1
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Frampton SL, Sutcliffe C, Baldock C, Ashe HL. Modelling the structure of Short Gastrulation and generation of a toolkit for studying its function in Drosophila. Biol Open 2022; 11:275491. [PMID: 35603711 PMCID: PMC9194680 DOI: 10.1242/bio.059199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
A BMP gradient is essential for patterning the dorsal-ventral axis of invertebrate and vertebrate embryos. The extracellular BMP binding protein Short Gastrulation (Sog) in Drosophila plays a key role in BMP gradient formation. In this study, we combine genome editing, structural and developmental approaches to study Sog function in Drosophila. We generate a sog knockout fly stock, which allows simple reintegration of altered versions of the sog coding sequence. As proof-of-principle, we test the requirement for two cysteine residues that were previously identified as targets for palmitoylation, which has been proposed to enhance Sog secretion. However, we show that the sogC27,28S mutant is viable with only very mild phenotypes, indicating that these residues and their potential modification are not critical for Sog secretion in vivo. Additionally, we use experimental negative stain EM imaging and hydrodynamic data to validate the AlphaFold structure prediction for Sog. The model suggests a more compact shape than the vertebrate ortholog Chordin and conformational flexibility between the C-terminal von Willebrand C domains. We discuss how this altered compactness may contribute to mechanistic differences in Sog and Chordin function during BMP gradient formation. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sophie L. Frampton
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Catherine Sutcliffe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK
| | - Clair Baldock
- Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK,Authors for correspondence (, )
| | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PT, UK,Authors for correspondence (, )
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2
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Sandler JE, Irizarry J, Stepanik V, Dunipace L, Amrhein H, Stathopoulos A. A Developmental Program Truncates Long Transcripts to Temporally Regulate Cell Signaling. Dev Cell 2019; 47:773-784.e6. [PMID: 30562515 DOI: 10.1016/j.devcel.2018.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/30/2018] [Accepted: 11/13/2018] [Indexed: 11/29/2022]
Abstract
Rapid mitotic divisions and a fixed transcription rate limit the maximal length of transcripts in early Drosophila embryos. Previous studies suggested that transcription of long genes is initiated but aborted, as early nuclear divisions have short interphases. Here, we identify long genes that are expressed during short nuclear cycles as truncated transcripts. The RNA binding protein Sex-lethal physically associates with transcripts for these genes and is required to support early termination to specify shorter transcript isoforms in early embryos of both sexes. In addition, one truncated transcript for the gene short-gastrulation encodes a product in embryos that functionally relates to a previously characterized dominant-negative form, which maintains TGF-β signaling in the off-state. In summary, our results reveal a developmental program of short transcripts functioning to help temporally regulate Drosophila embryonic development, keeping cell signaling at early stages to a minimum in order to support its proper initiation at cellularization.
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Affiliation(s)
- Jeremy E Sandler
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jihyun Irizarry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vincent Stepanik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Leslie Dunipace
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henry Amrhein
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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3
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Kim AR, Choi EB, Kim MY, Choi KW. Angiotensin-converting enzyme Ance is cooperatively regulated by Mad and Pannier in Drosophila imaginal discs. Sci Rep 2017; 7:13174. [PMID: 29030610 PMCID: PMC5640665 DOI: 10.1038/s41598-017-13487-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/26/2017] [Indexed: 02/02/2023] Open
Abstract
Angiotensin-converting enzyme (ACE) is an evolutionarily conserved peptidyl dipeptidase. Mammalian ACE converts angiotensin I to the active vasoconstrictor angiotensin II, thus playing a critical role for homeostasis of the renin-angiotensin system. In Drosophila, the ACE homolog Ance is expressed in specific regions of developing organs, but its regulatory mechanism has not been identified. Here we provide evidence that Ance expression is regulated by a combination of Mad and Pannier (Pnr) in imaginal discs. We demonstrate that Ance expression in eye and wing discs depends on Dpp signaling. The Mad binding site of Ance regulatory region is essential for Ance expression. Ance expression in imaginal discs is also regulated by the GATA family transcription factor Pnr. Pnr directly regulates Ance expression by binding to a GATA site of Ance enhancer. In addition, Pnr and Mad physically and genetically interact. Ance null mutants are morphologically normal but show genetic interaction with dpp mutants. Furthermore, we show that human SMAD2 and GATA4 physically interact and ACE expression in HEK293 cells is regulated by SMAD2 and GATA4. Taken together, this study reveals a cooperative mechanism of Ance regulation by Mad and Pnr. Our data also suggest a conserved transcriptional regulation of human ACE.
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Affiliation(s)
- Ah-Ram Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Eun-Bee Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Mi-Young Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea.
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4
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Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J. Drosophila poised enhancers are generated during tissue patterning with the help of repression. Genome Res 2016; 27:64-74. [PMID: 27979994 PMCID: PMC5204345 DOI: 10.1101/gr.209486.116] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 11/08/2016] [Indexed: 12/18/2022]
Abstract
Histone modifications are frequently used as markers for enhancer states, but how to interpret enhancer states in the context of embryonic development is not clear. The poised enhancer signature, involving H3K4me1 and low levels of H3K27ac, has been reported to mark inactive enhancers that are poised for future activation. However, future activation is not always observed, and alternative reasons for the widespread occurrence of this enhancer signature have not been investigated. By analyzing enhancers during dorsal-ventral (DV) axis formation in the Drosophila embryo, we find that the poised enhancer signature is specifically generated during patterning in the tissue where the enhancers are not induced, including at enhancers that are known to be repressed by a transcriptional repressor. These results suggest that, rather than serving exclusively as an intermediate step before future activation, the poised enhancer state may be a mark for spatial regulation during tissue patterning. We discuss the possibility that the poised enhancer state is more generally the result of repression by transcriptional repressors.
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Affiliation(s)
- Nina Koenecke
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Jeff Johnston
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Qiye He
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Samuel Meier
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA.,University of Kansas Medical Center, Department of Pathology, Kansas City, Kansas 66160, USA
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5
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Target genes of Dpp/BMP signaling pathway revealed by transcriptome profiling in the early D. melanogaster embryo. Gene 2016; 591:191-200. [DOI: 10.1016/j.gene.2016.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/05/2016] [Accepted: 07/05/2016] [Indexed: 01/23/2023]
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6
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Quijano JC, Wisotzkey RG, Tran NL, Huang Y, Stinchfield MJ, Haerry TE, Shimmi O, Newfeld SJ. lolal Is an Evolutionarily New Epigenetic Regulator of dpp Transcription during Dorsal-Ventral Axis Formation. Mol Biol Evol 2016; 33:2621-32. [PMID: 27401231 PMCID: PMC5026256 DOI: 10.1093/molbev/msw132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Secreted ligands in the Dpp/BMP family drive dorsal–ventral (D/V) axis formation in all Bilaterian species. However, maternal factors regulating Dpp/BMP transcription in this process are largely unknown. We identified the BTB domain protein longitudinals lacking-like (lolal) as a modifier of decapentaplegic (dpp) mutations. We show that Lolal is evolutionarily related to the Trithorax group of chromatin regulators and that lolal interacts genetically with the epigenetic factor Trithorax-like during Dpp D/V signaling. Maternally driven LolalHA is found in oocytes and translocates to zygotic nuclei prior to the point at which dpp transcription begins. lolal maternal and zygotic mutant embryos display significant reductions in dpp, pMad, and zerknullt expression, but they are never absent. The data suggest that lolal is required to maintain dpp transcription during D/V patterning. Phylogenetic data revealed that lolal is an evolutionarily new gene present only in insects and crustaceans. We conclude that Lolal is the first maternal protein identified with a role in dpp D/V transcriptional maintenance, that Lolal and the epigenetic protein Trithorax-like are essential for Dpp D/V signaling and that the architecture of the Dpp D/V pathway evolved in the arthropod lineage after the separation from vertebrates via the incorporation of new genes such as lolal.
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Affiliation(s)
| | | | | | - Yunxian Huang
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Theodor E Haerry
- Center for Molecular Biology and Biotechnology, Florida Atlantic University
| | - Osamu Shimmi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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7
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Deignan L, Pinheiro MT, Sutcliffe C, Saunders A, Wilcockson SG, Zeef LAH, Donaldson IJ, Ashe HL. Regulation of the BMP Signaling-Responsive Transcriptional Network in the Drosophila Embryo. PLoS Genet 2016; 12:e1006164. [PMID: 27379389 PMCID: PMC4933369 DOI: 10.1371/journal.pgen.1006164] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/10/2016] [Indexed: 12/24/2022] Open
Abstract
The BMP signaling pathway has a conserved role in dorsal-ventral axis patterning during embryonic development. In Drosophila, graded BMP signaling is transduced by the Mad transcription factor and opposed by the Brinker repressor. In this study, using the Drosophila embryo as a model, we combine RNA-seq with Mad and Brinker ChIP-seq to decipher the BMP-responsive transcriptional network underpinning differentiation of the dorsal ectoderm during dorsal-ventral axis patterning. We identify multiple new BMP target genes, including positive and negative regulators of EGF signaling. Manipulation of EGF signaling levels by loss- and gain-of-function studies reveals that EGF signaling negatively regulates embryonic BMP-responsive transcription. Therefore, the BMP gene network has a self-regulating property in that it establishes a balance between its activity and that of the antagonistic EGF signaling pathway to facilitate correct patterning. In terms of BMP-dependent transcription, we identify key roles for the Zelda and Zerknüllt transcription factors in establishing the resulting expression domain, and find widespread binding of insulator proteins to the Mad and Brinker-bound genomic regions. Analysis of embryos lacking the BEAF-32 insulator protein shows reduced transcription of a peak BMP target gene and a reduction in the number of amnioserosa cells, the fate specified by peak BMP signaling. We incorporate our findings into a model for Mad-dependent activation, and discuss its relevance to BMP signal interpretation in vertebrates. Embryogenesis involves the patterning of many different cell fates by a limited number of types of signals. One way that these signals promote a particular cell fate is through the induction of a complex, yet highly reproducible, gene expression programme that instructs changes in the cell. For example, there is a conserved role for BMP signals in specifying cell fates during dorsal-ventral axis patterning. Here, we have used genomics approaches to identify the gene expression programme implemented in response to BMP signaling during axis patterning in the Drosophila embryo. Part of the gene network downstream of BMP signaling includes members of the EGF signaling pathway, with our data highlighting reciprocal interactions between these two pathways. We have also determined genome-wide binding of BMP-responsive transcription factors to gain new insights into how the BMP gene network is activated. Our data reveal roles for specific transcription factors and insulator binding proteins, with the latter traditionally associated with the separation of transcriptional domains. Overall, our data will provide a platform for exploiting the tractability of the Drosophila embryo to determine which features of the network are critical drivers of BMP-induced cell fate changes during embryogenesis.
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Affiliation(s)
- Lisa Deignan
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Marco T. Pinheiro
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Catherine Sutcliffe
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Abbie Saunders
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Scott G. Wilcockson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Leo A. H. Zeef
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ian J. Donaldson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Hilary L. Ashe
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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8
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Hodar C, Zuñiga A, Pulgar R, Travisany D, Chacon C, Pino M, Maass A, Cambiazo V. Comparative gene expression analysis of Dtg, a novel target gene of Dpp signaling pathway in the early Drosophila melanogaster embryo. Gene 2013; 535:210-7. [PMID: 24321690 DOI: 10.1016/j.gene.2013.11.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 10/30/2013] [Accepted: 11/14/2013] [Indexed: 10/25/2022]
Abstract
In the early Drosophila melanogaster embryo, Dpp, a secreted molecule that belongs to the TGF-β superfamily of growth factors, activates a set of downstream genes to subdivide the dorsal region into amnioserosa and dorsal epidermis. Here, we examined the expression pattern and transcriptional regulation of Dtg, a new target gene of Dpp signaling pathway that is required for proper amnioserosa differentiation. We showed that the expression of Dtg was controlled by Dpp and characterized a 524-bp enhancer that mediated expression in the dorsal midline, as well as, in the differentiated amnioserosa in transgenic reporter embryos. This enhancer contained a highly conserved region of 48-bp in which bioinformatic predictions and in vitro assays identified three Mad binding motifs. Mutational analysis revealed that these three motifs were necessary for proper expression of a reporter gene in transgenic embryos, suggesting that short and highly conserved genomic sequences may be indicative of functional regulatory regions in D. melanogaster genes. Dtg orthologs were not detected in basal lineages of Dipterans, which unlike D. melanogaster develop two extra-embryonic membranes, amnion and serosa, nevertheless Dtg orthologs were identified in the transcriptome of Musca domestica, in which dorsal ectoderm patterning leads to the formation of a single extra-embryonic membrane. These results suggest that Dtg was recruited as a new component of the network that controls dorsal ectoderm patterning in the lineage leading to higher Cyclorrhaphan flies, such as D. melanogaster and M. domestica.
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Affiliation(s)
- Christian Hodar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Alejandro Zuñiga
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Rodrigo Pulgar
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- Laboratorio de Bioinformática y Matemática del Genoma, Center for Mathematical Modeling, FCFM-Universidad de Chile, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile
| | - Carlos Chacon
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile
| | - Michael Pino
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile
| | - Alejandro Maass
- Laboratorio de Bioinformática y Matemática del Genoma, Center for Mathematical Modeling, FCFM-Universidad de Chile, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile; Department of Mathematical Engineering, FCFM-Universidad de Chile, Santiago, Chile
| | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, El Líbano 5524, Santiago, Chile; Fondap Center for Genome Regulation (CGR), Universidad de Chile, Santiago, Chile.
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9
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Stolfi A, Wagner E, Taliaferro JM, Chou S, Levine M. Neural tube patterning by Ephrin, FGF and Notch signaling relays. Development 2012; 138:5429-39. [PMID: 22110057 DOI: 10.1242/dev.072108] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The motor ganglion (MG) controls the rhythmic swimming behavior of the Ciona intestinalis tadpole. Despite its cellular simplicity (five pairs of neurons), the MG exhibits conservation of transcription factor expression with the spinal cord of vertebrates. Evidence is presented that the developing MG is patterned by sequential Ephrin/FGF/MAPK and Delta/Notch signaling events. FGF/MAPK attenuation by a localized EphrinAb signal specifies posterior neuronal subtypes, which in turn relay a Delta2/Notch signal that specifies anterior fates. This short-range relay is distinct from the patterning of the vertebrate spinal cord, which is a result of opposing BMP and Shh morphogen gradients. Nonetheless, both mechanisms lead to localized expression of related homeodomain codes for the specification of distinct neuronal subtypes. This MG regulatory network provides a foundation for elucidating the genetic and cellular basis of a model chordate central pattern generator.
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Affiliation(s)
- Alberto Stolfi
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA.
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10
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Blitz IL, Cho KWY. Finding partners: how BMPs select their targets. Dev Dyn 2009; 238:1321-31. [PMID: 19441058 DOI: 10.1002/dvdy.21984] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The bone morphogenetic protein (BMP) signaling pathway is a conserved and evolutionarily ancient regulatory module affecting a large variety of cellular behaviors. The evolutionary flexibility in using BMP responses presumably arose by co-option of a canonical BMP signaling cascade to regulate the transcription of diverse batteries of target genes. This begs the question of how seemingly interchangeable BMP signaling components elicit widely different outputs in different cell types, an important issue in the context of understanding how BMP signaling integrates with gene regulatory networks to control development. Because a molecular understanding of how BMP signaling activates different batteries of target genes is an essential prerequisite to comprehending the roles of BMPs in regulating cellular responses, here we review the current knowledge of how BMP-regulated target genes are selected by the signal transduction machinery. We highlight recent studies suggesting the evolutionary conservation of BMP target gene regulation signaling by Schnurri family zinc finger proteins. Developmental Dynamics 238:1321-1331, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology and the Developmental Biology Center, University of California, Irvine, California, USA.
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11
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Liberman LM, Stathopoulos A. Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence. Dev Biol 2008; 327:578-89. [PMID: 19135437 DOI: 10.1016/j.ydbio.2008.12.020] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/13/2008] [Accepted: 12/16/2008] [Indexed: 11/18/2022]
Abstract
In early Drosophila embryos, the transcription factor Dorsal regulates patterns of gene expression and cell fate specification along the dorsal-ventral axis. How gene expression is produced within the broad lateral domain of the presumptive neurogenic ectoderm is not understood. To investigate transcriptional control during neurogenic ectoderm specification, we examined divergence and function of an embryonic cis-regulatory element controlling the gene short gastrulation (sog). While transcription factor binding sites are not completely conserved, we demonstrate that these sequences are bona fide regulatory elements, despite variable regulatory architecture. Mutation of conserved sequences revealed that putative transcription factor binding sites for Dorsal and Zelda, a ubiquitous maternal transcription factor, are required for proper sog expression. When Zelda and Dorsal sites are paired in a synthetic regulatory element, broad lateral expression results. However, synthetic regulatory elements that contain Dorsal and an additional activator also drive expression throughout the neurogenic ectoderm. Our results suggest that interaction between Dorsal and Zelda drives expression within the presumptive neurogenic ectoderm, but they also demonstrate that regulatory architecture directing expression in this domain is flexible. We propose a model for neurogenic ectoderm specification in which gene regulation occurs at the intersection of temporal and spatial transcription factor inputs.
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Affiliation(s)
- Louisa M Liberman
- California Institute of Technology, Division of Biology, 1200 E. California Blvd., MC 114-96, Pasadena, CA 91125, USA
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12
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Blanco J, Gehring WJ. Analysis of twin of eyeless regulation during early embryogenesis in Drosophila melanogaster. Gene Expr Patterns 2008; 8:523-7. [DOI: 10.1016/j.gep.2008.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 05/27/2008] [Accepted: 06/01/2008] [Indexed: 11/27/2022]
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13
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Extraembryonic development in insects and the acrobatics of blastokinesis. Dev Biol 2008; 313:471-91. [DOI: 10.1016/j.ydbio.2007.11.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 10/11/2007] [Accepted: 11/02/2007] [Indexed: 01/04/2023]
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14
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Isaac RE, Lamango NS, Ekbote U, Taylor CA, Hurst D, Weaver RJ, Carhan A, Burnham S, Shirras AD. Angiotensin-converting enzyme as a target for the development of novel insect growth regulators. Peptides 2007; 28:153-62. [PMID: 17157962 DOI: 10.1016/j.peptides.2006.08.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Revised: 08/14/2006] [Accepted: 08/14/2006] [Indexed: 11/25/2022]
Abstract
Insect angiotensin converting enzyme (ACE) is a zinc metallopeptidase capable of inactivating a variety of small to medium size peptide hormones by cleavage of C-terminal dipeptides and dipeptideamides. High levels of ACE activity are found in the hemolymph and in reproductive tissues of insects, where the enzyme is considered to have an important role in the metabolism of bioactive peptides. Therefore, inhibiting ACE activity is expected to interfere with the peptidergic endocrine system and to have detrimental effects on growth, development and reproduction. We will review the studies showing that ACE inhibitors do indeed disrupt growth and reproduction in various insect species. We will also present some new genetic and pharmacological data that strengthens our conclusion that ACE should be considered as a potential target for the development of new insect growth regulators.
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Affiliation(s)
- R Elwyn Isaac
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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15
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Anderson J, Salzer CL, Kumar JP. Regulation of the retinal determination gene dachshund in the embryonic head and developing eye of Drosophila. Dev Biol 2006; 297:536-49. [PMID: 16780828 PMCID: PMC2717003 DOI: 10.1016/j.ydbio.2006.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 04/13/2006] [Accepted: 05/03/2006] [Indexed: 11/29/2022]
Abstract
The retinal determination gene dachshund is distantly related to the family of Ski/Sno proto-oncogenes and influences the development of a wide range of tissues including the embryonic head, optic lobes, brain, central nervous system as well as the post-embryonic leg, wing, genital and eye-antennal discs. We were interested in the regulatory mechanisms that control the dynamic expression pattern of dachshund and in this report we set out to ascertain how the transcription of dachshund is modulated in the embryonic head and developing eye-antennal imaginal disc. We demonstrate that the TGFbeta signaling cascade, the transcription factor zerknullt and several other patterning genes prevent dachshund from being expressed inappropriately within the embryonic head. Additionally, we show that several members of the eye specification cascade influence the transcription of dachshund during normal and ectopic eye development. Our results suggest that dachshund is regulated by a complex combinatorial code of transcription factors and signaling pathways. Unraveling this code may lead to an understanding of how dachshund regulates the development of many diverse tissue types including the eye.
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16
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Mizutani CM, Nie Q, Wan FY, Zhang YT, Vilmos P, Sousa-Neves R, Bier E, Marsh JL, Lander AD. Formation of the BMP activity gradient in the Drosophila embryo. Dev Cell 2005; 8:915-24. [PMID: 15935780 PMCID: PMC1829168 DOI: 10.1016/j.devcel.2005.04.009] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2004] [Revised: 03/22/2005] [Accepted: 04/20/2005] [Indexed: 11/28/2022]
Abstract
The dorsoventral axis of the Drosophila embryo is patterned by a gradient of bone morphogenetic protein (BMP) ligands. In a process requiring at least three additional extracellular proteins, a broad domain of weak signaling forms and then abruptly sharpens into a narrow dorsal midline peak. Using experimental and computational approaches, we investigate how the interactions of a multiprotein network create the unusual shape and dynamics of formation of this gradient. Starting from observations suggesting that receptor-mediated BMP degradation is an important driving force in gradient dynamics, we develop a general model that is capable of capturing both subtle aspects of gradient behavior and a level of robustness that agrees with in vivo results.
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Affiliation(s)
- Claudia Mieko Mizutani
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
| | - Qing Nie
- Department of Mathematics, University of California, Irvine Irvine, California 92697
- Center for Complex Biological Systems, University of California, Irvine Irvine, California 92697
| | - Frederic Y.M. Wan
- Department of Mathematics, University of California, Irvine Irvine, California 92697
- Center for Complex Biological Systems, University of California, Irvine Irvine, California 92697
| | - Yong-Tao Zhang
- Department of Mathematics, University of California, Irvine Irvine, California 92697
- Center for Complex Biological Systems, University of California, Irvine Irvine, California 92697
| | - Peter Vilmos
- Department of Developmental and Cell Biology, University of California, Irvine Irvine, California 92697
- Developmental Biology Center University of California, Irvine Irvine, California 92697
| | - Rui Sousa-Neves
- Department of Developmental and Cell Biology, University of California, Irvine Irvine, California 92697
- Developmental Biology Center University of California, Irvine Irvine, California 92697
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
- *Correspondence: (A.D.L.); (E.B.)
| | - J. Lawrence Marsh
- Center for Complex Biological Systems, University of California, Irvine Irvine, California 92697
- Department of Developmental and Cell Biology, University of California, Irvine Irvine, California 92697
- Developmental Biology Center University of California, Irvine Irvine, California 92697
| | - Arthur D. Lander
- Center for Complex Biological Systems, University of California, Irvine Irvine, California 92697
- Department of Developmental and Cell Biology, University of California, Irvine Irvine, California 92697
- Developmental Biology Center University of California, Irvine Irvine, California 92697
- *Correspondence: (A.D.L.); (E.B.)
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17
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Wharton SJ, Basu SP, Ashe HL. Smad affinity can direct distinct readouts of the embryonic extracellular Dpp gradient in Drosophila. Curr Biol 2005; 14:1550-8. [PMID: 15341741 DOI: 10.1016/j.cub.2004.08.053] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2004] [Revised: 07/19/2004] [Accepted: 07/20/2004] [Indexed: 10/26/2022]
Abstract
BACKGROUND The TGF-beta signaling molecule Decapentaplegic (Dpp) is an essential morphogen that patterns many tissues during Drosophila development, including the embryonic dorsal ectoderm and larval wing imaginal disk. An activity gradient of Dpp specifies distinct cell fates in the dorsal ectoderm of the embryo through the activation of different transcriptional threshold responses. RESULTS We have analyzed the gene Race, which is expressed in response to peak levels of Dpp signaling in gastrulating embryos. We show that the Smad transcription factors, which are intracellular transducers of Dpp signaling, are essential activators of Race in vivo. Furthermore, increasing the affinity of the Smad binding sites in the Race enhancer broadens the expression pattern of a linked reporter gene and alters its behavior in mutant embryos to that characteristic of a distinct threshold response. CONCLUSIONS Smad activator affinity is a critical determinant of the threshold response to the extracellular Dpp gradient in the embryo. Our results identify a mechanism for interpreting the Dpp gradient in the embryo which is different to the reciprocal repressor gradient model proposed for the wing disk. We suggest that transcription factor binding site affinity will be a general strategy used in the interpretation of other extracellular morphogen gradients.
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Affiliation(s)
- Stephen J Wharton
- School of Biological Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom
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18
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Hamaguchi T, Yabe S, Uchiyama H, Murakami R. Drosophila Tbx6-related gene, Dorsocross, mediates high levels of Dpp and Scw signal required for the development of amnioserosa and wing disc primordium. Dev Biol 2004; 265:355-68. [PMID: 14732398 DOI: 10.1016/j.ydbio.2003.09.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Regional differentiation along the dorsoventral (DV) axis of the Drosophila embryo primarily depends on a graded BMP signaling activity generated by Decapentaplegic (Dpp) and Screw (Scw). We have identified triplicated Dpp and Scw target genes Dorsocross1, 2 and 3 (Doc1, 2, 3) that have a conserved T-box domain related to the vertebrate Tbx6 subfamily and act redundantly to induce dorsal structures. Doc genes are expressed in the dorsal region in the early blastoderm. After gastrulation, newly expressed Doc appears in a segmental pattern in the ectoderm. This expression correlates spatially with the second phase of Dpp expression in the ectoderm. Doc expression in the early blastoderm is abolished in either dpp or scw mutant embryos, whereas the ectodermal segmented expression depends only on Dpp. Inactivation of Doc genes with RNAi dramatically affected the development of amnioserosa and wing disc primordia, both of which depend on high levels of BMP signaling, although leg disc primordium, which depends on low levels of BMP, remained intact. Doc1 mRNA expressed in Xenopus embryos induced ventral mesoderm, suppressed activin-induced events and induced Xvent genes, which are analogous to the effects of native Tbx6 and its upstream regulator, BMP-4. These results suggest that the Tbx6 subfamily act in the BMP signaling pathway required for embryonic patterning in both animals.
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Affiliation(s)
- Takashi Hamaguchi
- Department of Physics, Biology, and Informatics, Yamaguchi University, Yamaguchi 753-8512, Japan
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19
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Chang T, Shy D, Hartenstein V. Antagonistic relationship between Dpp and EGFR signaling in Drosophila head patterning. Dev Biol 2003; 263:103-13. [PMID: 14568549 DOI: 10.1016/s0012-1606(03)00448-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Drosophila eye field that gives rise to the visual system and dorsal head epidermis forms an unpaired anlage located in the dorsal head ectoderm. The eye field expresses and requires both Dpp and EGFR signaling for its development. As shown in previous studies, EGFR is required for cell maintenance in the developing visual system. Dpp initially switches on the early eye genes so and eya in the eye field. Consecutively, high levels of Dpp in the dorsal midline inhibit these genes and promote development of head epidermis. We show that Dpp negatively regulates EGFR signaling, thereby increasing the amount of cell death in the dorsal midline. By this mechanism, Dpp controls the formation of a bilateral visual system and indirectly modulates cell death, which is essential for normal head morphogenesis. Loss of either Dpp or its downstream target, Zen, abolishes head epidermis fate and leads to the misexpression of dp-ERK in the dorsal midline. The resulting morphological phenotype consists of cyclopia, reduction of cell death, and failure of head involution. Ectopic expression of activated EGFR inhibits the Dpp target race and thereby causes cyclopia and defective head involution. We discuss possible mechanisms of Dpp and EGFR interaction in the embryo.
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Affiliation(s)
- Ting Chang
- Department of Molecular Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
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20
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Stathopoulos A, Van Drenth M, Erives A, Markstein M, Levine M. Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo. Cell 2002; 111:687-701. [PMID: 12464180 DOI: 10.1016/s0092-8674(02)01087-5] [Citation(s) in RCA: 231] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The maternal Dorsal regulatory gradient initiates the differentiation of several tissues in the early Drosophila embryo. Whole-genome microarray assays identified as many as 40 new Dorsal target genes, which encode a broad spectrum of cell signaling proteins and transcription factors. Evidence is presented that a tissue-specific form of the NF-Y transcription complex is essential for the activation of gene expression in the mesoderm. Tissue-specific enhancers were identified for new Dorsal target genes, and bioinformatics methods identified conserved cis-regulatory elements for coordinately regulated genes that respond to similar thresholds of the Dorsal gradient. The new Dorsal target genes and enhancers represent one of the most extensive gene networks known for any developmental process.
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Affiliation(s)
- Angelike Stathopoulos
- Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, Berkeley, CA 94720, USA
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21
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Lasko P. Diabetic flies? Using Drosophila melanogaster to understand the causes of monogenic and genetically complex diseases. Clin Genet 2002; 62:358-67. [PMID: 12431248 DOI: 10.1034/j.1399-0004.2002.620502.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Approximately three-quarters of human disease loci have counterparts in the fruit fly Drosophila melanogaster. This model organism is therefore extremely valuable for using to understand the role of these loci in normal development, and for unravelling genetic pathways in which these loci take part. Important advantages for Drosophila in such studies are its completed genome, the unparalleled collection of mutations already in existence, the relative ease in which new mutations can be generated, the existence of convenient techniques for inactivating or overexpressing genes in dispensable tissues that are easily observed and measured, and the ability to readily carry out second-site modifier genetics. Recent work in Drosophila on the insulin-signaling pathway, a pathway of profound clinical importance, is reviewed as an illustration of how such research can provide fundamental insights into the functions of this pathway in regulating growth and development. Moreover, Drosophila research is now identifying heretofore unknown regulators of insulin signaling, as well as indicating novel functions for this pathway in suppressing benign tumor formation and regulating life span.
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Affiliation(s)
- P Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.
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22
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Abstract
Fos and Jun proteins homo- or heterodimerize to form functional AP-1 transcription factors. Drosophila mutants lacking either Jun or Fos display indistinguishable dorsal open phenotypes, indicating an essential function of both Jun and Fos for embryonic dorsal closure. Here we present experiments to determine the basis for this dual requirement. By combining mutant alleles and transgenes expressing Fos and Jun variants with altered dimerization preferences, fly lines were generated in which only specifically defined dimer variants can form. Phenotypic analysis of these mutants reveals that homodimers of Fos or of Jun cannot replace the function of the heterodimeric complex. This defect is not explained by the lower stability of homodimers as compared to heterodimers, because 'pseudo-homodimers' which are as stable as native Jun-Fos heterodimers cannot substitute for their function. We conclude that Jun and Fos play complementary roles that are both required for signal transduction and gene activation during dorsal closure.
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Affiliation(s)
- Laura Ciapponi
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.
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23
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Zhang H, Levine M, Ashe HL. Brinker is a sequence-specific transcriptional repressor in the Drosophila embryo. Genes Dev 2001; 15:261-6. [PMID: 11159907 PMCID: PMC312626 DOI: 10.1101/gad.861201] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A Dpp activity gradient specifies multiple thresholds of gene expression in the dorsal ectoderm of the early embryo. Some of these thresholds depend on a putative repressor, Brinker, which is expressed in the neurogenic ectoderm in response to the maternal Dorsal gradient and Dpp signaling. Here we show that Brinker is a sequence-specific transcriptional repressor. It binds the consensus sequence, TGGCGc/tc/t, and interacts with the Groucho corepressor through a conserved sequence motif, FKPY. An optimal Brinker binding site is contained within an 800-bp enhancer from the tolloid gene, which has been identified as a genetic target of the Brinker repressor. A tolloid-lacZ transgene containing point mutations in this site exhibits an expanded pattern of expression, suggesting that Brinker directly represses tolloid transcription. We discuss other examples of transcriptional repressors constraining the activities of signaling pathways.
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Affiliation(s)
- H Zhang
- Department Molecular Cell Biology, Division of Genetics and Development, University of California, Berkeley, California 94720, USA
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24
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Dearden P, Grbic M, Falciani F, Akam M. Maternal expression and early zygotic regulation of the Hox3/zen gene in the grasshopper Schistocerca gregaria. Evol Dev 2000; 2:261-70. [PMID: 11252555 DOI: 10.1046/j.1525-142x.2000.00065.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In insects, a key step in the early patterning of the egg is to distinguish the primordium of the embryo proper from those regions that will form extra-embryonic membranes. In Drosophila, where these processes are well understood, the structure of the extra-embryonic membranes is highly derived. The distinct amnion and serosa typical of lower insects is replaced by a single, fused, and much reduced membrane, the amnioserosa, which never secretes an embryonic cuticle. We have used the Zen gene as a marker to study the formation of the extra-embryonic membranes, and other aspects of early embryonic patterning, in the grasshopper Schistocerca gregaria (African Plague Locust). Zen genes are derived from Hox genes, but in Drosophila they appear to have lost any role in patterning the A/P axis of the embryo; instead, they are involved in D/V patterning and the specification of the extra-embryonic membranes. We show that the Schistocerca zen gene is expressed during embryogenesis in three distinct phases. The first of these is during cleavage, when Sgzen is transiently expressed in all energids that reach the cell surface. The second phase of expression initiates in a ring of "necklace cells" that surround the forming embryo, and demarcate the boundary between the amnion and serosa. This leads to expression throughout the serosa. The final phase of expression is in the amnion, after this has separated from the serosa. This complex pattern implies that the role of Sgzen in Schistocerca is not limited solely to the specification of cell identity in the extra-embryonic membranes. We also report that the Schistocerca zen gene is expressed maternally, unlike its Drosophila and Tribolium counterparts. A distinct maternal transcript, and maternal Zen protein, accumulate in the developing oocyte from early post-meiotic stages. They remain uniformly distributed in the oocyte cytoplasm until late vitellogenic stages, when the protein and RNA become somewhat concentrated at the egg cortex and in the posterior polar cap of the oocyte, probably by passive exclusion from the yolk. The cytoplasmic localization of Sgzen protein in the oocyte, and at some stages during embryogenesis, implies that nuclear exclusion of this transcription factor is specifically controlled.
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Affiliation(s)
- P Dearden
- University Museum of Zoology, Department of Zoology, Cambridge, UK.
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25
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Ashe HL, Mannervik M, Levine M. Dpp signaling thresholds in the dorsal ectoderm of the Drosophila embryo. Development 2000; 127:3305-12. [PMID: 10887086 DOI: 10.1242/dev.127.15.3305] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The dorsal ectoderm of the Drosophila embryo is subdivided into different cell types by an activity gradient of two TGF(β) signaling molecules, Decapentaplegic (Dpp) and Screw (Scw). Patterning responses to this gradient depend on a secreted inhibitor, Short gastrulation (Sog) and a newly identified transcriptional repressor, Brinker (Brk), which are expressed in neurogenic regions that abut the dorsal ectoderm. Here we examine the expression of a number of Dpp target genes in transgenic embryos that contain ectopic stripes of Dpp, Sog and Brk expression. These studies suggest that the Dpp/Scw activity gradient directly specifies at least three distinct thresholds of gene expression in the dorsal ectoderm of gastrulating embryos. Brk was found to repress two target genes, tailup and pannier, that exhibit different limits of expression within the dorsal ectoderm. These results suggest that the Sog inhibitor and Brk repressor work in concert to establish sharp dorsolateral limits of gene expression. We also present evidence that the activation of Dpp/Scw target genes depends on the Drosophila homolog of the CBP histone acetyltransferase.
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Affiliation(s)
- H L Ashe
- Department of Molecular and Cell Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
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26
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Vonica A, Weng W, Gumbiner BM, Venuti JM. TCF is the nuclear effector of the beta-catenin signal that patterns the sea urchin animal-vegetal axis. Dev Biol 2000; 217:230-43. [PMID: 10625549 DOI: 10.1006/dbio.1999.9551] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mechanism of animal-vegetal (AV) axis formation in the sea urchin embryo is incompletely understood. Specification of the axis is thought to involve a combination of cell-cell signals and as yet unidentified maternal determinants. In Xenopus the Wnt pathway plays a crucial role in defining the embryonic axes. Recent experiments in sea urchins have shown that at least two components of the Wnt signaling pathway, GSK3beta and beta-catenin, are involved in embryonic AV axis patterning. These results support the notion that the developmental network that regulates axial patterning in deuterostomes is evolutionarily conserved. To further test this hypothesis, we have examined the role of beta-catenin nuclear binding partners, members of the TCF family of transcriptional regulators, in sea urchin AV axis patterning. To test the role of TCFs in mediating beta-catenin signals in sea urchin AV axis development we examined the consequences of microinjecting RNAs encoding altered forms of TCF on sea urchin development. We show that expression of a dominant negative TCF results in a classic "animalized" embryo. In contrast, microinjected RNA encoding an activated TCF produces a highly "vegetalized" embryo. We show that the transactivational activity of endogenous sea urchin TCF is potentiated by LiCl treatment, which vegetalizes embryos by inhibiting GSK3, consistent with an in vivo interaction between endogenous beta-catenin and TCF. We also provide evidence indicating that all of beta-catenin's activity in patterning the sea urchin AV axis is mediated by TCF. Using a glucocorticoid-responsive TCF, we show that TCF transcriptional activity affects specification along the AV axis between fertilization and the 60-cell stage.
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Affiliation(s)
- A Vonica
- Department of Anatomy, College of Physicians and Surgeons, New York, New York, 10032, USA
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27
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Ashburner M, Misra S, Roote J, Lewis SE, Blazej R, Davis T, Doyle C, Galle R, George R, Harris N, Hartzell G, Harvey D, Hong L, Houston K, Hoskins R, Johnson G, Martin C, Moshrefi A, Palazzolo M, Reese MG, Spradling A, Tsang G, Wan K, Whitelaw K, Celniker S. An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region. Genetics 1999; 153:179-219. [PMID: 10471707 PMCID: PMC1460734 DOI: 10.1093/genetics/153.1.179] [Citation(s) in RCA: 183] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926
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Affiliation(s)
- M Ashburner
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, England.
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28
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Ashe HL, Levine M. Local inhibition and long-range enhancement of Dpp signal transduction by Sog. Nature 1999; 398:427-31. [PMID: 10201373 DOI: 10.1038/18892] [Citation(s) in RCA: 148] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Extracellular gradients of signalling molecules can specify different thresholds of gene activity in development. A gradient of Decapentaplegic (Dpp) activity subdivides the dorsal ectoderm of the Drosophila embryo into amnioserosa and dorsal epidermis. The proteins Short gastrulation (Sog) and Tolloid (Tld) are required to shape this gradient. Sog has been proposed to form an inhibitory complex with either Dpp or the related ligand Screw, and is subsequently processed by the protease Tld. Paradoxically, Sog appears to be required for amnioserosa formation, which is specified by peak Dpp signalling activity. Here we show that the misexpression of sog using the even-skipped stripe-2 enhancer redistributes Dpp signalling in a mutant background in which dpp is expressed throughout the embryo. Dpp activity is diminished near the Sog stripe and peak Dpp signalling is detected far from this stripe. However, a tethered form of Sog suppresses local Dpp activity without augmenting Dpp activity at a distance, indicating that diffusion of Sog may be required for enhanced Dpp activity and consequent amnioserosa formation. The long-distance stimulation of Dpp activity by Sog requires Tld, whereas Sog-mediated inhibition of Dpp does not. The heterologous Dpp inhibitor Noggin inhibits Dpp signalling but fails to augment Dpp activity. These results suggest an unusual strategy for generating a gradient threshold of growth-factor activity, whereby Sog and its protease specify peak Dpp signalling far from a localized source of Sog.
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Affiliation(s)
- H L Ashe
- Department of Molecular and Cellular Biology, University of California, Berkeley 94720, USA
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29
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Zhang H, Levine M. Groucho and dCtBP mediate separate pathways of transcriptional repression in the Drosophila embryo. Proc Natl Acad Sci U S A 1999; 96:535-40. [PMID: 9892668 PMCID: PMC15171 DOI: 10.1073/pnas.96.2.535] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The precellular Drosophila embryo contains approximately 10 well characterized transcriptional repressors. At least half are short-range repressors that must bind within 100 bp of either upstream activators or the core transcription complex to inhibit (or quench) gene expression. The two long-range repressors can function over distances of 1 kilobase or more to silence transcription. Previous studies have shown that three of the five short-range repressors interact with a common corepressor protein, dCtBP. In contrast, the two long-range repressors, Hairy and Dorsal, recruit a different corepressor protein, Groucho. Hairy also was shown to interact with dCtBP, thereby raising the possibility that Groucho and dCtBP are components of a common corepressor complex. To investigate this issue, we have misexpressed wild-type and mutant forms of Hairy in transgenic embryos. Evidence is presented that Hairy-mediated repression depends on the Groucho interaction sequence (WRPW) but not the weak dCtBP motif (PLSLV) present in the native protein. Conversion of the PLSLV motif into an optimal dCtBP interaction sequence (PLDLS) disrupts the activity of an otherwise normal Hairy protein. These results suggest that dCtBP and Groucho mediate separate pathways of transcriptional repression and that the two proteins can inhibit one another when both bind the same repressor.
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Affiliation(s)
- H Zhang
- Department of Molecular and Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
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30
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Fujiwara S, Corbo JC, Levine M. The snail repressor establishes a muscle/notochord boundary in the Ciona embryo. Development 1998; 125:2511-20. [PMID: 9609834 DOI: 10.1242/dev.125.13.2511] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Previous studies have identified a minimal 434 bp enhancer from the promoter region of the Ciona Brachyury gene (Ci-Bra), which is sufficient to direct a notochord-specific pattern of gene expression. Here we present evidence that a Ciona homolog of snail (Ci-sna) encodes a repressor of the Ci-Bra enhancer in the tail muscles. DNA-binding assays identified four Ci-Sna-binding sites in the Ci-Bra enhancer, and mutations in these sites cause otherwise normal Ci-Bra/lacZ transgenes to be misexpressed in ectopic tissues, particularly the tail muscles. Selective misexpression of Ci-sna using a heterologous promoter results in the repression of Ci-Bra/lacZ transgenes in the notochord. Moreover, the conversion of the Ci-Sna repressor into an activator results in the ectopic induction of Ci-Bra/lacZ transgenes in the muscles, and also causes an intermixing of notochord and muscle cells during tail morphogenesis. These results suggest that Ci-Sna functions as a boundary repressor, which subdivides the mesoderm into separate notochord and tail muscle lineages.
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Affiliation(s)
- S Fujiwara
- Department of Molecular and Cell Biology, Division of Genetics, University of California, Berkeley, CA 94720, USA
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31
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Abstract
The Drosophila homolog of c-Jun regulates epithelial cell shape changes during the process of dorsal closure in mid-embryogenesis. Here, mutations in the DFos gene are described. In dorsal closure, DFos cooperates with DJun by regulating the expression of dpp; Dpp acts as a relay signal that triggers cell shape changes and DFos expression in neighboring cells. In addition to the joint requirement of DFos and DJun during dorsal closure, DFos functions independently of DJun during early stages of embryogenesis. These findings demonstrate common and distinct roles of DFos and DJun during embryogenesis and suggest a conserved link between AP-1 (activating protein-1) and TGF-beta (transforming growth factor-beta) signaling during epithelial cell shape changes.
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Affiliation(s)
- J R Riesgo-Escovar
- Zoologisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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32
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Huang AM, Rusch J, Levine M. An anteroposterior Dorsal gradient in the Drosophila embryo. Genes Dev 1997; 11:1963-73. [PMID: 9271119 PMCID: PMC316408 DOI: 10.1101/gad.11.15.1963] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/1997] [Accepted: 06/19/1997] [Indexed: 02/05/2023]
Abstract
Dorsoventral (DV) patterning of the Drosophila embryo is initiated by a broad Dorsal (Dl) nuclear gradient, which is regulated by a conserved signaling pathway that includes the Toll receptor and Pelle kinase. We investigate the consequences of expressing a constitutively activated form of the Toll receptor, Toll(10b), in anterior regions of the early embryo using the bicoid 3' UTR. Localized Toll(10b) products result in the formation of an ectopic, anteroposterior (AP) Dl nuclear gradient along the length of the embryo. The analysis of both authentic dorsal target genes and defined synthetic promoters suggests that the ectopic gradient is sufficient to generate the full repertory of DV patterning responses along the AP axis of the embryo. For example, mesoderm determinants are activated in the anterior third of the embryo, whereas neurogenic genes are expressed in central regions. These results raise the possibility that Toll signaling components diffuse in the plasma membrane or syncytial cytoplasm of the early embryo. This study also provides evidence that neurogenic repressors may be important for the establishment of the sharp mesoderm/neuroectoderm boundary in the early embryo.
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Affiliation(s)
- A M Huang
- Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
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33
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Hou XS, Goldstein ES, Perrimon N. Drosophila Jun relays the Jun amino-terminal kinase signal transduction pathway to the Decapentaplegic signal transduction pathway in regulating epithelial cell sheet movement. Genes Dev 1997; 11:1728-37. [PMID: 9224721 DOI: 10.1101/gad.11.13.1728] [Citation(s) in RCA: 146] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have characterized mutations in the Drosophila homolog of the mammalian proto-oncogene c-Jun gene (Djun). We demonstrate that DJUN in the embryo is a downstream target of the JNK signal transduction pathway during dorsal closure formation, and that the function of the JNK/DJUN pathway is to control the localized expression of decapentalegic (dpp), a member of the TGF-beta growth factor family. In contrast to previous observations, we find that both in the embryo and during photoreceptor cell determination, DJUN is not regulated by a pathway that involves MAPK.
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Affiliation(s)
- X S Hou
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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