the genome, we are faced with serious challenges in analysing the underlying molecular mechanisms of Notch signal control.
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Affiliation(s)
- K G Guruharsha
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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15
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Hainaut M, Sagnier T, Berenger H, Pradel J, Graba Y, Miotto B. The MYST-containing protein Chameau is required for proper sensory organ specification during Drosophila thorax morphogenesis. PLoS One 2012; 7:e32882. [PMID: 22412942 PMCID: PMC3295779 DOI: 10.1371/journal.pone.0032882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 02/04/2012] [Indexed: 12/15/2022] Open
Abstract
The adult thorax of Drosophila melanogaster is covered by a stereotyped pattern of mechanosensory bristles called macrochaetes. Here, we report that the MYST containing protein Chameau (Chm) contributes to the establishment of this pattern in the most dorsal part of the thorax. Chm mutant pupae present extra-dorsocentral (DC) and scutellar (SC) macrochaetes, but a normal number of the other macrochaetes. We provide evidences that chm restricts the singling out of sensory organ precursors from proneural clusters and genetically interacts with transcriptional regulators involved in the regulation of achaete and scute in the DC and SC proneural cluster. This function of chm likely relies on chromatin structure regulation since a protein with a mutation in the conserved catalytic site fails to rescue the formation of supernumerary DC and SC bristles in chm mutant flies. This is further supported by the finding that mutations in genes encoding chromatin modifiers and remodeling factors, including Polycomb group (PcG) and Trithorax group (TrxG) members, dominantly modulate the penetrance of chm extra bristle phenotype. These data support a critical role for chromatin structure modulation in the establishment of the stereotyped sensory bristle pattern in the fly thorax.
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Affiliation(s)
- Matthieu Hainaut
- Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France
| | - Thierry Sagnier
- Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France
| | - Hélène Berenger
- Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France
| | - Jacques Pradel
- Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France
| | - Yacine Graba
- Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France
- * E-mail: (YG); (BM)
| | - Benoit Miotto
- Institut de Biologie du Développement de Marseille-Luminy, CNRS UMR6216/Université de la Méditerranée, Marseille, France
- * E-mail: (YG); (BM)
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Notch signaling is antagonized by SAO-1, a novel GYF-domain protein that interacts with the E3 ubiquitin ligase SEL-10 in Caenorhabditis elegans. Genetics 2012; 190:1043-57. [PMID: 22209900 DOI: 10.1534/genetics.111.136804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Notch signaling pathways can be regulated through a variety of cellular mechanisms, and genetically compromised systems provide useful platforms from which to search for the responsible modulators. The Caenorhabditis elegans gene aph-1 encodes a component of γ-secretase, which is essential for Notch signaling events throughout development. By looking for suppressors of the incompletely penetrant aph-1(zu147) mutation, we identify a new gene, sao-1 (suppressor of aph-one), that negatively regulates aph-1(zu147) activity in the early embryo. The sao-1 gene encodes a novel protein that contains a GYF protein-protein interaction domain and interacts specifically with SEL-10, an Fbw7 component of SCF E3 ubiquitin ligases. We demonstrate that the embryonic lethality of aph-1(zu147) mutants can be suppressed by removing sao-1 activity or by mutations that disrupt the SAO-1-SEL-10 protein interaction. Decreased sao-1 activity also influences Notch signaling events when they are compromised at different molecular steps of the pathway, such as at the level of the Notch receptor GLP-1 or the downstream transcription factor LAG-1. Combined analysis of the SAO-1-SEL-10 protein interaction and comparisons of sao-1 and sel-10 genetic interactions suggest a possible role for SAO-1 as an accessory protein that participates with SEL-10 in downregulation of Notch signaling. This work provides the first mutant analysis of a GYF-domain protein in either C. elegans or Drosophila and introduces a new type of Fbw7-interacting protein that acts in a subset of Fbw7 functions.
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Rotstein B, Molnar D, Adryan B, Llimargas M. Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PLoS One 2011; 6:e28985. [PMID: 22216153 PMCID: PMC3245245 DOI: 10.1371/journal.pone.0028985] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/17/2011] [Indexed: 11/18/2022] Open
Abstract
The Drosophila transcription factor Tramtrack (Ttk) is involved in a wide range of developmental decisions, ranging from early embryonic patterning to differentiation processes in organogenesis. Given the wide spectrum of functions and pleiotropic effects that hinder a comprehensive characterisation, many of the tissue specific functions of this transcription factor are only poorly understood. We recently discovered multiple roles of Ttk in the development of the tracheal system on the morphogenetic level. Here, we sought to identify some of the underlying genetic components that are responsible for the tracheal phenotypes of Ttk mutants. We therefore profiled gene expression changes after Ttk loss- and gain-of-function in whole embryos and cell populations enriched for tracheal cells. The analysis of the transcriptomes revealed widespread changes in gene expression. Interestingly, one of the most prominent gene classes that showed significant opposing responses to loss- and gain-of-function was annotated with functions in chitin metabolism, along with additional genes that are linked to cellular responses, which are impaired in ttk mutants. The expression changes of these genes were validated by quantitative real-time PCR and further functional analysis of these candidate genes and other genes also expected to control tracheal tube size revealed at least a partial explanation of Ttk's role in tube size regulation. The computational analysis of our tissue-specific gene expression data highlighted the sensitivity of the approach and revealed an interesting set of novel putatively tracheal genes.
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Affiliation(s)
- Barbara Rotstein
- Institut de Biologia Molecular de Barcelona, CSIC, Barcelona, Spain
| | - David Molnar
- Department of Genetics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Boris Adryan
- Department of Genetics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (BA); (ML)
| | - Marta Llimargas
- Institut de Biologia Molecular de Barcelona, CSIC, Barcelona, Spain
- * E-mail: (BA); (ML)
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Marygold SJ, Walker C, Orme M, Leevers S. Genetic characterization of ebi reveals its critical role in Drosophila wing growth. Fly (Austin) 2011; 5:291-303. [PMID: 22041576 DOI: 10.4161/fly.5.4.18276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The ebi gene of Drosophila melanogaster has been implicated in diverse signalling pathways, cellular functions and developmental processes. However, a thorough genetic analysis of this gene has been lacking and the true extent of its biological roles is unclear. Here, we characterize eleven ebi mutations and find that ebi has a novel role in promoting growth of the wing imaginal disc: viable combinations of mutant alleles give rise to adults with small wings. Wing discs with reduced EBI levels are correspondingly small and exhibit down-regulation of Notch target genes. Furthermore, we show that EBI colocalizes on polytene chromosomes with Smrter (SMR), a transcriptional corepressor, and Suppressor of Hairless (SU(H)), the primary transcription factor involved in Notch signalling. Interestingly, the mammalian orthologs of ebi, transducin β-like 1 (TBL1) and TBL-related 1 (TBLR1), function as corepressor/coactivator exchange factors and are required for transcriptional activation of Notch target genes. We hypothesize that EBI acts to activate (de-repress) transcription of Notch target genes important for Drosophila wing growth by functioning as a corepressor/coactivator exchange factor for SU(H).
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Jiang M, Instrell R, Saunders B, Berven H, Howell M. Tales from an academic RNAi screening facility; FAQs. Brief Funct Genomics 2011; 10:227-37. [PMID: 21527443 DOI: 10.1093/bfgp/elr016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNAi technology is now a well-established and widely employed research technique that has been adopted by many researchers for use in large-scale screening campaigns. Here, we offer our experience of genome-wide siRNA screening from the perspective of a facility providing screening as a service to a wide range of researchers with diverse interests and approaches. We have experienced the emotional rollercoaster of screening from the exuberant early promise of a screen, the messy reality of the data through to the recognition of screen data as a potential information goldmine. Here, we use some of the questions we most frequently encounter to highlight the initial concerns of many researchers embarking on a siRNA screen and conclude that an informed view of what can be reasonably expected from a screen is essential to the most effective implementation of the technology. Along the way, we suggest that for this area of research at least, either centralization of the resources or close and open collaboration between interested parties offers distinct advantages.
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Affiliation(s)
- Ming Jiang
- High-Throughput Screening facility, Cancer Research UK, London Research Institute
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