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Miller M, Chen A, Gobert V, Augé B, Beau M, Burlet-Schiltz O, Haenlin M, Waltzer L. Control of RUNX-induced repression of Notch signaling by MLF and its partner DnaJ-1 during Drosophila hematopoiesis. PLoS Genet 2017; 13:e1006932. [PMID: 28742844 PMCID: PMC5549762 DOI: 10.1371/journal.pgen.1006932] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/08/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
A tight regulation of transcription factor activity is critical for proper development. For instance, modifications of RUNX transcription factors dosage are associated with several diseases, including hematopoietic malignancies. In Drosophila, Myeloid Leukemia Factor (MLF) has been shown to control blood cell development by stabilizing the RUNX transcription factor Lozenge (Lz). However, the mechanism of action of this conserved family of proteins involved in leukemia remains largely unknown. Here we further characterized MLF's mode of action in Drosophila blood cells using proteomic, transcriptomic and genetic approaches. Our results show that MLF and the Hsp40 co-chaperone family member DnaJ-1 interact through conserved domains and we demonstrate that both proteins bind and stabilize Lz in cell culture, suggesting that MLF and DnaJ-1 form a chaperone complex that directly regulates Lz activity. Importantly, dnaj-1 loss causes an increase in Lz+ blood cell number and size similarly as in mlf mutant larvae. Moreover we find that dnaj-1 genetically interacts with mlf to control Lz level and Lz+ blood cell development in vivo. In addition, we show that mlf and dnaj-1 loss alters Lz+ cell differentiation and that the increase in Lz+ blood cell number and size observed in these mutants is caused by an overactivation of the Notch signaling pathway. Finally, using different conditions to manipulate Lz activity, we show that high levels of Lz are required to repress Notch transcription and signaling. All together, our data indicate that the MLF/DnaJ-1-dependent increase in Lz level allows the repression of Notch expression and signaling to prevent aberrant blood cell development. Thus our findings establish a functional link between MLF and the co-chaperone DnaJ-1 to control RUNX transcription factor activity and Notch signaling during blood cell development in vivo.
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Affiliation(s)
- Marion Miller
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Aichun Chen
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vanessa Gobert
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Benoit Augé
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mathilde Beau
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marc Haenlin
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucas Waltzer
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
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Regulation of Notch Signaling by the Heterogeneous Nuclear Ribonucleoprotein Hrp48 and Deltex in Drosophila melanogaster. Genetics 2017; 206:905-918. [PMID: 28396507 DOI: 10.1534/genetics.116.198879] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/03/2017] [Indexed: 01/03/2023] Open
Abstract
Notch signaling is an evolutionarily conserved pathway that is found to be involved in a number of cellular events throughout development. The deployment of the Notch signaling pathway in numerous cellular contexts is possible due to its regulation at multiple levels. In an effort to identify the novel components integrated into the molecular circuitry affecting Notch signaling, we carried out a protein-protein interaction screen based on the identification of cellular protein complexes using co-immunoprecipitation followed by mass-spectrometry. We identified Hrp48, a heterogeneous nuclear ribonucleoprotein in Drosophila, as a novel interacting partner of Deltex (Dx), a cytoplasmic modulator of Notch signaling. Immunocytochemical analysis revealed that Dx and Hrp48 colocalize in cytoplasmic vesicles. The dx mutant also showed strong genetic interactions with hrp48 mutant alleles. The coexpression of Dx and Hrp48 resulted in the depletion of cytoplasmic Notch in larval wing imaginal discs and downregulation of Notch targets cut and wingless Previously, it has been shown that Sex-lethal (Sxl), on binding with Notch mRNA, negatively regulates Notch signaling. The overexpression of Hrp48 was found to inhibit Sxl expression and consequently rescued Notch signaling activity. In the present study, we observed that Dx together with Hrp48 can regulate Notch signaling in an Sxl-independent manner. In addition, Dx and Hrp48 displayed a synergistic effect on caspase-mediated cell death. Our results suggest that Dx and Hrp48 together negatively regulate Notch signaling in Drosophila melanogaster.
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Drosophila dyskerin is required for somatic stem cell homeostasis. Sci Rep 2017; 7:347. [PMID: 28337032 PMCID: PMC5428438 DOI: 10.1038/s41598-017-00446-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 02/27/2017] [Indexed: 02/07/2023] Open
Abstract
Drosophila represents an excellent model to dissect the roles played by the evolutionary conserved family of eukaryotic dyskerins. These multifunctional proteins are involved in the formation of H/ACA snoRNP and telomerase complexes, both involved in essential cellular tasks. Since fly telomere integrity is guaranteed by a different mechanism, we used this organism to investigate the specific role played by dyskerin in somatic stem cell maintenance. To this aim, we focussed on Drosophila midgut, a hierarchically organized and well characterized model for stemness analysis. Surprisingly, the ubiquitous loss of the protein uniquely affects the formation of the larval stem cell niches, without altering other midgut cell types. The number of adult midgut precursor stem cells is dramatically reduced, and this effect is not caused by premature differentiation and is cell-autonomous. Moreover, a few dispersed precursors found in the depleted midguts can maintain stem identity and the ability to divide asymmetrically, nor show cell-growth defects or undergo apoptosis. Instead, their loss is mainly specifically dependent on defective amplification. These studies establish a strict link between dyskerin and somatic stem cell maintenance in a telomerase-lacking organism, indicating that loss of stemness can be regarded as a conserved, telomerase-independent effect of dyskerin dysfunction.
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Johnston MJ, Bar-Cohen S, Paroush Z, Nystul TG. Phosphorylated Groucho delays differentiation in the follicle stem cell lineage by providing a molecular memory of EGFR signaling in the niche. Development 2016; 143:4631-4642. [PMID: 27836963 PMCID: PMC5201033 DOI: 10.1242/dev.143263] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/31/2016] [Indexed: 01/03/2023]
Abstract
In the epithelial follicle stem cells (FSCs) of the Drosophila ovary, Epidermal Growth Factor Receptor (EGFR) signaling promotes self-renewal, whereas Notch signaling promotes differentiation of the prefollicle cell (pFC) daughters. We have identified two proteins, Six4 and Groucho (Gro), that link the activity of these two pathways to regulate the earliest cell fate decision in the FSC lineage. Our data indicate that Six4 and Gro promote differentiation towards the polar cell fate by promoting Notch pathway activity. This activity of Gro is antagonized by EGFR signaling, which inhibits Gro-dependent repression via p-ERK mediated phosphorylation. We have found that the phosphorylated form of Gro persists in newly formed pFCs, which may delay differentiation and provide these cells with a temporary memory of the EGFR signal. Collectively, these findings demonstrate that phosphorylated Gro labels a transition state in the FSC lineage and describe the interplay between Notch and EGFR signaling that governs the differentiation processes during this period.
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Affiliation(s)
- Michael J Johnston
- The University of California, San Francisco, Departments of Anatomy and OB-GYN/RS, CA 94122, USA
| | - Shaked Bar-Cohen
- The Hebrew University, Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Jerusalem 9112102, Israel
| | - Ze'ev Paroush
- The Hebrew University, Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, Jerusalem 9112102, Israel
| | - Todd G Nystul
- The University of California, San Francisco, Departments of Anatomy and OB-GYN/RS, CA 94122, USA
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55
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The silent information regulator 1 (Sirt1) is a positive regulator of the Notch pathway in Drosophila. Biochem J 2016; 473:4129-4143. [DOI: 10.1042/bcj20160563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/26/2016] [Accepted: 09/12/2016] [Indexed: 02/07/2023]
Abstract
The silent information regulator 1 (Sirt1) has been shown to have negative effects on the Notch pathway in several contexts. We bring evidence that Sirt1 has a positive effect on Notch activation in Drosophila, in the context of sensory organ precursor specification and during wing development. The phenotype of Sirt1 mutant resembles weak Notch loss-of-function phenotypes, and genetic interactions of Sirt1 with the components of the Notch pathway also suggest a positive role for Sirt1 in Notch signalling. Sirt1 is necessary for the efficient activation of enhancer of split [E(spl)] genes by Notch in S2N cells. Additionally, the Notch-dependent response of several E(spl) genes is sensitive to metabolic stress caused by 2-deoxy-d-glucose treatment, in a Sirt1-dependent manner. We found Sirt1 associated with several proteins involved in Notch repression as well as activation, including the cofactor exchange factor Ebi (TBL1), the RLAF/LAF histone chaperone complex and the Tip60 acetylation complex. Moreover, Sirt1 participates in the deacetylation of the CSL transcription factor Suppressor of Hairless. The role of Sirt1 in Notch signalling is, therefore, more complex than previously recognized, and its diverse effects may be explained by a plethora of Sirt1 substrates involved in the regulation of Notch signalling.
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Slaninova V, Krafcikova M, Perez-Gomez R, Steffal P, Trantirek L, Bray SJ, Krejci A. Notch stimulates growth by direct regulation of genes involved in the control of glycolysis and the tricarboxylic acid cycle. Open Biol 2016; 6:150155. [PMID: 26887408 PMCID: PMC4772804 DOI: 10.1098/rsob.150155] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Glycolytic shift is a characteristic feature of rapidly proliferating cells, such as cells during development and during immune response or cancer cells, as well as of stem cells. It results in increased glycolysis uncoupled from mitochondrial respiration, also known as the Warburg effect. Notch signalling is active in contexts where cells undergo glycolytic shift. We decided to test whether metabolic genes are direct transcriptional targets of Notch signalling and whether upregulation of metabolic genes can help Notch to induce tissue growth under physiological conditions and in conditions of Notch-induced hyperplasia. We show that genes mediating cellular metabolic changes towards the Warburg effect are direct transcriptional targets of Notch signalling. They include genes encoding proteins involved in glucose uptake, glycolysis, lactate to pyruvate conversion and repression of the tricarboxylic acid cycle. The direct transcriptional upregulation of metabolic genes is PI3K/Akt independent and occurs not only in cells with overactivated Notch but also in cells with endogenous levels of Notch signalling and in vivo. Even a short pulse of Notch activity is able to elicit long-lasting metabolic changes resembling the Warburg effect. Loss of Notch signalling in Drosophila wing discs as well as in human microvascular cells leads to downregulation of glycolytic genes. Notch-driven tissue overgrowth can be rescued by downregulation of genes for glucose metabolism. Notch activity is able to support growth of wing during nutrient-deprivation conditions, independent of the growth of the rest of the body. Notch is active in situations that involve metabolic reprogramming, and the direct regulation of metabolic genes may be a common mechanism that helps Notch to exert its effects in target tissues.
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Affiliation(s)
- Vera Slaninova
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic Institute of Entomology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
| | - Michaela Krafcikova
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Raquel Perez-Gomez
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Pavel Steffal
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sarah J Bray
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Alena Krejci
- Faculty of Science, University of South Bohemia, Branisovska 31, 37005 Ceske Budejovice, Czech Republic Institute of Entomology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
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Abstract
The study of Drosophila imaginal discs has contributed to a number of discoveries in developmental and cellular biology. In addition to the elucidation of the role of tissue compartments and organ-specific master regulator genes during development, imaginal discs have also become well established as models for studying cellular interactions and complex genetic pathways. Here, we review key discoveries resulting from investigations of these epithelial precursor organs, ranging from cell fate determination and transdetermination to tissue patterning. Furthermore, the design of increasingly sophisticated genetic tools over the last decades has added value to the use of imaginal discs as model systems. As a result of tissue-specific genetic screens, several components of developmentally regulated signaling pathways were identified and epistasis revealed the levels at which they function. Discs have been widely used to assess cellular interactions in their natural tissue context, contributing to a better understanding of growth regulation, tissue regeneration, and cancer. With the continuous implementation of novel tools, imaginal discs retain significant potential as model systems to address emerging questions in biology and medicine.
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The Ecdysone and Notch Pathways Synergistically Regulate Cut at the Dorsal-Ventral Boundary in Drosophila Wing Discs. J Genet Genomics 2016; 43:179-86. [PMID: 27117286 DOI: 10.1016/j.jgg.2016.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/05/2016] [Accepted: 03/04/2016] [Indexed: 11/23/2022]
Abstract
Metazoan development requires coordination of signaling pathways to regulate patterns of gene expression. In Drosophila, the wing imaginal disc provides an excellent model for the study of how signaling pathways interact to regulate pattern formation. The determination of the dorsal-ventral (DV) boundary of the wing disc depends on the Notch pathway, which is activated along the DV boundary and induces the expression of the homeobox transcription factor, Cut. Here, we show that Broad (Br), a zinc-finger transcription factor, is also involved in regulating Cut expression in the DV boundary region. However, Br expression is not regulated by Notch signaling in wing discs, while ecdysone signaling is the upstream signal that induces Br for Cut upregulation. Also, we find that the ecdysone-Br cascade upregulates cut-lacZ expression, a reporter containing a 2.7 kb cut enhancer region, implying that ecdysone signaling, similar to Notch, regulates cut at the transcriptional level. Collectively, our findings reveal that the Notch and ecdysone signaling pathways synergistically regulate Cut expression for proper DV boundary formation in the wing disc. Additionally, we show br promotes Delta, a Notch ligand, near the DV boundary to suppress aberrant high Notch activity, indicating further interaction between the two pathways for DV patterning of the wing disc.
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Mamińska A, Bartosik A, Banach-Orłowska M, Pilecka I, Jastrzębski K, Zdżalik-Bielecka D, Castanon I, Poulain M, Neyen C, Wolińska-Nizioł L, Toruń A, Szymańska E, Kowalczyk A, Piwocka K, Simonsen A, Stenmark H, Fürthauer M, González-Gaitán M, Miaczynska M. ESCRT proteins restrict constitutive NF-κB signaling by trafficking cytokine receptors. Sci Signal 2016; 9:ra8. [PMID: 26787452 DOI: 10.1126/scisignal.aad0848] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because signaling mediated by the transcription factor nuclear factor κB (NF-κB) is initiated by ligands and receptors that can undergo internalization, we investigated how endocytic trafficking regulated this key physiological pathway. We depleted all of the ESCRT (endosomal sorting complexes required for transport) subunits, which mediate receptor trafficking and degradation, and found that the components Tsg101, Vps28, UBAP1, and CHMP4B were essential to restrict constitutive NF-κB signaling in human embryonic kidney 293 cells. In the absence of exogenous cytokines, depletion of these proteins led to the activation of both canonical and noncanonical NF-κB signaling, as well as the induction of NF-κB-dependent transcriptional responses in cultured human cells, zebrafish embryos, and fat bodies in flies. These effects depended on cytokine receptors, such as the lymphotoxin β receptor (LTβR) and tumor necrosis factor receptor 1 (TNFR1). Upon depletion of ESCRT subunits, both receptors became concentrated on and signaled from endosomes. Endosomal accumulation of LTβR induced its ligand-independent oligomerization and signaling through the adaptors TNFR-associated factor 2 (TRAF2) and TRAF3. These data suggest that ESCRTs constitutively control the distribution of cytokine receptors in their ligand-free state to restrict their signaling, which may represent a general mechanism to prevent spurious activation of NF-κB.
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Affiliation(s)
- Agnieszka Mamińska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Anna Bartosik
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Iwona Pilecka
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Kamil Jastrzębski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | | | - Irinka Castanon
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Morgane Poulain
- Institut de Biologie Valrose, CNRS UMR 7277, INSERM 1091, University of Nice Sophia Antipolis, 06108 Nice, France
| | - Claudine Neyen
- École Polytechnique Fédérale de Lausanne (EPFL), Global Health Institute, 1015 Lausanne, Switzerland
| | | | - Anna Toruń
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Ewelina Szymańska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
| | - Agata Kowalczyk
- Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | | | - Anne Simonsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Harald Stenmark
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, 0379 Oslo, Norway
| | - Maximilian Fürthauer
- Institut de Biologie Valrose, CNRS UMR 7277, INSERM 1091, University of Nice Sophia Antipolis, 06108 Nice, France
| | | | - Marta Miaczynska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.
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Aradhya R, Zmojdzian M, Da Ponte JP, Jagla K. Muscle niche-driven Insulin-Notch-Myc cascade reactivates dormant Adult Muscle Precursors in Drosophila. eLife 2015; 4. [PMID: 26650355 PMCID: PMC4749548 DOI: 10.7554/elife.08497] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/28/2015] [Indexed: 01/25/2023] Open
Abstract
How stem cells specified during development keep their non-differentiated quiescent state, and how they are reactivated, remain poorly understood. Here, we applied a Drosophila model to follow in vivo behavior of adult muscle precursors (AMPs), the transient fruit fly muscle stem cells. We report that emerging AMPs send out thin filopodia that make contact with neighboring muscles. AMPs keep their filopodia-based association with muscles throughout their dormant state but also when they start to proliferate, suggesting that muscles could play a role in AMP reactivation. Indeed, our genetic analyses indicate that muscles send inductive dIlp6 signals that switch the Insulin pathway ON in closely associated AMPs. This leads to the activation of Notch, which regulates AMP proliferation via dMyc. Altogether, we report that Drosophila AMPs display homing behavior to muscle niche and that the niche-driven Insulin-Notch-dMyc cascade plays a key role in setting the activated state of AMPs. DOI:http://dx.doi.org/10.7554/eLife.08497.001 Muscles experience wear and tear over our lifetimes and therefore need to be regularly repaired and replenished by new cells. These cells are produced by stem cells, which often reside in a special microenvironment called the stem cell niche. This niche may also contain support cells that produce signals to attract stem cells and then maintain them in a dormant state. When the muscle is damaged, its resident stem cells are activated so that they divide to produce new cells. Understanding how this happens is an important goal for regenerative medicine, but many of the details remain unclear. In fruit flies, stem cells called adult muscle precursor cells (or AMPs for short) lie dormant in the embryo and larva, but are then activated to form the muscles of the adult fly. These cells share many features with the muscle stem cells of mammals, which prompted Aradhya, Zmojdzian et al. to use them as a model to investigate how stem cells find their niche and are later activated. For the experiments, the AMPs in fruit fly larvae were labelled with a fluorescent protein. Aradhya, Zmojdzian et al. observed that these cells produce long extensions that connect them to each other, to nearby muscle and to nerve cells. During development, these extensions are gradually lost until they contact only the muscles that are closest to the AMPs, which indicates that these muscles provide a niche for the AMPs and are perhaps involved in their activation. Further experiments show that neighbouring muscles do indeed help to activate AMPs, as they produce a signal that activates a cell communication system called the insulin pathway inside the AMPs. Insulin signalling – which is sensitive to the availability of nutrients in the body – turns on another signalling pathway, called Notch, that then stimulate the AMPs to divide. Aradhya, Zmojdzian et al. propose that this signalling cascade might help to ensure that AMPs are only activated at the right time in development. The next step is to find out whether stem cells in human muscles are activated in a similar way. DOI:http://dx.doi.org/10.7554/eLife.08497.002
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Affiliation(s)
- Rajaguru Aradhya
- Génétique Reproduction et Développement, INSERM U1103, CNRS UMR6293, Clermont-Ferrand, France
| | - Monika Zmojdzian
- Génétique Reproduction et Développement, INSERM U1103, CNRS UMR6293, Clermont-Ferrand, France
| | - Jean Philippe Da Ponte
- Génétique Reproduction et Développement, INSERM U1103, CNRS UMR6293, Clermont-Ferrand, France
| | - Krzysztof Jagla
- Génétique Reproduction et Développement, INSERM U1103, CNRS UMR6293, Clermont-Ferrand, France
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Yang D, Abdallah A, Li Z, Lu Y, Almeida S, Gao FB. FTD/ALS-associated poly(GR) protein impairs the Notch pathway and is recruited by poly(GA) into cytoplasmic inclusions. Acta Neuropathol 2015; 130:525-35. [PMID: 26031661 PMCID: PMC4575383 DOI: 10.1007/s00401-015-1448-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/16/2015] [Accepted: 05/17/2015] [Indexed: 12/14/2022]
Abstract
C9ORF72 repeat expansion is the most common genetic mutation in frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). Abnormal dipeptide repeat proteins (DPRs) generated from repeat-associated non-AUG (RAN) translation of repeat-containing RNAs are thought to be pathogenic; however, the mechanisms are unknown. Here we report that (GR)80 and (PR)80 are toxic in neuronal and non-neuronal cells in Drosophila. In contrast to reported shorter poly(GR) forms, (GR)80 is mostly localized throughout the cytosol without detectable accumulation in the nucleolus, accompanied by suppression of Notch signaling and cell loss in the wing. Some Notch target genes are also downregulated in brains and iPSC-derived cortical neurons of C9ORF72 patients. Increased Notch expression largely suppressed (GR)80-induced cell loss in the wing. When co-expressed in Drosophila, HeLa cells, or human neurons, (GA)80 recruited (GR)80 into cytoplasmic inclusions, partially decreasing the toxicity of (GR)80 and restoring Notch signaling in Drosophila. Thus, different DPRs have opposing roles in cell loss and we identify the Notch pathway as one of the receptor signaling pathways that might be compromised in C9ORF72 FTD/ALS.
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Affiliation(s)
- Dejun Yang
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Abbas Abdallah
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Zhaodong Li
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02216, USA
| | - Yubing Lu
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Sandra Almeida
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
| | - Fen-Biao Gao
- Department of Neurology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA.
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Regulation of Notch Signaling by an Evolutionary Conserved DEAD Box RNA Helicase, Maheshvara in Drosophila melanogaster. Genetics 2015; 201:1071-85. [PMID: 26400611 DOI: 10.1534/genetics.115.181214] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/09/2015] [Indexed: 02/01/2023] Open
Abstract
Notch signaling is an evolutionary conserved process that influences cell fate determination, cell proliferation, and cell death in a context-dependent manner. Notch signaling is fine-tuned at multiple levels and misregulation of Notch has been implicated in a variety of human diseases. We have characterized maheshvara (mahe), a novel gene in Drosophila melanogaster that encodes a putative DEAD box protein that is highly conserved across taxa and belongs to the largest group of RNA helicase. A dynamic pattern of mahe expression along with the maternal accumulation of its transcripts is seen during early stages of embryogenesis. In addition, a strong expression is also seen in the developing nervous system. Ectopic expression of mahe in a wide range of tissues during development results in a variety of defects, many of which resemble a typical Notch loss-of-function phenotype. We illustrate that ectopic expression of mahe in the wing imaginal discs leads to loss of Notch targets, Cut and Wingless. Interestingly, Notch protein levels are also lowered, whereas no obvious change is seen in the levels of Notch transcripts. In addition, mahe overexpression can significantly rescue ectopic Notch-mediated proliferation of eye tissue. Further, we illustrate that mahe genetically interacts with Notch and its cytoplasmic regulator deltex in trans-heterozygous combination. Coexpression of Deltex and Mahe at the dorso-ventral boundary results in a wing-nicking phenotype and a more pronounced loss of Notch target Cut. Taken together we report identification of a novel evolutionary conserved RNA helicase mahe, which plays a vital role in regulation of Notch signaling.
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64
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Reduction of Cullin-2 in somatic cells disrupts differentiation of germline stem cells in the Drosophila ovary. Dev Biol 2015. [DOI: 10.1016/j.ydbio.2015.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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65
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Ho DM, Pallavi SK, Artavanis-Tsakonas S. The Notch-mediated hyperplasia circuitry in Drosophila reveals a Src-JNK signaling axis. eLife 2015. [PMID: 26222204 PMCID: PMC4517436 DOI: 10.7554/elife.05996] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Notch signaling controls a wide range of cell fate decisions during development and disease via synergistic interactions with other signaling pathways. Here, through a genome-wide genetic screen in Drosophila, we uncover a highly complex Notch-dependent genetic circuitry that profoundly affects proliferation and consequently hyperplasia. We report a novel synergistic relationship between Notch and either of the non-receptor tyrosine kinases Src42A and Src64B to promote hyperplasia and tissue disorganization, which results in cell cycle perturbation, JAK/STAT signal activation, and differential regulation of Notch targets. Significantly, the JNK pathway is responsible for the majority of the phenotypes and transcriptional changes downstream of Notch-Src synergy. We previously reported that Notch-Mef2 also activates JNK, indicating that there are commonalities within the Notch-dependent proliferation circuitry; however, the current data indicate that Notch-Src accesses JNK in a significantly different fashion than Notch-Mef2. DOI:http://dx.doi.org/10.7554/eLife.05996.001 The cells within animals are organized into tissues and organs that perform particular roles. To develop and maintain these structures, the ability of individual cells to divide and grow is strictly controlled by the activities of many proteins, including one called Notch. This protein is found in all multicellular organisms and allows cells to communicate with each other. Mutations in the gene that encodes Notch can cause cells to divide excessively and lead to cancer and other diseases. Notch regulates the growth and division of cells by interacting with many other proteins. For example, Mef2 works with Notch to activate a communication system called the JNK pathway. This pathway is involved in controlling cell division, cell death, and cell movement. However, it is thought that Notch may also interact with other proteins that have not yet been identified. Now, Ho et al. have conducted a genome-wide screen in fruit flies to find proteins that interact with Notch. The experiments used flies that develop abnormally large eyes because they have an over-active Notch protein. Ho et al. identified hundreds of fruit fly genes that could increase or decrease the size of the flies' eyes in the presence of Notch activity. Many of these genes are known to be involved in development, cell division, or in controlling the activity of other genes. Ho et al. found that two of these genes encode similar proteins called Src42A and Src64B, which are similar to the Src proteins that are involved in many types of human cancers. The experiments show that both proteins interact with Notch to promote uncontrolled cell division and lead to tissues in the flies becoming more disorganized. The JNK pathway is also activated by Notch working with Src42A or Src64B, but in a different manner to how it is activated by Mef2 and Notch, and with different consequences for cells. This study provides new insights into how genes work together in order to influence cell division and other events in development. Also, it suggests that Notch activity may regulate the growth of cancers linked with defects in the Src proteins. DOI:http://dx.doi.org/10.7554/eLife.05996.002
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Affiliation(s)
- Diana M Ho
- Department of Cell Biology, Harvard Medical School, Boston, United States
| | - S K Pallavi
- Department of Cell Biology, Harvard Medical School, Boston, United States
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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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Acquisition of estrogen independence induces TOB1-related mechanisms supporting breast cancer cell proliferation. Oncogene 2015; 35:1643-56. [PMID: 26165839 DOI: 10.1038/onc.2015.226] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/19/2015] [Accepted: 05/04/2015] [Indexed: 12/19/2022]
Abstract
Resistance to therapies targeting the estrogen pathway remains a challenge in the treatment of estrogen receptor-positive breast cancer. To address this challenge, a systems biology approach was used. A library of small interfering RNAs targeting an estrogen receptor (ER)- and aromatase-centered network identified 46 genes that are dispensable in estrogen-dependent MCF7 cells, but are selectively required for the survival of estrogen-independent MCF7-derived cells and multiple additional estrogen-independent breast cancer cell lines. Integration of this information identified a tumor suppressor gene TOB1 as a critical determinant of estrogen-independent ER-positive breast cell survival. Depletion of TOB1 selectively promoted G1 phase arrest and sensitivity to AKT and mammalian target of rapmycin (mTOR) inhibitors in estrogen-independent cells but not in estrogen-dependent cells. Phosphoproteomic profiles from reverse-phase protein array analysis supported by mRNA profiling identified a significant signaling network reprogramming by TOB1 that differed in estrogen-sensitive and estrogen-resistant cell lines. These data support a novel function for TOB1 in mediating survival of estrogen-independent breast cancers. These studies also provide evidence for combining TOB1 inhibition and AKT/mTOR inhibition as a therapeutic strategy, with potential translational significance for the management of patients with ER-positive breast cancers.
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Chou MH, Hsieh YC, Huang CW, Chen PH, Chan SP, Tsao YP, Lee HH, Wu JT, Chen SL. BCAS2 Regulates Delta-Notch Signaling Activity through Delta Pre-mRNA Splicing in Drosophila Wing Development. PLoS One 2015; 10:e0130706. [PMID: 26091239 PMCID: PMC4475048 DOI: 10.1371/journal.pone.0130706] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 05/23/2015] [Indexed: 11/19/2022] Open
Abstract
Previously, we showed that BCAS2 is essential for Drosophila viability and functions in pre-mRNA splicing. In this study, we provide strong evidence that BCAS2 regulates the activity of Delta-Notch signaling via Delta pre-mRNA splicing. Depletion of dBCAS2 reduces Delta mRNA expression and leads to accumulation of Delta pre-mRNA, resulting in diminished transcriptions of Delta-Notch signaling target genes, such as cut and E(spl)m8. Furthermore, ectopic expression of human BCAS2 (hBCAS2) and Drosophila BCAS2 (dBCAS2) in a dBCAS2-deprived fly can rescue dBCAS2 depletion-induced wing damage to the normal phenotypes. These rescued phenotypes are correlated with the restoration of Delta pre-mRNA splicing, which affects Delta-Notch signaling activity. Additionally, overexpression of Delta can rescue the wing deformation by deprivation of dBCAS2; and the depletion of dBCAS2 can restore the aberrant eye associated with Delta-overexpressing retinas; providing supporting evidence for the regulation of Delta-Notch signaling by dBCAS2. Taken together, dBCAS2 participates in Delta pre-mRNA splicing that affects the regulation of Delta-Notch signaling in Drosophila wing development.
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Affiliation(s)
- Meng-Hsuan Chou
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Yi-Chen Hsieh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Chu-Wei Huang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Po-Han Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Shih-Peng Chan
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - Yeou-Ping Tsao
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, 104, Taiwan
| | - Hsiu-Hsiang Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
| | - June-Tai Wu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
- Department of Medical Research, National Taiwan University Hospital, Taipei, 100, Taiwan
- * E-mail: (SLC); (JTW)
| | - Show-Li Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
- * E-mail: (SLC); (JTW)
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69
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Abstract
The ability to visualize Notch pathway activity in vivo is invaluable for studying the functions and mechanisms of Notch signaling. A variety of tools have been developed to enable monitoring of pathway activity in Drosophila, including endogenous Notch-responsive genes and synthetic transcriptional reporter constructs. Here we summarize some of the different Notch signaling reporters that are available, discuss their relative merits, and describe two methods for visualizing their expression (immunostaining and X-gal staining). These approaches are widely applicable to a range of tissues and stages in Drosophila development.
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Abstract
The study of Drosophila oogenesis provides invaluable information about signaling pathway regulation and cell cycle programming. During Drosophila oogenesis, a string of egg chambers in each ovariole progressively develops toward maturity. Egg chamber development consists of 14 stages. From stage 1 to stage 6 (mitotic cycle), main-body follicle cells undergo mitotic divisions. From stage 7 to stage 10a (endocycle), follicle cells cease mitosis but continue three rounds of endoreduplication. From stage 10b to stage 13 (gene amplification), instead of whole genome duplication, follicle cells selectively amplify specific genomic regions, mostly for chorion production. So far, Drosophila oogenesis is one of the most well studied model systems used to understand cell cycle switches, which furthers our knowledge about cell cycle control machinery and sheds new light on potential cancer treatments. Here, we give a brief summary of cell cycle switches, the associated signaling pathways and factors, and the detailed experimental procedures used to study the cell cycle switches.
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Affiliation(s)
- Dongyu Jia
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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71
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Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell 2014; 159:200-214. [PMID: 25259927 PMCID: PMC4298142 DOI: 10.1016/j.cell.2014.09.002] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/04/2014] [Accepted: 09/02/2014] [Indexed: 12/31/2022]
Abstract
Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.
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Affiliation(s)
- Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Institute of Computer Science, Warsaw University of Technology, 00-661 Warsaw, Poland
| | - Ender Karaca
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Kuchuan Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Upasana Gala
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joep de Ligt
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Yajing Xie
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yesim Parman
- Neurology Department and Neuropathology Laboratory, Istanbul University Medical School, Istanbul 34390, Turkey
| | - Merve Sivaci
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Esra Battaloglu
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Donna Muzny
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, BCM, Houston, TX 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA
| | | | - Robin D Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Cynthia J Curry
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA; Genetic Medicine Central California, Fresno, CA 93701, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Karen L Schulze
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Human Genetics Center, University of Texas, Health Science Center, Houston, TX 77030, USA
| | - William B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Neurology, University of Washington, Seattle WA 98195, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA.
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Uninflatable and Notch control the targeting of Sara endosomes during asymmetric division. Curr Biol 2014; 24:2142-2148. [PMID: 25155514 DOI: 10.1016/j.cub.2014.07.054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 06/11/2014] [Accepted: 07/21/2014] [Indexed: 11/21/2022]
Abstract
Cell fate decision during asymmetric division is mediated by the biased partition of cell fate determinants during mitosis [1-6]. In the case of the asymmetric division of the fly sensory organ precursor cells, directed Notch signaling from pIIb to the pIIa daughter endows pIIa with its distinct fate [1-6]. We have previously shown that Notch/Delta molecules internalized in the mother cell traffic through Sara endosomes and are directed to the pIIa daughter [6]. Here we show that the receptor Notch itself is required during the asymmetric targeting of the Sara endosomes to pIIa. Notch binds Uninflatable, and both traffic together through Sara endosomes, which is essential to direct asymmetric endosomes motility and Notch-dependent cell fate assignation. Our data uncover a part of the core machinery required for the asymmetric motility of a vesicular structure that is essential for the directed dispatch of Notch signaling molecules during asymmetric mitosis.
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73
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Shimizu H, Woodcock SA, Wilkin MB, Trubenová B, Monk NAM, Baron M. Compensatory flux changes within an endocytic trafficking network maintain thermal robustness of Notch signaling. Cell 2014; 157:1160-74. [PMID: 24855951 PMCID: PMC4032575 DOI: 10.1016/j.cell.2014.03.050] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 01/15/2014] [Accepted: 03/14/2014] [Indexed: 11/03/2022]
Abstract
Developmental signaling is remarkably robust to environmental variation, including temperature. For example, in ectothermic animals such as Drosophila, Notch signaling is maintained within functional limits across a wide temperature range. We combine experimental and computational approaches to show that temperature compensation of Notch signaling is achieved by an unexpected variety of endocytic-dependent routes to Notch activation which, when superimposed on ligand-induced activation, act as a robustness module. Thermal compensation arises through an altered balance of fluxes within competing trafficking routes, coupled with temperature-dependent ubiquitination of Notch. This flexible ensemble of trafficking routes supports Notch signaling at low temperature but can be switched to restrain Notch signaling at high temperature and thus compensates for the inherent temperature sensitivity of ligand-induced activation. The outcome is to extend the physiological range over which normal development can occur. Similar mechanisms may provide thermal robustness for other developmental signals.
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Affiliation(s)
- Hideyuki Shimizu
- University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon A Woodcock
- University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Marian B Wilkin
- University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Barbora Trubenová
- University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Nicholas A M Monk
- School of Mathematics and Statistics, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH, UK
| | - Martin Baron
- University of Manchester, Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK.
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74
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Xie G, Yu Z, Jia D, Jiao R, Deng WM. E(y)1/TAF9 mediates the transcriptional output of Notch signaling in Drosophila. J Cell Sci 2014; 127:3830-9. [PMID: 25015288 DOI: 10.1242/jcs.154583] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcriptional activation of Notch signaling targets requires the formation of a ternary complex that involves the intracellular domain of the Notch receptor (NICD), DNA-binding protein Suppressor of Hairless [Su(H), RPBJ in mammals] and coactivator Mastermind (Mam). Here, we report that E(y)1/TAF9, a component of the transcription factor TFIID complex, interacts specifically with the NICD-Su(H)-Mam complex to facilitate the transcriptional output of Notch signaling. We identified E(y)1/TAF9 in a large-scale in vivo RNA interference (RNAi) screen for genes that are involved in a Notch-dependent mitotic-to-endocycle transition in Drosophila follicle cells. Knockdown of e(y)1/TAF9 displayed Notch-mutant-like phenotypes and defects in target gene and activity reporter expression in both the follicle cells and wing imaginal discs. Epistatic analyses in these two tissues indicated that E(y)1/TAF9 functions downstream of Notch cleavage. Biochemical studies in S2 cells demonstrated that E(y)1/TAF9 physically interacts with the transcriptional effectors of Notch signaling Su(H) and NICD. Taken together, our data suggest that the association of the NICD-Su(H)-Mastermind complex with E(y)1/TAF9 in response to Notch activation recruits the transcription initiation complex to induce Notch target genes, coupling Notch signaling with the transcription machinery.
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Affiliation(s)
- Gengqiang Xie
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
| | - Zhongsheng Yu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, the Chinese Academy of Sciences, Datun Road 15, Beijing 100101, China
| | - Dongyu Jia
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
| | - Renjie Jiao
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL 32304-4295, USA
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75
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Mitochondria modify exercise-induced development of stem cell-derived neurons in the adult brain. J Neurosci 2014; 34:6624-33. [PMID: 24806687 DOI: 10.1523/jneurosci.4972-13.2014] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Neural stem cells in the adult mammalian hippocampus continuously generate new functional neurons, which modify the hippocampal network and significantly contribute to cognitive processes and mood regulation. Here, we show that the development of new neurons from stem cells in adult mice is paralleled by extensive changes to mitochondrial mass, distribution, and shape. Moreover, exercise-a strong modifier of adult hippocampal neurogenesis-accelerates neuronal maturation and induces a profound increase in mitochondrial content and the presence of mitochondria in dendritic segments. Genetic inhibition of the activity of the mitochondrial fission factor dynamin-related protein 1 (Drp1) inhibits neurogenesis under basal and exercise conditions. Conversely, enhanced Drp1 activity furthers exercise-induced acceleration of neuronal maturation. Collectively, these results indicate that adult hippocampal neurogenesis requires adaptation of the mitochondrial compartment and suggest that mitochondria are targets for enhancing neurogenesis-dependent hippocampal plasticity.
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76
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Lőrincz P, Lakatos Z, Maruzs T, Szatmári Z, Kis V, Sass M. Atg6/UVRAG/Vps34-containing lipid kinase complex is required for receptor downregulation through endolysosomal degradation and epithelial polarity during Drosophila wing development. BIOMED RESEARCH INTERNATIONAL 2014; 2014:851349. [PMID: 25006588 PMCID: PMC4074780 DOI: 10.1155/2014/851349] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/01/2014] [Indexed: 11/18/2022]
Abstract
Atg6 (Beclin 1 in mammals) is a core component of the Vps34 PI3K (III) complex, which promotes multiple vesicle trafficking pathways. Atg6 and Vps34 form two distinct PI3K (III) complexes in yeast and mammalian cells, either with Atg14 or with UVRAG. The functions of these two complexes are not entirely clear, as both Atg14 and UVRAG have been suggested to regulate both endocytosis and autophagy. In this study, we performed a microscopic analysis of UVRAG, Atg14, or Atg6 loss-of-function cells in the developing Drosophila wing. Both autophagy and endocytosis are seriously impaired and defective endolysosomes accumulate upon loss of Atg6. We show that Atg6 is required for the downregulation of Notch and Wingless signaling pathways; thus it is essential for normal wing development. Moreover, the loss of Atg6 impairs cell polarity. Atg14 depletion results in autophagy defects with no effect on endocytosis or cell polarity, while the silencing of UVRAG phenocopies all but the autophagy defect of Atg6 depleted cells. Thus, our results indicate that the UVRAG-containing PI3K (III) complex is required for receptor downregulation through endolysosomal degradation and for the establishment of proper cell polarity in the developing wing, while the Atg14-containing complex is involved in autophagosome formation.
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Affiliation(s)
- Péter Lőrincz
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest 1117, Hungary
| | - Zsolt Lakatos
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest 1117, Hungary
| | - Tamás Maruzs
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest 1117, Hungary
| | - Zsuzsanna Szatmári
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest 1117, Hungary
| | - Viktor Kis
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest 1117, Hungary
| | - Miklós Sass
- Department of Anatomy, Cell and Developmental Biology, Eotvos Lorand University, Budapest 1117, Hungary
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77
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Tzou WS, Lo YT, Pai TW, Hu CH, Li CH. Stochastic simulation of notch signaling reveals novel factors that mediate the differentiation of neural stem cells. J Comput Biol 2014; 21:548-67. [PMID: 24798230 DOI: 10.1089/cmb.2014.0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Notch signaling controls cell fate decisions and regulates multiple biological processes, such as cell proliferation, differentiation, and apoptosis. Computational modeling of the deterministic simulation of Notch signaling has provided important insight into the possible molecular mechanisms that underlie the switch from the undifferentiated stem cell to the differentiated cell. Here, we constructed a stochastic model of a Notch signaling model containing Hes1, Notch1, RBP-Jk, Mash1, Hes6, and Delta. mRNA and protein were represented as a discrete state, and 334 reactions were employed for each biochemical reaction using a graphics processing unit-accelerated Gillespie scheme. We employed the tuning of 40 molecular mechanisms and revealed several potential mediators capable of enabling the switch from cell stemness to differentiation. These effective mediators encompass different aspects of cellular regulations, including the nuclear transport of Hes1, the degradation of mRNA (Hes1 and Notch1) and protein (Notch1), the association between RBP-Jk and Notch intracellular domain (NICD), and the cleavage efficiency of the NICD. These mechanisms overlap with many modifiers that have only recently been discovered to modulate the Notch signaling output, including microRNA action, ubiquitin-mediated proteolysis, and the competitive binding of the RBP-Jk-DNA complex. Moreover, we identified the degradation of Hes1 mRNA and nuclear transport of Hes1 as the dominant mechanisms that were capable of abolishing the cell state transition induced by other molecular mechanisms.
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Affiliation(s)
- Wen-Shyong Tzou
- 1 Department of Life Sciences, National Taiwan Ocean University , Taiwan, R.O.C
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78
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Dominguez M. Oncogenic programmes and Notch activity: an 'organized crime'? Semin Cell Dev Biol 2014; 28:78-85. [PMID: 24780858 DOI: 10.1016/j.semcdb.2014.04.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/02/2014] [Indexed: 10/25/2022]
Abstract
The inappropriate Notch signalling can influence virtually all aspect of cancer, including tumour-cell growth, survival, apoptosis, angiogenesis, invasion and metastasis, although it does not do this alone. Hence, elucidating the partners of Notch that are active in cancer is now the focus of much intense research activity. The genetic toolkits available, coupled to the small size and short life of the fruit fly Drosophila melanogaster, makes this an inexpensive and effective animal model, suited to large-scale cancer gene discovery studies. The fly eye is not only a non-vital organ but its stereotyped size and disposition also means it is easy to screen for mutations that cause tumours and metastases and provides ample opportunities to test cancer theories and to unravel unanticipated nexus between Notch and other cancer genes, or to discover unforeseen Notch's partners in cancer. These studies suggest that Notch's oncogenic capacity is brought about not simply by increasing signal strength but through partnerships, whereby oncogenes gain more by cooperating than acting individually, as in a ring 'organized crime'.
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79
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Chi Z, Byrne ST, Dolinko A, Harraz MM, Kim MS, Umanah G, Zhong J, Chen R, Zhang J, Xu J, Chen L, Pandey A, Dawson TM, Dawson VL. Botch is a γ-glutamyl cyclotransferase that deglycinates and antagonizes Notch. Cell Rep 2014; 7:681-8. [PMID: 24767995 DOI: 10.1016/j.celrep.2014.03.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 02/12/2014] [Accepted: 03/19/2014] [Indexed: 11/27/2022] Open
Abstract
Botch promotes embryonic neurogenesis by inhibiting the initial S1 furin-like cleavage step of Notch maturation. The biochemical process by which Botch inhibits Notch maturation is not known. Here, we show that Botch has γ-glutamyl cyclotransferase (GGCT) activity that deglycinates Notch, which prevents the S1 furin-like cleavage. Moreover, Notch is monoglycinated on the γ-glutamyl carbon of glutamate 1,669. The deglycinase activity of Botch is required for inhibition of Notch signaling both in vitro and in vivo. When the γ-glutamyl-glycine at position 1,669 of Notch is degylcinated, it is replaced by 5-oxy-proline. These results reveal that Botch regulates Notch signaling through deglycination and identify a posttranslational modification of Notch that plays an important role in neurogenesis.
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Affiliation(s)
- Zhikai Chi
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Sean T Byrne
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Andrew Dolinko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Maged M Harraz
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Min-Sik Kim
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - George Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Jun Zhong
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Rong Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Jianmin Zhang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jinchong Xu
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Li Chen
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Department of Biological Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, 600 North Wolfe Street, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, 401 North Broadway, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, 855 North Wolfe Street, Baltimore, MD 21205, USA.
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80
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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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81
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Sievers C, Comoglio F, Seimiya M, Merdes G, Paro R. A deterministic analysis of genome integrity during neoplastic growth in Drosophila. PLoS One 2014; 9:e87090. [PMID: 24516544 PMCID: PMC3916295 DOI: 10.1371/journal.pone.0087090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/19/2013] [Indexed: 11/18/2022] Open
Abstract
The development of cancer has been associated with the gradual acquisition of genetic alterations leading to a progressive increase in malignancy. In various cancer types this process is enabled and accelerated by genome instability. While genome sequencing-based analysis of tumor genomes becomes increasingly a standard procedure in human cancer research, the potential necessity of genome instability for tumorigenesis in Drosophila melanogaster has, to our knowledge, never been determined at DNA sequence level. Therefore, we induced formation of tumors by depletion of the Drosophila tumor suppressor Polyhomeotic and subjected them to genome sequencing. To achieve a highly resolved delineation of the genome structure we developed the Deterministic Structural Variation Detection (DSVD) algorithm, which identifies structural variations (SVs) with high accuracy and at single base resolution. The employment of long overlapping paired-end reads enables DSVD to perform a deterministic, i.e. fragment size distribution independent, identification of a large size spectrum of SVs. Application of DSVD and other algorithms to our sequencing data reveals substantial genetic variation with respect to the reference genome reflecting temporal separation of the reference and laboratory strains. The majority of SVs, constituted by small insertions/deletions, is potentially caused by erroneous replication or transposition of mobile elements. Nevertheless, the tumor did not depict a loss of genome integrity compared to the control. Altogether, our results demonstrate that genome stability is not affected inevitably during sustained tumor growth in Drosophila implying that tumorigenesis, in this model organism, can occur irrespective of genome instability and the accumulation of specific genetic alterations.
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Affiliation(s)
- Cem Sievers
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Gunter Merdes
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zurich, Basel, Switzerland ; Faculty of Science, University of Basel, Basel, Switzerland
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82
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Giagtzoglou N. Genetic screens to identify new Notch pathway mutants in Drosophila. Methods Mol Biol 2014; 1187:15-28. [PMID: 25053478 DOI: 10.1007/978-1-4939-1139-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Notch signaling controls a wide range of developmental processes, including proliferation, apoptosis, and cell fate specification during both development and adult tissue homeostasis. The functional versatility of the Notch signaling pathway is tightly linked with the complexity of its regulation in different cellular contexts. To unravel the complexity of Notch signaling, it is important to identify the different components of the Notch signaling pathway. A powerful strategy to accomplish this task is based on genetic screens. Given that the developmental context of signaling is important, these screens should be customized to specific cell populations or tissues. Here, I describe how to perform F1 clonal forward genetic screens in Drosophila to identify novel components of the Notch signaling pathway. These screens combine a classical EMS (ethyl methanesulfonate) chemical mutagenesis protocol along with clonal analysis via FRT-mediated mitotic recombination. These F1 clonal screens allow rapid phenotypic screening within clones of mutant cells induced at specific developmental stages and in tissues of interest, bypassing the pleiotropic effects of isolated mutations. More importantly, since EMS mutations have been notoriously difficult to map to specific genes in the past, I briefly discuss mapping methods that allow rapid identification of the causative mutations.
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Affiliation(s)
- Nikolaos Giagtzoglou
- Department of Neurology, Jan and Dan Duncan Neurological Institute, Baylor College of Medicine, 1250 Moursund St. Ste. 1150, Houston, TX, 77030, USA,
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83
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In Vivo RNAi-Based Screens: Studies in Model Organisms. Genes (Basel) 2013; 4:646-65. [PMID: 24705267 PMCID: PMC3927573 DOI: 10.3390/genes4040646] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 10/29/2013] [Accepted: 11/14/2013] [Indexed: 11/23/2022] Open
Abstract
RNA interference (RNAi) is a technique widely used for gene silencing in organisms and cultured cells, and depends on sequence homology between double-stranded RNA (dsRNA) and target mRNA molecules. Numerous cell-based genome-wide screens have successfully identified novel genes involved in various biological processes, including signal transduction, cell viability/death, and cell morphology. However, cell-based screens cannot address cellular processes such as development, behavior, and immunity. Drosophila and Caenorhabditis elegans are two model organisms whose whole bodies and individual body parts have been subjected to RNAi-based genome-wide screening. Moreover, Drosophila RNAi allows the manipulation of gene function in a spatiotemporal manner when it is implemented using the Gal4/UAS system. Using this inducible RNAi technique, various large-scale screens have been performed in Drosophila, demonstrating that the method is straightforward and valuable. However, accumulated results reveal that the results of RNAi-based screens have relatively high levels of error, such as false positives and negatives. Here, we review in vivo RNAi screens in Drosophila and the methods that could be used to remove ambiguity from screening results.
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84
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Glycolysis supports embryonic muscle growth by promoting myoblast fusion. Proc Natl Acad Sci U S A 2013; 110:18982-7. [PMID: 24191061 DOI: 10.1073/pnas.1301262110] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Muscles ensure locomotion behavior of invertebrate and vertebrate organisms. They are highly specialized and form using conserved developmental programs. To identify new players in muscle development we screened Drosophila and zebrafish gene expression databases for orthologous genes expressed in embryonic muscles. We selected more than 100 candidates. Among them is the glycolysis gene Pglym78/pgam2, the attenuated expression of which results in the formation of thinner muscles in Drosophila embryos. This phenotype is also observed in fast muscle fibers of pgam2 zebrafish morphants, suggesting affected myoblast fusion. Indeed, a detailed analysis of developing muscles in Pglym78 RNAi embryos reveals loss of fusion-associated actin foci and an inefficient Notch decay in fusion competent myoblasts, both known to be required for fusion. In addition to Pglym78, our screen identifies six other genes involved in glycolysis or in pyruvate metabolism (Pfk, Tpi, Gapdh, Pgk, Pyk, and Impl3). They are synchronously activated in embryonic muscles and attenuation of their expression leads to similar muscle phenotypes, which are characterized by fibers with reduced size and the presence of unfused myoblasts. Our data also show that the cell size triggering insulin pathway positively regulates glycolysis in developing muscles and that blocking the insulin or target of rapamycin pathways phenocopies the loss of function phenotypes of glycolytic genes, leading to myoblast fusion arrest and reduced muscle size. Collectively, these data suggest that setting metabolism to glycolysis-stimulated biomass production is part of a core myogenic program that operates in both invertebrate and vertebrate embryos and promotes formation of syncytial muscles.
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85
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Cheruiyot A, Lee JA, Gao FB, Ahmad ST. Expression of mutant CHMP2B, an ESCRT-III component involved in frontotemporal dementia, causes eye deformities due to Notch misregulation in Drosophila. FASEB J 2013; 28:667-75. [PMID: 24158394 DOI: 10.1096/fj.13-234138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Endosomal sorting complexes required for transport (ESCRTs) mediate sorting of ubiquitinated membrane proteins into multivesicular bodies en route to lysosomes for degradation. A mutation in CHMP2B (CHMP2B(Intron5), an ESCRT-III component) that is associated with a hereditary form of frontotemporal dementia (FTD3) disrupts the endosomal-lysosomal pathway and causes accumulation of autophagosomes and multilamellar structures. We previously demonstrated that expression of CHMP2B(Intron5) in the Drosophila eye using GMR-Gal4 causes misregulation of the Toll receptor pathway. Here, we show that ectopic expression of CHMP2B(Intron5) using eyeless-Gal4 (ey>CHMP2B(Intron5)), a driver with different spatiotemporal expression attributes than GMR-Gal4 in the Drosophila eye, causes eye deformities when compared to expression of wild-type CHMP2B (CHMP2B(WT)) and the Drosophila homologue of CHMP2B (CG4618). In addition, ey>CHMP2B(Intron5) flies showed defects in photoreceptor cell patterning and phototactic behavior. Furthermore, ey>CHMP2B(Intron5) flies showed accumulation of Notch in enlarged endosomes and up-regulation of Notch activity. Partial loss of Notch activity in ey>CHMP2B(Intron5) flies significantly rescued eye deformities, photoreceptor patterning defect, and phototactic behavior defect, indicating that these defects are primarily due to Notch misregulation. These results demonstrate that CHMP2B(Intron5) preferentially affects different receptor signaling pathways in a cellular and developmental context-dependent manner.
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Affiliation(s)
- Abigael Cheruiyot
- 2Department of Biology, Colby College, 5720 Mayflower Hill Dr., Waterville, ME 04901, USA.
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86
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Montarras D, L'honoré A, Buckingham M. Lying low but ready for action: the quiescent muscle satellite cell. FEBS J 2013; 280:4036-50. [DOI: 10.1111/febs.12372] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 05/24/2013] [Accepted: 05/28/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Didier Montarras
- Department of Developmental and Stem Cell Biology; CNRS URA 2578; Institut Pasteur; Paris; France
| | - Aurore L'honoré
- Department of Developmental and Stem Cell Biology; CNRS URA 2578; Institut Pasteur; Paris; France
| | - Margaret Buckingham
- Department of Developmental and Stem Cell Biology; CNRS URA 2578; Institut Pasteur; Paris; France
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87
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Schaaf CA, Misulovin Z, Gause M, Koenig A, Gohara DW, Watson A, Dorsett D. Cohesin and polycomb proteins functionally interact to control transcription at silenced and active genes. PLoS Genet 2013; 9:e1003560. [PMID: 23818863 PMCID: PMC3688520 DOI: 10.1371/journal.pgen.1003560] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 04/24/2013] [Indexed: 12/05/2022] Open
Abstract
Cohesin is crucial for proper chromosome segregation but also regulates gene transcription and organism development by poorly understood mechanisms. Using genome-wide assays in Drosophila developing wings and cultured cells, we find that cohesin functionally interacts with Polycomb group (PcG) silencing proteins at both silenced and active genes. Cohesin unexpectedly facilitates binding of Polycomb Repressive Complex 1 (PRC1) to many active genes, but their binding is mutually antagonistic at silenced genes. PRC1 depletion decreases phosphorylated RNA polymerase II and mRNA at many active genes but increases them at silenced genes. Depletion of cohesin reduces long-range interactions between Polycomb Response Elements in the invected-engrailed gene complex where it represses transcription. These studies reveal a previously unrecognized role for PRC1 in facilitating productive gene transcription and provide new insights into how cohesin and PRC1 control development.
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Affiliation(s)
- Cheri A. Schaaf
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Ziva Misulovin
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Maria Gause
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Amanda Koenig
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - David W. Gohara
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Audrey Watson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
| | - Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America
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88
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Ubiquitinations in the notch signaling pathway. Int J Mol Sci 2013; 14:6359-81. [PMID: 23519106 PMCID: PMC3634445 DOI: 10.3390/ijms14036359] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/11/2013] [Accepted: 03/14/2013] [Indexed: 12/22/2022] Open
Abstract
The very conserved Notch pathway is used iteratively during development and adulthood to regulate cell fates. Notch activation relies on interactions between neighboring cells, through the binding of Notch receptors to their ligands, both transmembrane molecules. This inter-cellular contact initiates a cascade of events eventually transforming the cell surface receptor into a nuclear factor acting on the transcription of specific target genes. This review highlights how the various processes undergone by Notch receptors and ligands that regulate the pathway are linked to ubiquitination events.
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89
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Interactions between VEGFR and Notch signaling pathways in endothelial and neural cells. Cell Mol Life Sci 2013; 70:1779-92. [PMID: 23479133 DOI: 10.1007/s00018-013-1312-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 02/25/2013] [Accepted: 02/25/2013] [Indexed: 12/25/2022]
Abstract
Notch cell interaction mechanism governs cell fate decisions in many different cell contexts throughout the lifetime of all Metazoan species. It links the fate of one cell to that of its neighbors through cell-to-cell contacts, and binding of Notch receptors expressed on one cell to their membrane bound ligands on an adjacent cell. Environmental cues, such as growth factors and extracellular matrix molecules, superimpose a dynamic regulation on this canonical Notch signaling pathway. In this review, we will focus on Notch signaling in the vertebrate vascular and nervous systems and examine its role in angiogenesis, neurogenesis, and neurovascular interactions. We will also highlight the molecular relationships of the Notch pathway with vascular endothelial growth factors (VEGFs) and their high-affinity tyrosine kinase VEGF receptors, key regulators of both angiogenesis and neurogenesis.
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90
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Dai Q, Ren A, Westholm JO, Serganov AA, Patel DJ, Lai EC. The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. Genes Dev 2013; 27:602-14. [PMID: 23468431 DOI: 10.1101/gad.213314.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We recently reported that Drosophila Insensitive (Insv) promotes sensory organ development and has activity as a nuclear corepressor for the Notch transcription factor Suppressor of Hairless [Su(H)]. Insv lacks domains of known biochemical function but contains a single BEN domain (i.e., a "BEN-solo" protein). Our chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) analysis confirmed binding of Insensitive to Su(H) target genes in the Enhancer of split gene complex [E(spl)-C]; however, de novo motif analysis revealed a novel site strongly enriched in Insv peaks (TCYAATHRGAA). We validate binding of endogenous Insv to genomic regions bearing such sites, whose associated genes are enriched for neural functions and are functionally repressed by Insv. Unexpectedly, we found that the Insv BEN domain binds specifically to this sequence motif and that Insv directly regulates transcription via this motif. We determined the crystal structure of the BEN-DNA target complex, revealing homodimeric binding of the BEN domain and extensive nucleotide contacts via α helices and a C-terminal loop. Point mutations in key DNA-contacting residues severely impair DNA binding in vitro and capacity for transcriptional regulation in vivo. We further demonstrate DNA-binding and repression activities by the mammalian neural BEN-solo protein BEND5. Altogether, we define novel DNA-binding activity in a conserved family of transcriptional repressors, opening a molecular window on this extensive gene family.
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Affiliation(s)
- Qi Dai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
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91
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Fisher KH, Brown S, Zeidler MP. Designing RNAi screens to identify JAK/STAT pathway components. Methods Mol Biol 2013; 967:81-97. [PMID: 23296723 DOI: 10.1007/978-1-62703-242-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The JAK/STAT signaling pathway has essential roles in multiple developmental processes, including stem cell maintenance, immune responses, and cellular proliferation. As a result, it has been extensively studied in both vertebrate systems and lower complexity models, such as Drosophila. Given its connection with such a wide range of biological functions, it is no surprise that pathway misregulation is frequently associated with multiple human diseases including cancer. While the core components of the pathway, and a number of negative regulators, are well known and conserved in many organisms, more subtle levels of regulation and inter-pathway crosstalk are less well understood. With the emergence of RNA interference (RNAi) as a tool to knock down gene expression and so evaluate protein function, high-throughput screens have been developed to identify pathway regulators on a genome-wide scale. Here we discuss the approaches and methods employed thus far for identification of pathway regulators using RNAi in Drosophila. Furthermore, we discuss possible approaches for future screens and the significant potential for applying RNAi technology in vertebrate models.
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Affiliation(s)
- Katherine H Fisher
- MRC Centre of Developmental Biology and Genetics, Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, UK
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92
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Knorr E, Bingsohn L, Kanost MR, Vilcinskas A. Tribolium castaneum as a model for high-throughput RNAi screening. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 136:163-78. [PMID: 23748349 DOI: 10.1007/10_2013_208] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Coleopteran insects are a highly diverse and successful order, and many beetle species are significant agricultural pests. New biorational strategies for managing populations of beetles and other insect species are needed as pests develop resistance to chemical insecticides and Bt toxins. There is now an opportunity to use genome sequence data to identify genes that are essential for insect growth, development, or survival as new targets for designing control technology. This goal requires a method for high-throughput in vivo screening of thousands of genes to identify candidate genes that, when their expression is disrupted, have a phenotype that may be useful in insect pest control. Tribolium castaneum, the red flour beetle, is a model organism that offers considerable advantages for such screening, including ease of rearing in large numbers, a sequenced genome, and a strong, systemic RNAi response for specific depletion of gene transcripts. The RNAi effect in T. castaneum can be elicited in any tissue and any stage by the injection of dsRNA into the hemocoel, and injection of dsRNA into adult females can even be used to identify phenotypes in offspring. A pilot RNAi screen (iBeetle) is underway. Several T. castaneum genes with promising RNAi phenotypes for further development as mechanisms for plant protection have been identified. These include heat shock protein 90, chitin synthase, the segmentation gene hairy, and a matrix metalloprotease. Candidate genes identified in T. castaneum screens can then be tested in agricultural pest species (in which screening is not feasible), to evaluate their effectiveness for use in potential plant-based RNAi control strategies. Delivery of dsRNA expressed by genetically modified crops to the midgut of phytophagous insects is under investigation as a new tool for very specific protection of plants from insect pest species. The T. castaneum screening platform offers a system for discovery of candidate genes with high potential benefit.
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Affiliation(s)
- Eileen Knorr
- Institute of Phytopathology and Applied Zoology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, 39592, Giessen, Germany
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93
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A targeted in vivo RNAi screen reveals deubiquitinases as new regulators of Notch signaling. G3-GENES GENOMES GENETICS 2012; 2:1563-75. [PMID: 23275879 PMCID: PMC3516478 DOI: 10.1534/g3.112.003780] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/27/2012] [Indexed: 01/11/2023]
Abstract
Notch signaling is highly conserved in all metazoan animals and plays critical roles in cell fate specification, cell proliferation, apoptosis, and stem cell maintenance. Although core components of the Notch signaling cascade have been identified, many gaps in the understanding of the Notch signaling pathway remain to be filled. One form of posttranslational regulation, which is controlled by the ubiquitin-proteasome system, is known to modulate Notch signaling. The ubiquitination pathway is a highly coordinated process in which the ubiquitin moiety is either conjugated to or removed from target proteins by opposing E3 ubiquitin ligases and deubiquitinases (DUBs). Several E3 ubiquitin ligases have been implicated in ubiquitin conjugation to the receptors and the ligands of the Notch signaling cascade. In contrast, little is known about a direct role of DUBs in Notch signaling in vivo. Here, we report an in vivo RNA interference screen in Drosophila melanogaster targeting all 45 DUBs that we annotated in the fly genome. We show that at least four DUBs function specifically in the formation of the fly wing margin and/or the specification of the scutellar sensory organ precursors, two processes that are strictly dependent on the balanced Notch signaling activity. Furthermore, we provide genetic evidence suggesting that these DUBs are necessary to positively modulate Notch signaling activity. Our study reveals a conserved molecular mechanism by which protein deubiquitination process contributes to the complex posttranslational regulation of Notch signaling in vivo.
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94
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Schwarz TJ, Ebert B, Lie DC. Stem cell maintenance in the adult mammalian hippocampus: a matter of signal integration? Dev Neurobiol 2012; 72:1006-15. [PMID: 22488809 DOI: 10.1002/dneu.22026] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The continuous generation of new neurons from stem cells in the hippocampal dentate gyrus is considered an important contributor to hippocampal plasticity. A prerequisite for the life-long generation of new dentate granule neurons is the maintenance of the neural stem cell pool. A number of essential molecular regulators and signals for hippocampal neural stem cell maintenance have been identified, but how these pathways interact to prevent precocious differentiation or exhaustion of the stem cell pool is currently unknown. Here, we summarize the current knowledge on the molecular regulation of the hippocampal stem cell pool and discuss the possibility that signal integration through Notch signaling controls stem cell maintenance in the adult hippocampus.
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Affiliation(s)
- Tobias J Schwarz
- Research Group Adult Neurogenesis and Neural Stem Cells, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
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95
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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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96
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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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97
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Chen KF, Crowther DC. Functional genomics in Drosophila models of human disease. Brief Funct Genomics 2012; 11:405-15. [PMID: 22914042 DOI: 10.1093/bfgp/els038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
It is occasionally observed that common sporadic diseases have rare familial counterparts in which mutations at a single locus result in a similar disorder exhibiting simple Mendelian inheritance. Such an observation is often sufficient justification for the creation of a disease model in the fly. Whether the system is based on the over-expression of a toxic variant of a human protein or requires the loss of function of an orthologous fly gene, the consequent phenotypes can be used to understand pathogenesis through the discovery of genetic modifiers. Such genetic screening can be completed rapidly in the fly and in this review we outline how libraries of mutants are generated and how consequent changes in disease-related phenotypes are assessed. The bioinformatic approaches to processing the copious amounts of data so generated are also presented. The next phase of fly modelling will tackle the challenges of complex diseases in which many genes are associated with risk in the human. There is growing interest in the use of interactomics and epigenetics to provide proteome- and genome-scale descriptions of the regulatory dysfunction that results in disease.
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Affiliation(s)
- Ko-Fan Chen
- Department of Genetics, University of Cambridge, Cambridge, UK
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98
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Jiang Y, Reichert H. Analysis of neural stem cell self-renewal and differentiation by transgenic RNAi in Drosophila. Arch Biochem Biophys 2012; 534:38-43. [PMID: 22906721 DOI: 10.1016/j.abb.2012.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/03/2012] [Accepted: 08/04/2012] [Indexed: 12/21/2022]
Abstract
The fruit fly, Drosophila melanogaster, has proved to be a useful model organism for studying the biology of neural stem cells. Notably, significant progress has been made in identifying the molecular mechanisms that regulate the asymmetric cell divisions of the neural stem cell-like neuroblasts during brain development. Recently, the emerging technology of genome-wide transgenic RNA interference (RNAi), which makes it possible to analyze complicated developmental processes in a targeted, tissue-specific way, has been used for the analysis of gene function in Drosophila neuroblasts. Here, we review the key molecular mechanisms that regulate the asymmetric cell divisions of neuroblasts during brain development in Drosophila. We then summarize recent genome-wide transgenic RNAi screens in Drosophila and report on the identification of new regulators and gene networks that are required in balancing neuroblast self-renewal and differentiation.
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Affiliation(s)
- Yanrui Jiang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.
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99
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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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100
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Moretti J, Chastagner P, Liang CC, Cohn MA, Israël A, Brou C. The ubiquitin-specific protease 12 (USP12) is a negative regulator of notch signaling acting on notch receptor trafficking toward degradation. J Biol Chem 2012; 287:29429-41. [PMID: 22778262 DOI: 10.1074/jbc.m112.366807] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Notch signaling is critical for development and adult tissue physiology, controlling cell fate in a context-dependent manner. Upon ligand binding, the transmembrane Notch receptor undergoes two ordered proteolytic cleavages releasing Notch intracellular domain, which regulates the transcription of Notch target genes. The strength of Notch signaling is of crucial importance and depends notably on the quantity of Notch receptor at the cell surface. Using an shRNA library screen monitoring Notch trafficking and degradation in the absence of ligand, we identified mammalian USP12 and its Drosophila melanogaster homolog as novel negative regulators of Notch signaling. USP12 silencing specifically interrupts Notch trafficking to the lysosomes and, as a consequence, leads to an increased amount of receptor at the cell surface and to a higher Notch activity. At the biochemical level, USP12 with its activator UAF1 deubiquitinate the nonactivated form of Notch in cell culture and in vitro. These results characterize a new level of conserved regulation of Notch signaling by the ubiquitin system.
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Affiliation(s)
- Julien Moretti
- Institut Pasteur and CNRS Unité de Recherche Associée (URA) 2582, Signalisation Moléculaire et Activation Cellulaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France
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