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Khan A, Paro S, McGurk L, Sambrani N, Hogg MC, Brindle J, Pennetta G, Keegan LP, O'Connell MA. Membrane and synaptic defects leading to neurodegeneration in Adar mutant Drosophila are rescued by increased autophagy. BMC Biol 2020; 18:15. [PMID: 32059717 PMCID: PMC7020516 DOI: 10.1186/s12915-020-0747-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/05/2020] [Indexed: 11/10/2022] Open
Abstract
Background In fly brains, the Drosophila Adar (adenosine deaminase acting on RNA) enzyme edits hundreds of transcripts to generate edited isoforms of encoded proteins. Nearly all editing events are absent or less efficient in larvae but increase at metamorphosis; the larger number and higher levels of editing suggest editing is most required when the brain is most complex. This idea is consistent with the fact that Adar mutations affect the adult brain most dramatically. However, it is unknown whether Drosophila Adar RNA editing events mediate some coherent physiological effect. To address this question, we performed a genetic screen for suppressors of Adar mutant defects. Adar5G1 null mutant flies are partially viable, severely locomotion defective, aberrantly accumulate axonal neurotransmitter pre-synaptic vesicles and associated proteins, and develop an age-dependent vacuolar brain neurodegeneration. Results A genetic screen revealed suppression of all Adar5G1 mutant phenotypes tested by reduced dosage of the Tor gene, which encodes a pro-growth kinase that increases translation and reduces autophagy in well-fed conditions. Suppression of Adar5G1 phenotypes by reduced Tor is due to increased autophagy; overexpression of Atg5, which increases canonical autophagy initiation, reduces aberrant accumulation of synaptic vesicle proteins and suppresses all Adar mutant phenotypes tested. Endosomal microautophagy (eMI) is another Tor-inhibited autophagy pathway involved in synaptic homeostasis in Drosophila. Increased expression of the key eMI protein Hsc70-4 also reduces aberrant accumulation of synaptic vesicle proteins and suppresses all Adar5G1 mutant phenotypes tested. Conclusions These findings link Drosophila Adar mutant synaptic and neurotransmission defects to more general cellular defects in autophagy; presumably, edited isoforms of CNS proteins are required for optimum synaptic response capabilities in the brain during the behaviorally complex adult life stage.
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Affiliation(s)
- Anzer Khan
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Simona Paro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Leeanne McGurk
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Nagraj Sambrani
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic
| | - Marion C Hogg
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - James Brindle
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Giuseppa Pennetta
- Centre for Integrative Physiology, Euan MacDonald Centre for Motor Neurone Disease Research, Hugh Robson Building, University of Edinburgh, George Square, Edinburgh, EH8 9XD, UK
| | - Liam P Keegan
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
| | - Mary A O'Connell
- CEITEC Masaryk University, Kamenice 735/5, A35, CZ 62 500, Brno, Czech Republic. .,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.
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Sinigaglia K, Wiatrek D, Khan A, Michalik D, Sambrani N, Sedmík J, Vukić D, O'Connell MA, Keegan LP. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2019; 1862:356-369. [DOI: 10.1016/j.bbagrm.2018.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/12/2018] [Accepted: 10/27/2018] [Indexed: 01/24/2023]
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Lai YT, Deem KD, Borràs-Castells F, Sambrani N, Rudolf H, Suryamohan K, El-Sherif E, Halfon MS, McKay DJ, Tomoyasu Y. Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum. Development 2018. [PMID: 29540499 DOI: 10.1242/dev.160663] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Evolution of cis-regulatory elements (such as enhancers) plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods for studying enhancers in species other than established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium using FAIRE (formaldehyde-assisted isolation of regulatory elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and at each stage. In addition, comparison of the FAIRE data with sets of computationally predicted (i.e. supervised cis-regulatory module-predicted) enhancers revealed a very high overlap between the two datasets. Second, using nubbin in the wing and hunchback in the embryo as case studies, we established the first universal reporter assay system that works in various contexts in Tribolium, and in a cross-species context. Together, these advances will facilitate investigation of cis-evolution and morphological diversity in Tribolium and other insects.
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Affiliation(s)
- Yi-Ting Lai
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Kevin D Deem
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | | | - Nagraj Sambrani
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Heike Rudolf
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Kushal Suryamohan
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Ezzat El-Sherif
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91058, Germany
| | - Marc S Halfon
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Daniel J McKay
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Götze M, Dufourt J, Ihling C, Rammelt C, Pierson S, Sambrani N, Temme C, Sinz A, Simonelig M, Wahle E. Translational repression of the Drosophila nanos mRNA involves the RNA helicase Belle and RNA coating by Me31B and Trailer hitch. RNA 2017; 23:1552-1568. [PMID: 28701521 PMCID: PMC5602113 DOI: 10.1261/rna.062208.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/10/2017] [Indexed: 05/10/2023]
Abstract
Translational repression of maternal mRNAs is an essential regulatory mechanism during early embryonic development. Repression of the Drosophila nanos mRNA, required for the formation of the anterior-posterior body axis, depends on the protein Smaug binding to two Smaug recognition elements (SREs) in the nanos 3' UTR. In a comprehensive mass spectrometric analysis of the SRE-dependent repressor complex, we identified Smaug, Cup, Me31B, Trailer hitch, eIF4E, and PABPC, in agreement with earlier data. As a novel component, the RNA-dependent ATPase Belle (DDX3) was found, and its involvement in deadenylation and repression of nanos was confirmed in vivo. Smaug, Cup, and Belle bound stoichiometrically to the SREs, independently of RNA length. Binding of Me31B and Tral was also SRE-dependent, but their amounts were proportional to the length of the RNA and equimolar to each other. We suggest that "coating" of the RNA by a Me31B•Tral complex may be at the core of repression.
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Affiliation(s)
- Michael Götze
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Jérémy Dufourt
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Christian Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Stephanie Pierson
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Nagraj Sambrani
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Claudia Temme
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Martine Simonelig
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34396 Montpellier Cedex 5, France
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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Sawanth SK, Gopinath G, Sambrani N, Arunkumar KP. The autoregulatory loop: A common mechanism of regulation of key sex determining genes in insects. J Biosci 2017; 41:283-94. [PMID: 27240989 DOI: 10.1007/s12038-016-9609-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sex determination in most insects is structured as a gene cascade, wherein a primary signal is passed through a series of sex-determining genes, culminating in a downstream double-switch known as doublesex that decides the sexual fate of the embryo. From the literature available on sex determination cascades, it becomes apparent that sex determination mechanisms have evolved rapidly. The primary signal that provides the cue to determine the sex of the embryo varies remarkably, not only among taxa, but also within taxa. Furthermore, the upstream key gene in the cascade also varies between species and even among closely related species. The order Insecta alone provides examples of astoundingly complex diversity of upstream key genes in sex determination mechanisms. Besides, unlike key upstream genes, the downstream double-switch gene is alternatively spliced to form functional sex-specific isoforms. This sex-specific splicing is conserved across insect taxa. The genes involved in the sex determination cascade such as Sex-lethal (Sxl) in Drosophila melanogaster, transformer (tra) in many other dipterans, coleopterans and hymenopterans, Feminizer (fem) in Apis mellifera, and IGF-II mRNA-binding protein (Bmimp) in Bombyx mori are reported to be regulated by an autoregulatory positive feedback loop. In this review, by taking examples from various insects, we propose the hypothesis that autoregulatory loop mechanisms of sex determination might be a general strategy. We also discuss the possible reasons for the evolution of autoregulatory loops in sex determination cascades and their impact on binary developmental choices.
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Affiliation(s)
- Suresh Kumar Sawanth
- Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 001, India
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Sawanth SK, Gopinath G, Sambrani N, Arunkumar KP. Erratum: The autoregulatory loop: A common mechanism of regulation ofkey sex determining genes in insects. J Biosci 2016. [DOI: 10.1007/s12038-016-9653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ravisankar P, Lai YT, Sambrani N, Tomoyasu Y. Comparative developmental analysis of Drosophila and Tribolium reveals conserved and diverged roles of abrupt in insect wing evolution. Dev Biol 2015; 409:518-29. [PMID: 26687509 DOI: 10.1016/j.ydbio.2015.12.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 11/16/2022]
Abstract
Morphological innovation is a fundamental process in evolution, yet its molecular basis is still elusive. Acquisition of elytra, highly modified beetle forewings, is an important innovation that has driven the successful radiation of beetles. Our RNAi screening for candidate genes has identified abrupt (ab) as a potential key player in elytron evolution. In this study, we performed a series of RNA interference (RNAi) experiments in both Tribolium and Drosophila to understand the contributions of ab to the evolution of beetle elytra. We found that (i) ab is essential for proper wing vein patterning both in Tribolium and Drosophila, (ii) ab has gained a novel function in determining the unique elytron shape in the beetle lineage, (iii) unlike Hippo and Insulin, other shape determining pathways, the shape determining function of ab is specific to the elytron and not required in the hindwing, (iv) ab has a previously undescribed role in the Notch signal-associated wing formation processes, which appears to be conserved between beetles and flies. These data suggest that ab has gained a new function during elytron evolution in beetles without compromising the conserved wing-related functions. Gaining a new function without losing evolutionarily conserved functions may be a key theme in the evolution of morphologically novel structures.
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Affiliation(s)
| | - Yi-Ting Lai
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Nagraj Sambrani
- Department of Biology, Miami University, Oxford, OH 45056, USA
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Sambrani N, Pradel J, Graba Y. Distinct genetic requirements for BX-C-mediated specification of abdominal denticles. Dev Dyn 2014; 243:192-200. [DOI: 10.1002/dvdy.24081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 10/09/2013] [Accepted: 10/09/2013] [Indexed: 11/07/2022] Open
Affiliation(s)
| | | | - Yacine Graba
- CNRS; Aix Marseille Université; Marseille France
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Sambrani N, Hudry B, Maurel-Zaffran C, Zouaz A, Mishra R, Merabet S, Graba Y. Distinct molecular strategies for Hox-mediated limb suppression in Drosophila: from cooperativity to dispensability/antagonism in TALE partnership. PLoS Genet 2013; 9:e1003307. [PMID: 23505377 PMCID: PMC3591290 DOI: 10.1371/journal.pgen.1003307] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/18/2012] [Indexed: 11/19/2022] Open
Abstract
The emergence following gene duplication of a large repertoire of Hox paralogue proteins underlies the importance taken by Hox proteins in controlling animal body plans in development and evolution. Sequence divergence of paralogous proteins accounts for functional specialization, promoting axial morphological diversification in bilaterian animals. Yet functionally specialized paralogous Hox proteins also continue performing ancient common functions. In this study, we investigate how highly divergent Hox proteins perform an identical function. This was achieved by comparing in Drosophila the mode of limb suppression by the central (Ultrabithorax and AbdominalA) and posterior class (AbdominalB) Hox proteins. Results highlight that Hox-mediated limb suppression relies on distinct modes of DNA binding and a distinct use of TALE cofactors. Control of common functions by divergent Hox proteins, at least in the case studied, relies on evolving novel molecular properties. Thus, changes in protein sequences not only provide the driving force for functional specialization of Hox paralogue proteins, but also provide means to perform common ancient functions in distinct ways.
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Affiliation(s)
- Nagraj Sambrani
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Bruno Hudry
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Corinne Maurel-Zaffran
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Amel Zouaz
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Rakesh Mishra
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
| | - Samir Merabet
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
| | - Yacine Graba
- Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Institut de Biologie du Développement de Marseille Luminy (IBDML, UMR 7288), Parc Scientifique de Luminy, Marseille, France
- * E-mail:
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Rivas ML, Espinosa-Vázquez JM, Sambrani N, Greig S, Merabet S, Graba Y, Castelli-Gair Hombría J. Antagonism versus cooperativity with TALE cofactors at the base of the functional diversification of Hox protein function. PLoS Genet 2013; 9:e1003252. [PMID: 23408901 PMCID: PMC3567137 DOI: 10.1371/journal.pgen.1003252] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022] Open
Abstract
Extradenticle (Exd) and Homothorax (Hth) function as positive transcriptional cofactors of Hox proteins, helping them to bind specifically their direct targets. The posterior Hox protein Abdominal-B (Abd-B) does not require Exd/Hth to bind DNA; and, during embryogenesis, Abd-B represses hth and exd transcription. Here we show that this repression is necessary for Abd-B function, as maintained Exd/Hth expression results in transformations similar to those observed in loss-of-function Abd-B mutants. We characterize the cis regulatory module directly regulated by Abd-B in the empty spiracles gene and show that the Exd/Hth complex interferes with Abd-B binding to this enhancer. Our results suggest that this novel Exd/Hth function does not require the complex to bind DNA and may be mediated by direct Exd/Hth binding to the Abd-B homeodomain. Thus, in some instances, the main positive cofactor complex for anterior Hox proteins can act as a negative factor for the posterior Hox protein Abd-B. This antagonistic interaction uncovers an alternative way in which MEIS and PBC cofactors can modulate Abd-B like posterior Hox genes during development.
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Affiliation(s)
| | | | - Nagraj Sambrani
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
| | - Stephen Greig
- Akam Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Samir Merabet
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
| | - Yacine Graba
- IBDML, CNRS/Université de la Méditerranée, Marseille, France
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Abstract
Deciphering the molecular bases of animal body plan construction is a central question in developmental and evolutionary biology. Genome analyses of a number of metazoans indicate that widely conserved regulatory molecules underlie the amazing diversity of animal body plans, suggesting that these molecules are reiteratively used for multiple purposes. Hox proteins constitute a good example of such molecules and provide the framework to address the mechanisms underlying transcriptional specificity and diversity in development and evolution. Here we examine the current knowledge of the molecular bases of Hox-mediated transcriptional control, focusing on how this control is encoded within protein sequences and structures. The survey suggests that the homeodomain is part of an extended multifunctional unit coordinating DNA binding and activity regulation and highlights the need for further advances in our understanding of Hox protein activity.
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Affiliation(s)
- Samir Merabet
- Institute of Developmental Biology of Marseille Luminy, University of the Mediterranean, Marseille, France.
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Bajpai R, Sambrani N, Stadelmayer B, Shashidhara LS. Identification of a novel target of D/V signaling in Drosophila wing disc: Wg-independent function of the organizer. Gene Expr Patterns 2005; 5:113-21. [PMID: 15533826 DOI: 10.1016/j.modgep.2004.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2004] [Accepted: 05/24/2004] [Indexed: 01/12/2023]
Abstract
Growth and patterning during Drosophila wing development are mediated by signaling from its dorso-ventral (D/V) organizer. Wingless is expressed in the D/V boundary and functions as a morphogen to activate target genes at a distance. Wingless pathway and thereby D/V signaling is negatively regulated by the homeotic gene Ultrabithorax (Ubx) to mediate haltere development. In an enhancer-trap screen to identify genes that show differential expression between wing and haltere discs, we identified CG32062, which codes for a RNA-binding protein. In wing discs, CG32062 is expressed only in non-D/V cells. CG32062 expression in non-D/V cells is dependent on Notch-mediated signaling from the D/V boundary. However, CG32062 expression is independent of Wingless function, thus providing evidence for a second long-range signaling mechanism of the D/V organizer. In haltere discs, CG32062 is negatively regulated by Ubx. The non-cell autonomous nature of Ubx-mediated repression of CG32062 expression suggests that the novel component of D/V signaling is also negatively regulated during haltere specification.
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Affiliation(s)
- Ruchi Bajpai
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India 500 007
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