1
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Denaud S, Bardou M, Papadopoulos GL, Grob S, Di Stefano M, Sabarís G, Nollmann M, Schuettengruber B, Cavalli G. A PRE loop at the dac locus acts as a topological chromatin structure that restricts and specifies enhancer-promoter communication. Nat Struct Mol Biol 2024:10.1038/s41594-024-01375-7. [PMID: 39152239 DOI: 10.1038/s41594-024-01375-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Three-dimensional (3D) genome folding has a fundamental role in the regulation of developmental genes by facilitating or constraining chromatin interactions between cis-regulatory elements (CREs). Polycomb response elements (PREs) are a specific kind of CRE involved in the memory of transcriptional states in Drosophila melanogaster. PREs act as nucleation sites for Polycomb group (PcG) proteins, which deposit the repressive histone mark H3K27me3, leading to the formation of a class of topologically associating domain (TAD) called a Polycomb domain. PREs can establish looping contacts that stabilize the gene repression of key developmental genes during development. However, the mechanism by which PRE loops fine-tune gene expression is unknown. Using clustered regularly interspaced short palindromic repeats and Cas9 genome engineering, we specifically perturbed PRE contacts or enhancer function and used complementary approaches including 4C-seq, Hi-C and Hi-M to analyze how chromatin architecture perturbation affects gene expression. Our results suggest that the PRE loop at the dac gene locus acts as a constitutive 3D chromatin scaffold during Drosophila development that forms independently of gene expression states and has a versatile function; it restricts enhancer-promoter communication and contributes to enhancer specificity.
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Affiliation(s)
- Sandrine Denaud
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France
| | - Marion Bardou
- Centre de Biologie Structurale, IUMR5048 CNRS, INSERM U1054, University of Montpellier, Montpellier, France
| | | | - Stefan Grob
- Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Marco Di Stefano
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France
| | - Gonzalo Sabarís
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France
| | - Marcelo Nollmann
- Centre de Biologie Structurale, IUMR5048 CNRS, INSERM U1054, University of Montpellier, Montpellier, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002 CNRS, University of Montpellier, Montpellier, France.
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2
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Pouliou M, Koutsi MA, Champezou L, Giannopoulou AI, Vatsellas G, Piperi C, Agelopoulos M. MYCN Amplifications and Metabolic Rewiring in Neuroblastoma. Cancers (Basel) 2023; 15:4803. [PMID: 37835497 PMCID: PMC10571721 DOI: 10.3390/cancers15194803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/20/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Cancer is a disease caused by (epi)genomic and gene expression abnormalities and characterized by metabolic phenotypes that are substantially different from the normal phenotypes of the tissues of origin. Metabolic reprogramming is one of the key features of tumors, including those established in the human nervous system. In this work, we emphasize a well-known cancerous genomic alteration: the amplification of MYCN and its downstream effects in neuroblastoma phenotype evolution. Herein, we extend our previous computational biology investigations by conducting an integrative workflow applied to published genomics datasets and comprehensively assess the impact of MYCN amplification in the upregulation of metabolism-related transcription factor (TF)-encoding genes in neuroblastoma cells. The results obtained first emphasized overexpressed TFs, and subsequently those committed in metabolic cellular processes, as validated by gene ontology analyses (GOs) and literature curation. Several genes encoding for those TFs were investigated at the mechanistic and regulatory levels by conducting further omics-based computational biology assessments applied on published ChIP-seq datasets retrieved from MYCN-amplified- and MYCN-enforced-overexpression within in vivo systems of study. Hence, we approached the mechanistic interrelationship between amplified MYCN and overexpression of metabolism-related TFs in neuroblastoma and showed that many are direct targets of MYCN in an amplification-inducible fashion. These results illuminate how MYCN executes its regulatory underpinnings on metabolic processes in neuroblastoma.
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Affiliation(s)
- Marialena Pouliou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Marianna A. Koutsi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Lydia Champezou
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Angeliki-Ioanna Giannopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527 Athens, Greece;
| | - Giannis Vatsellas
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527 Athens, Greece;
| | - Marios Agelopoulos
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou St., 11527 Athens, Greece; (M.P.); (M.A.K.); (L.C.); (G.V.)
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3
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Beaven R, Denholm B. Early patterning followed by tissue growth establishes distal identity in Drosophila Malpighian tubules. Front Cell Dev Biol 2022; 10:947376. [PMID: 36060795 PMCID: PMC9437309 DOI: 10.3389/fcell.2022.947376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/28/2022] [Indexed: 12/03/2022] Open
Abstract
Specification and elaboration of proximo-distal (P-D) axes for structures or tissues within a body occurs secondarily from that of the main axes of the body. Our understanding of the mechanism(s) that pattern P-D axes is limited to a few examples such as vertebrate and invertebrate limbs. Drosophila Malpighian/renal tubules (MpTs) are simple epithelial tubules, with a defined P-D axis. How this axis is patterned is not known, and provides an ideal context to understand patterning mechanisms of a secondary axis. Furthermore, epithelial tubules are widespread, and their patterning is not well understood. Here, we describe the mechanism that establishes distal tubule and show this is a radically different mechanism to that patterning the proximal MpT. The distal domain is patterned in two steps: distal identity is specified in a small group of cells very early in MpT development through Wingless/Wnt signalling. Subsequently, this population is expanded by proliferation to generate the distal MpT domain. This mechanism enables distal identity to be established in the tubule in a domain of cells much greater than the effective range of Wingless.
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Affiliation(s)
| | - Barry Denholm
- Deanery of Biomedical Sciences, The University of Edinburgh, Edinburgh, United Kingdom
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4
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Fujiwara T, Brotas M, Chiappe ME. Walking strides direct rapid and flexible recruitment of visual circuits for course control in Drosophila. Neuron 2022; 110:2124-2138.e8. [PMID: 35525243 PMCID: PMC9275417 DOI: 10.1016/j.neuron.2022.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/31/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022]
Abstract
Flexible mapping between activity in sensory systems and movement parameters is a hallmark of motor control. This flexibility depends on the continuous comparison of short-term postural dynamics and the longer-term goals of an animal, thereby necessitating neural mechanisms that can operate across multiple timescales. To understand how such body-brain interactions emerge across timescales to control movement, we performed whole-cell patch recordings from visual neurons involved in course control in Drosophila. We show that the activity of leg mechanosensory cells, propagating via specific ascending neurons, is critical for stride-by-stride steering adjustments driven by the visual circuit, and, at longer timescales, it provides information about the moving body's state to flexibly recruit the visual circuit for course control. Thus, our findings demonstrate the presence of an elegant stride-based mechanism operating at multiple timescales for context-dependent course control. We propose that this mechanism functions as a general basis for the adaptive control of locomotion.
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Affiliation(s)
- Terufumi Fujiwara
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Margarida Brotas
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - M Eugenia Chiappe
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal.
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5
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Pechmann M, Prpic NM. The T-box gene optomotor-blind organizes proximodistal leg patterning in the beetle Tribolium castaneum by repressing dorsal Dpp pathway activity. Dev Biol 2021; 482:124-134. [PMID: 34942194 DOI: 10.1016/j.ydbio.2021.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/26/2021] [Accepted: 12/16/2021] [Indexed: 11/03/2022]
Abstract
Leg axis formation in Drosophila is organized by Wingless (Wg) and Decapentaplegic (Dpp) that control a number of downstream factors to pattern the dorsoventral (DV) and proximodistal (PD) axis. The T-box genes are important downstream factors mainly involved in dorsoventral leg axis formation. The ventral side is specified by H15 and midline, whereas optomotor-blind (omb) and Dorsocross (Doc1) are factors to specify dorsal cell fates. We show here that omb also organizes PD leg axis patterning in the beetle Tribolium castaneum. In the legs, Tc-omb is expressed along the dorsal side and represses ventral factors like wg and H15. Intriguingly, removing Tc-omb function leads to the activation of the Dpp pathway along the dorsal side of the legs, thus mimicking normal dpp expression in Drosophila. Dpp activity along the dorsal side leads to altered expression of proximal-distal patterning genes such as Distal-less (Dll) and dachshund (dac). Our results indicate a cell-autonomous activation of Dll and repression of dac by dpp. These findings are compatible with the cross-regulatory "cascade model" of proximal-distal leg imaginal disc patterning of Drosophila.
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Affiliation(s)
- Matthias Pechmann
- Universität zu Köln, Biozentrum Köln, Institut für Zoologie, Zülpicher Straße 47b, 50674, Köln, Germany.
| | - Nikola-Michael Prpic
- Justus-Liebig-Universität Gießen, Institut für Allgemeine Zoologie und Entwicklungsbiologie, AG Zoologie mit dem Schwerpunkt Molekulare Entwicklungsbiologie, Heinrich-Buff-Ring 38, 35392, Gießen, Germany.
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6
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Ruiz-Losada M, Pérez-Reyes C, Estella C. Role of the Forkhead Transcription Factors Fd4 and Fd5 During Drosophila Leg Development. Front Cell Dev Biol 2021; 9:723927. [PMID: 34409041 PMCID: PMC8365472 DOI: 10.3389/fcell.2021.723927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Appendage development requires the coordinated function of signaling pathways and transcription factors to pattern the leg along the three main axes: the antero-posterior (AP), proximo-distal (PD), and dorso-ventral (DV). The Drosophila leg DV axis is organized by two morphogens, Decapentaplegic (Dpp), and Wingless (Wg), which direct dorsal and ventral cell fates, respectively. However, how these signals regulate the differential expression of its target genes is mostly unknown. In this work, we found that two members of the Drosophila forkhead family of transcription factors, Fd4 and Fd5 (also known as fd96Ca and fd96Cb), are identically expressed in the ventro-lateral domain of the leg imaginal disc in response to Dpp signaling. Here, we analyze the expression regulation and function of these genes during leg development. We have generated specific mutant alleles for each gene and a double fd4/fd5 mutant chromosome to study their function during development. We highlight the redundant role of the fd4/fd5 genes during the formation of the sex comb, a male specific structure that appears in the ventro-lateral domain of the prothoracic leg.
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Affiliation(s)
- Mireya Ruiz-Losada
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Madrid, Spain
| | - Cristian Pérez-Reyes
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Estella
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Madrid, Spain
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7
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Zhang R, Zhang Z, Huang Y, Qian A, Tan A. A single ortholog of teashirt and tiptop regulates larval pigmentation and adult appendage patterning in Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 121:103369. [PMID: 32243904 DOI: 10.1016/j.ibmb.2020.103369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/07/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Two paralogous genes, teashirt (tsh) and tiptop (tio), encode zinc-finger transcription factors and play important roles in insect growth and development. In the fruit fly, Drosophila melanogaster, tsh promotes trunk segmental identities and contributes to the patterning of other tissues during the embryonic stage. During the adult stage, tsh contributes to the specification and patterning of appendages, including the leg, wing and eye. While tio acts redundantly with tsh, flies lacking tio function are viable without deleterious phenotypes. This gene pair is present in the genomes of all Drosophila species but only as a single homologue in several other insect species. In Oncopeltus fasciatus and Tribolium castaneum, tsh/tio has been functionally characterized as specifying the identity of the leg during the adult stage. However, in lepidopteran insects which include large numbers of pests in agriculture and forestry, as well as the major silk producer silkworm Bombyx mori, the biological functions of tsh/tio are still poorly understood. In the current study, we performed functional analysis of tsh/tio by using both CRISPR/Cas9-mediated mutagenesis and transposon-mediated ectopic expression in B. mori. The results show that loss of tsh/tio function affected pigmentation during the larval stage and appendage pattering during the adult stage. RNA-seq analysis and subsequent q-RT-PCR analysis revealed that depletion of tsh/tio significantly elevated the expression of the kynurenine 3-monooxygenase gene, as well as melanin synthase-related genes during the larval stage. Furthermore, ubiquitous ectopic expression of tsh/tio induces developmental retardation and eventually larval lethality. These data reveal evolutionarily conserved functions of tsh/tio in controlling adult appendage patterning, as well as the novel function of regulating larval pigmentation in B. mori, providing novel insights into how tsh/tio regulates insect growth and development.
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Affiliation(s)
- Ru Zhang
- Faculty of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China; Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhongjie Zhang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Airong Qian
- Faculty of Life Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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8
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Role of Notch Signaling in Leg Development in Drosophila melanogaster. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1218:103-127. [PMID: 32060874 DOI: 10.1007/978-3-030-34436-8_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Notch pathway plays diverse and fundamental roles during animal development. One of the most relevant, which arises directly from its unique mode of activation, is the specification of cell fates and tissue boundaries. The development of the leg of Drosophila melanogaster is a fine example of this Notch function, as it is required to specify the fate of the cells that will eventually form the leg joints, the flexible structures that separate the different segments of the adult leg. Notch activity is accurately activated and maintained at the distal end of each segment in response to the proximo-distal patterning gene network of the developing leg. Region-specific downstream targets of Notch in turn regulate the formation of the different types of joints. We discuss recent findings that shed light on the molecular and cellular mechanisms that are ultimately governed by Notch to achieve epithelial fold and joint morphogenesis. Finally, we briefly summarize the role that Notch plays in inducing the nonautonomous growth of the leg. Overall, this book chapter aims to highlight leg development as a useful model to study how patterning information is translated into specific cell behaviors that shape the final form of an adult organ.
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9
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Arbouzova NI, Fulford AD, Zhang H, McNeill H. Fat regulates expression of four-jointed reporters in vivo through a 20 bp element independently of the Hippo pathway. Dev Biol 2019; 450:23-33. [DOI: 10.1016/j.ydbio.2019.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/15/2023]
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10
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Sugime Y, Oguchi K, Gotoh H, Hayashi Y, Matsunami M, Shigenobu S, Koshikawa S, Miura T. Termite soldier mandibles are elongated by dachshund under hormonal and Hox gene controls. Development 2019; 146:dev.171942. [PMID: 30833380 DOI: 10.1242/dev.171942] [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: 09/26/2018] [Accepted: 02/12/2019] [Indexed: 11/20/2022]
Abstract
In social insects, interactions among colony members trigger caste differentiation with morphological modifications. In termite soldier differentiation, the mandible size considerably increases through two moltings (via the presoldier stage) under the control of juvenile hormone (JH). Regulatory genes are predicted to provide patterning information that induces the mandible-specific cell proliferation. To identify factors responsible for the mandibular enlargement, expression analyses of 18 candidate genes were carried out in the termite Hodotermopsis sjostedti Among those, dachshund (dac), which identifies the intermediate domain along the proximodistal appendage axis, showed mandible-specific upregulation prior to the molt into presoldiers, which can explain the pattern of cell proliferation for the mandibular elongation. Knockdown of dac by RNAi reduced the mandibular length and distorted its morphology. Furthermore, the epistatic relationships among Methoprene tolerant, Insulin receptor, Deformed (Dfd) and dac were revealed by combined RNAi and qRT-PCR analyses, suggesting that dac is regulated by Dfd, downstream of the JH and insulin signaling pathways. Thus, caste-specific morphogenesis is controlled by interactions between the factors that provide spatial information and physiological status.
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Affiliation(s)
- Yasuhiro Sugime
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Kohei Oguchi
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.,Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, Miura, Kanagawa, 238-0225, Japan
| | - Hiroki Gotoh
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.,Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoshinobu Hayashi
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.,Department of Biology, Keio University, Yokohama, Kanagawa, 223-8521, Japan
| | - Masatoshi Matsunami
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.,Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 903-0215, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Shigeyuki Koshikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| | - Toru Miura
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan .,Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, Miura, Kanagawa, 238-0225, Japan
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11
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Newcomb S, Voutev R, Jory A, Delker RK, Slattery M, Mann RS. cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg. PLoS Genet 2018; 14:e1007568. [PMID: 30142157 PMCID: PMC6147608 DOI: 10.1371/journal.pgen.1007568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/20/2018] [Accepted: 07/16/2018] [Indexed: 12/19/2022] Open
Abstract
We characterized the establishment of an Epidermal Growth Factor Receptor (EGFR) organizing center (EOC) during leg development in Drosophila melanogaster. Initial EGFR activation occurs in the center of leg discs by expression of the EGFR ligand Vn and the EGFR ligand-processing protease Rho, each through single enhancers, vnE and rhoE, that integrate inputs from Wg, Dpp, Dll and Sp1. Deletion of vnE and rhoE eliminates vn and rho expression in the center of the leg imaginal discs, respectively. Animals with deletions of both vnE and rhoE (but not individually) show distal but not medial leg truncations, suggesting that the distal source of EGFR ligands acts at short-range to only specify distal-most fates, and that multiple additional ‘ring’ enhancers are responsible for medial fates. Further, based on the cis-regulatory logic of vnE and rhoE we identified many additional leg enhancers, suggesting that this logic is broadly used by many genes during Drosophila limb development. The EGFR signaling pathway plays a major role in innumerable developmental processes in all animals and its deregulation leads to different types of cancer, as well as many other developmental diseases in humans. Here we explored the integration of inputs from the Wnt- and TGF-beta signaling pathways and the leg-specifying transcription factors Distal-less and Sp1 at enhancer elements of EGFR ligands. These enhancers trigger a specific EGFR-dependent developmental output in the fly leg that is limited to specifying distal-most fates. Our findings suggest that activation of the EGFR pathway during fly leg development occurs through the activation of multiple EGFR ligand enhancers that are active at different positions along the proximo-distal axis. Similar enhancer elements are likely to control EGFR activation in humans as well. Such DNA elements might be ‘hot spots’ that cause formation of EGFR-dependent tumors if mutations in them occur. Thus, understanding the molecular characteristics of such DNA elements could facilitate the detection and treatment of cancer.
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Affiliation(s)
- Susan Newcomb
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Roumen Voutev
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY, United States of America
- * E-mail: (RV); (RSM)
| | - Aurelie Jory
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Rebecca K. Delker
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Matthew Slattery
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY, United States of America
| | - Richard S. Mann
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY, United States of America
- * E-mail: (RV); (RSM)
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12
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Ruiz-Losada M, Blom-Dahl D, Córdoba S, Estella C. Specification and Patterning of Drosophila Appendages. J Dev Biol 2018; 6:jdb6030017. [PMID: 30011921 PMCID: PMC6162442 DOI: 10.3390/jdb6030017] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023] Open
Abstract
Appendages are external projections of the body that serve the animal for locomotion, feeding, or environment exploration. The appendages of the fruit fly Drosophilamelanogaster are derived from the imaginal discs, epithelial sac-like structures specified in the embryo that grow and pattern during larva development. In the last decades, genetic and developmental studies in the fruit fly have provided extensive knowledge regarding the mechanisms that direct the formation of the appendages. Importantly, many of the signaling pathways and patterning genes identified and characterized in Drosophila have similar functions during vertebrate appendage development. In this review, we will summarize the genetic and molecular mechanisms that lead to the specification of appendage primordia in the embryo and their posterior patterning during imaginal disc development. The identification of the regulatory logic underlying appendage specification in Drosophila suggests that the evolutionary origin of the insect wing is, in part, related to the development of ventral appendages.
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Affiliation(s)
- Mireya Ruiz-Losada
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM/CSIC), Nicolás Cabrera 1, 28049 Madrid, Spain.
| | - David Blom-Dahl
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM/CSIC), Nicolás Cabrera 1, 28049 Madrid, Spain.
| | - Sergio Córdoba
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM/CSIC), Nicolás Cabrera 1, 28049 Madrid, Spain.
| | - Carlos Estella
- Departamento de Biología Molecular and Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (UAM/CSIC), Nicolás Cabrera 1, 28049 Madrid, Spain.
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13
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Zhou CY, Zha XF, Liu HW, Xia QY. Zinc finger protein rotund deficiency affects development of the thoracic leg in Bombyx mori. INSECT SCIENCE 2017; 24:385-396. [PMID: 26970216 DOI: 10.1111/1744-7917.12334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 12/21/2015] [Accepted: 01/04/2016] [Indexed: 06/05/2023]
Abstract
The insect limb develops from the imaginal disc or larval leg during metamorphosis. The molecular mechanisms involved in the development from the larval to the adult leg are poorly understood. Herein, we cloned the full length of a zinc finger gene rotund from Bombyx mori (Bmrn), which contained a 1419 bp open reading frame, and encoded a 473 amino acid protein. Reverse transcription polymerase chain reaction and Western blot analyses demonstrated that Bmrn was expressed at higher levels in the epidermis than in other tissues tested, and it showed a very high expression level during metamorphosis. Knock-down of Bmrn produced defects in the tarsus and pretarsus, including the fusion and reduction of tarsomeres, and the developmental arrest of pretarsus. Our data showed that Bmrn is involved in the formation of the tarsus and pretarsus, whereas its homologous gene in Drosophila has been shown to affect three tarsal segments (t2-t4), suggesting that the remodeling of the leg has involved changes in the patterning of gene regulation during evolution.
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Affiliation(s)
- Chun-Yan Zhou
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Xing-Fu Zha
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Hua-Wei Liu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
| | - Qing-You Xia
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, China
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A faithful internal representation of walking movements in the Drosophila visual system. Nat Neurosci 2016; 20:72-81. [PMID: 27798632 DOI: 10.1038/nn.4435] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022]
Abstract
The integration of sensorimotor signals to internally estimate self-movement is critical for spatial perception and motor control. However, which neural circuits accurately track body motion and how these circuits control movement remain unknown. We found that a population of Drosophila neurons that were sensitive to visual flow patterns typically generated during locomotion, the horizontal system (HS) cells, encoded unambiguous quantitative information about the fly's walking behavior independently of vision. Angular and translational velocity signals were integrated with a behavioral-state signal and generated direction-selective and speed-sensitive graded changes in the membrane potential of these non-spiking cells. The nonvisual direction selectivity of HS cells cooperated with their visual selectivity only when the visual input matched that expected from the fly's movements, thereby revealing a circuit for internally monitoring voluntary walking. Furthermore, given that HS cells promoted leg-based turning, the activity of these cells could be used to control forward walking.
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Li Q, Barish S, Okuwa S, Maciejewski A, Brandt AT, Reinhold D, Jones CD, Volkan PC. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity. PLoS Genet 2016; 12:e1005780. [PMID: 26765103 PMCID: PMC4713227 DOI: 10.1371/journal.pgen.1005780] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity.
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Affiliation(s)
- Qingyun Li
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Scott Barish
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Sumie Okuwa
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Abigail Maciejewski
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Alicia T. Brandt
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dominik Reinhold
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Mathematics and Computer Science, Clark University, Worcester, Massachusetts, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Pelin Cayirlioglu Volkan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Duke Institute for Brain Sciences, Duke University, Durham, North Carolina, United States of America
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Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules. PLoS Genet 2015; 11:e1005376. [PMID: 26468882 PMCID: PMC4607503 DOI: 10.1371/journal.pgen.1005376] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/19/2015] [Indexed: 12/28/2022] Open
Abstract
The subdivision of cell populations in compartments is a key event during animal development. In Drosophila, the gene apterous (ap) divides the wing imaginal disc in dorsal vs ventral cell lineages and is required for wing formation. ap function as a dorsal selector gene has been extensively studied. However, the regulation of its expression during wing development is poorly understood. In this study, we analyzed ap transcriptional regulation at the endogenous locus and identified three cis-regulatory modules (CRMs) essential for wing development. Only when the three CRMs are combined, robust ap expression is obtained. In addition, we genetically and molecularly analyzed the trans-factors that regulate these CRMs. Our results propose a three-step mechanism for the cell lineage compartment expression of ap that includes initial activation, positive autoregulation and Trithorax-mediated maintenance through separable CRMs. The separation of cell populations into distinct functional units is essential for both vertebrate and invertebrate animal development. A classical paradigm for this phenomenon is the establishment of developmental compartments during Drosophila wing development. These compartments depend on the restricted expression of two selector genes, engrailed in the posterior compartment and apterous (ap) in the dorsal compartment. Yet, despite the central role these genes and their restricted expression patterns play in Drosophila development, we still do not understand how these patterns are established or maintained. Here, by dissecting the regulatory sequences required for ap expression, we solve this problem for this critical selector gene. We used a combination of experimental approaches to identify and functionally characterize the cis-regulatory modules (CRMs) that regulate ap expression during Drosophila wing development. For these analyses we implement a novel technique allowing us to study the function of these CRMs in vivo, at the native ap locus. We found three ap CRMs crucial for wing development: the Early (apE) and the D/V (apDV) enhancers and the ap PRE (apP). Only when all three regulatory elements are combined is a uniform and complete ap expression domain generated. In summary, our results indicate that ap is regulated in time and space by a three-step mechanism that generates a lineage compartment by integrating input from separate CRMs for the initiation, refinement and maintenance of its expression.
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Santos CG, Hartfelder K. Insights into the dynamics of hind leg development in honey bee (Apis mellifera L.) queen and worker larvae - A morphology/differential gene expression analysis. Genet Mol Biol 2015; 38:263-77. [PMID: 26500430 PMCID: PMC4612609 DOI: 10.1590/s1415-475738320140393] [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] [Received: 12/30/2014] [Accepted: 03/25/2015] [Indexed: 11/22/2022] Open
Abstract
Phenotypic plasticity is a hallmark of the caste systems of social insects, expressed in their life history and morphological traits. These are best studied in bees. In their co-evolution with angiosperm plants, the females of corbiculate bees have acquired a specialized structure on their hind legs for collecting pollen. In the highly eusocial bees (Apini and Meliponini), this structure is however only present in workers and absent in queens. By means of histological sections and cell proliferation analysis we followed the developmental dynamics of the hind legs of queens and workers in the fourth and fifth larval instars. In parallel, we generated subtractive cDNA libraries for hind leg discs of queen and worker larvae by means of a Representational Difference Analysis (RDA). From the total of 135 unique sequences we selected 19 for RT-qPCR analysis, where six of these were confirmed as differing significantly in their expression between the two castes in the larval spinning stage. The development of complex structures such as the bees' hind legs, requires diverse patterning mechanisms and signaling modules, as indicated by the set of differentially expressed genes related with cell adhesion and signaling pathways.
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Affiliation(s)
- Carolina Gonçalves Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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Ishimaru Y, Nakamura T, Bando T, Matsuoka Y, Ohuchi H, Noji S, Mito T. Involvement of dachshund and Distal-less in distal pattern formation of the cricket leg during regeneration. Sci Rep 2015; 5:8387. [PMID: 25669615 PMCID: PMC4323655 DOI: 10.1038/srep08387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/19/2015] [Indexed: 12/02/2022] Open
Abstract
Cricket nymphs have the remarkable ability to regenerate a functional leg following amputation, indicating that the regenerating blastemal cells contain information for leg morphology. However, the molecular mechanisms that underlie regeneration of leg patterns remain poorly understood. Here, we analyzed phenotypes of the tibia and tarsus (three tarsomeres) obtained by knockdown with regeneration-dependent RNA interference (rdRNAi) against Gryllus dachshund (Gb'dac) and Distal-less (Gb'Dll). We found that depletion of Gb'Dll mRNA results in loss of the tarsal segments, while rdRNAi against Gb'dac shortens the tibia at the two most distal tarsomeres. These results indicate that Gb'Dll expression is indispensable for formation of the tarsus, while Gb'dac expression is necessary for elongation of the tibia and formation of the most proximal tarsomere. These findings demonstrate that mutual transcriptional regulation between the two is indispensable for formation of the tarsomeres, whereas Gb'dac is involved in determination of tibial size through interaction with Gb'ds/Gb'ft.
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Affiliation(s)
- Yoshiyasu Ishimaru
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
| | - Taro Nakamura
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
| | - Tetsuya Bando
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama City, Okayama, 700-8530, Japan
| | - Yuji Matsuoka
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
| | - Hideyo Ohuchi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama City, Okayama, 700-8530, Japan
| | - Sumihare Noji
- Center for Collaboration among Agriculture, Industry and Commerce, The University of Tokushima, 2-24 Shinkura-cho, Tokushima City, Tokushima 770-8501, Japan
| | - Taro Mito
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
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19
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Hall ET, Verheyen EM. Ras-activated Dsor1 promotes Wnt signaling in Drosophila development. J Cell Sci 2015; 128:4499-511. [DOI: 10.1242/jcs.175240] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/29/2015] [Indexed: 12/20/2022] Open
Abstract
Wnt/Wingless (Wg) and Ras/MAPK signaling both play fundamental roles in growth, cell-fate determination, and when dysregulated, can lead to tumorigenesis. Several conflicting modes of interaction between Ras/MAPK and Wnt signaling have been identified in specific cellular contexts, causing synergistic or antagonistic effects on target genes. We find novel evidence that the dual specificity kinase MEK, Downstream of Raf1 (Dsor1), is required for Wnt signaling. Knockdown of Dsor1 results in loss of Wg target gene expression, as well as reductions in stabilized Armadillo (Arm; Drosophila β-catenin). We have identified a close physical interaction between Dsor1 and Arm, and find that catalytically inactive Dsor1 causes a reduction inactive Arm. These results suggest that Dsor1 normally counteracts the Axin-mediated destruction of Arm. We find that Ras-Dsor1 activity is independent of upstream activation by EGFR, rather it appears to be activated by the insulin-like growth factor receptor to promote Wg signaling. Together our results suggest novel crosstalk between Insulin and Wg signaling via Dsor1.
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Affiliation(s)
- Eric T. Hall
- Department of Molecular Biology and Biochemistry, Simon Fraser University, British Columbia, Canada
| | - Esther M. Verheyen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, British Columbia, Canada
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20
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Crocker J, Abe N, Rinaldi L, McGregor AP, Frankel N, Wang S, Alsawadi A, Valenti P, Plaza S, Payre F, Mann RS, Stern DL. Low affinity binding site clusters confer hox specificity and regulatory robustness. Cell 2014; 160:191-203. [PMID: 25557079 DOI: 10.1016/j.cell.2014.11.041] [Citation(s) in RCA: 245] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 09/11/2014] [Accepted: 11/13/2014] [Indexed: 11/26/2022]
Abstract
In animals, Hox transcription factors define regional identity in distinct anatomical domains. How Hox genes encode this specificity is a paradox, because different Hox proteins bind with high affinity in vitro to similar DNA sequences. Here, we demonstrate that the Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments. Although most individual Ubx binding sites are not evolutionarily conserved, the overall enhancer architecture-clusters of low affinity binding sites-is maintained and required for enhancer function. Natural selection therefore works at the level of the enhancer, requiring a particular density of low affinity Ubx sites to confer both specific and robust expression.
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Affiliation(s)
- Justin Crocker
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Namiko Abe
- Columbia University Medical Center, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA
| | - Lucrezia Rinaldi
- Columbia University Medical Center, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, UK
| | - Nicolás Frankel
- Departamento de Ecología, Genética y Evolución, IEGEBA-CONICET, Facultad, de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad, Universitaria, Pabellón 2, 1428 Buenos Aires, Argentina
| | - Shu Wang
- New Jersey Neuroscience Institute, 65 James Street, Edison, NJ 08820, USA
| | - Ahmad Alsawadi
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - Philippe Valenti
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - Serge Plaza
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - François Payre
- Centre de Biologie du Développement, Université de Toulouse, UPS, 31062 Cedex 9, France; CNRS, UMR5547, Centre de Biologie du Développement, Toulouse, 31062 Cedex 9, France
| | - Richard S Mann
- Columbia University Medical Center, 701 West 168(th) Street, HHSC 1104, New York, NY 10032, USA.
| | - David L Stern
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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Smith FW, Angelini DR, Gaudio MS, Jockusch EL. Metamorphic labral axis patterning in the beetle Tribolium castaneum requires multiple upstream, but few downstream, genes in the appendage patterning network. Evol Dev 2014; 16:78-91. [PMID: 24617987 DOI: 10.1111/ede.12066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The arthropod labrum is an anterior appendage-like structure that forms the dorsal side of the preoral cavity. Conflicting interpretations of fossil, nervous system, and developmental data have led to a proliferation of scenarios for labral evolution. The best supported hypothesis is that the labrum is a novel structure that shares development with appendages as a result of co-option. Here, we use RNA interference in the red flour beetle Tribolium castaneum to compare metamorphic patterning of the labrum to previously published data on ventral appendage patterning. As expected under the co-option hypothesis, depletion of several genes resulted in similar defects in the labrum and ventral appendages. These include proximal deletions and proximal-to-distal transformations resulting from depletion of the leg gap genes homothorax and extradenticle, large-scale deletions resulting from depletion of the leg gap gene Distal-less, and smaller distal deletions resulting from knockdown of the EGF ligand Keren. However, depletion of dachshund and many of the genes that function downstream of the leg gap genes in the ventral appendages had either subtle or no effects on labral axis patterning. This pattern of partial similarity suggests that upstream genes act through different downstream targets in the labrum. We also discovered that many appendage axis patterning genes have roles in patterning the epipharyngeal sensillum array, suggesting that they have become integrated into a novel regulatory network. These genes include Notch, Delta, and decapentaplegic, and the transcription factors abrupt, bric à brac, homothorax, extradenticle and the paralogs apterous a and apterous b.
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Affiliation(s)
- Frank W Smith
- Department of Ecology & Evolutionary Biology, University of Connecticut, 75 N. Eagleville Rd., U-3043, Storrs, CT, 06269-3043, USA
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The bHLH-PAS transcription factor dysfusion regulates tarsal joint formation in response to Notch activity during drosophila leg development. PLoS Genet 2014; 10:e1004621. [PMID: 25329825 PMCID: PMC4199481 DOI: 10.1371/journal.pgen.1004621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/19/2014] [Indexed: 01/22/2023] Open
Abstract
A characteristic of all arthropods is the presence of flexible structures called joints that connect all leg segments. Drosophila legs include two types of joints: the proximal or "true" joints that are motile due to the presence of muscle attachment and the distal joints that lack musculature. These joints are not only morphologically, functionally and evolutionarily different, but also the morphogenetic program that forms them is distinct. Development of both proximal and distal joints requires Notch activity; however, it is still unknown how this pathway can control the development of such homologous although distinct structures. Here we show that the bHLH-PAS transcription factor encoded by the gene dysfusion (dys), is expressed and absolutely required for tarsal joint development while it is dispensable for proximal joints. In the presumptive tarsal joints, Dys regulates the expression of the pro-apoptotic genes reaper and head involution defective and the expression of the RhoGTPases modulators, RhoGEf2 and RhoGap71E, thus directing key morphogenetic events required for tarsal joint development. When ectopically expressed, dys is able to induce some aspects of the morphogenetic program necessary for distal joint development such as fold formation and programmed cell death. This novel Dys function depends on its obligated partner Tango to activate the transcription of target genes. We also identified a dedicated dys cis-regulatory module that regulates dys expression in the tarsal presumptive leg joints through direct Su(H) binding. All these data place dys as a key player downstream of Notch, directing distal versus proximal joint morphogenesis.
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23
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Atallah J, Vurens G, Mavong S, Mutti A, Hoang D, Kopp A. Sex-specific repression of dachshund is required for Drosophila sex comb development. Dev Biol 2014; 386:440-7. [DOI: 10.1016/j.ydbio.2013.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 12/07/2013] [Accepted: 12/11/2013] [Indexed: 02/06/2023]
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24
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Lin X, Yao Y, Jin M, Li Q. Characterization of the Distal-less gene homologue, NlDll, in the brown planthopper, Nilaparvata lugens (Stål). Gene 2014; 535:112-8. [DOI: 10.1016/j.gene.2013.11.056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 10/25/2022]
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25
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Alexandre C, Baena-Lopez A, Vincent JP. Patterning and growth control by membrane-tethered Wingless. Nature 2014; 505:180-5. [PMID: 24390349 PMCID: PMC7611559 DOI: 10.1038/nature12879] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/12/2013] [Indexed: 01/20/2023]
Abstract
Wnts are evolutionarily conserved secreted signalling proteins that, in various developmental contexts, spread from their site of synthesis to form a gradient and activate target-gene expression at a distance. However, the requirement for Wnts to spread has never been directly tested. Here we used genome engineering to replace the endogenous wingless gene, which encodes the main Drosophila Wnt, with one that expresses a membrane-tethered form of the protein. Surprisingly, the resulting flies were viable and produced normally patterned appendages of nearly the right size, albeit with a delay. We show that, in the prospective wing, prolonged wingless transcription followed by memory of earlier signalling allows persistent expression of relevant target genes. We suggest therefore that the spread of Wingless is dispensable for patterning and growth even though it probably contributes to increasing cell proliferation.
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Affiliation(s)
- Cyrille Alexandre
- 1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2]
| | - Alberto Baena-Lopez
- 1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2]
| | - Jean-Paul Vincent
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Drosophila distal-less and Rotund bind a single enhancer ensuring reliable and robust bric-a-brac2 expression in distinct limb morphogenetic fields. PLoS Genet 2013; 9:e1003581. [PMID: 23825964 PMCID: PMC3694829 DOI: 10.1371/journal.pgen.1003581] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
Most identified Drosophila appendage-patterning genes encode DNA-binding proteins, whose cross-regulatory interactions remain to be better characterized at the molecular level, notably by studying their direct binding to tissue-specific transcriptional enhancers. A fine-tuned spatio-temporal expression of bric-a-brac2 (bab2) along concentric rings is essential for proper proximo-distal (P-D) differentiation of legs and antennae. However, within the genetic interaction landscape governing limb development, no transcription factor directly controlling bab2 expression has been identified to date. Using site-targeted GFP reporter assay and BAC recombineering, we show here that restricted bab2 expression in leg and antennal imaginal discs relies on a single 567-bp-long cis-regulatory module (CRM), termed LAE (for leg and antennal enhancer). We show that this CRM (i) is necessary and sufficient to ensure normal bab2 activity in developing leg and antenna, and (ii) is structurally and functionally conserved among Drosophilidae. Through deletion and site-directed mutagenesis approaches, we identified within the LAE essential sequence motifs required in both leg and antennal tissues. Using genetic and biochemical tests, we establish that in the LAE (i) a key TAAT-rich activator motif interacts with the homeodomain P-D protein Distal-less (Dll) and (ii) a single T-rich activator motif binds the C2H2 zinc-finger P-D protein Rotund (Rn), leading to bab2 up-regulation respectively in all or specifically in the proximal-most ring(s), both in leg and antenna. Joint ectopic expression of Dll and Rn is sufficient to cell-autonomously activate endogenous bab2 and LAE-driven reporter expression in wing and haltere cells. Our findings indicate that accuracy, reliability and robustness of developmental gene expression do not necessarily require cis-regulatory information redundancy. In insects, leg and antenna are homologous limbs, though derive from a single ancestral appendage. In Drosophila, leg and antennal development along the proximo-distal (P-D) axis relies on relatively-well known genetic cascades, in which most appendage-patterning genes encode transcription factors (TF). However, their cross-regulatory interactions remain to be better characterized at the molecular level. A fine-tuned expression of the bric-a-brac2 (bab2) gene is essential for normal leg and antennal segmentation. However, within the genetic cascades governing P-D limb development, no TF directly controlling bab2 expression has been identified to date. We show here that restricted bab2 expression in developing leg and antenna is governed by a single enhancer, termed LAE, which is necessary and sufficient in-vivo to ensure bab2 functions there. We show that leg and antennal cis-regulatory elements are closely associated and that essential LAE sites interact with Distal-less (Dll) and Rotund (Rn) TFs, leading to bab2 activation in all or specifically in the proximal-most expressing cells, respectively. Finally, joint ectopic expression of Dll and Rn is sufficient to instruct wing and haltere cells to up-regulate bab2. Taken together, our work indicates that a single enhancer is necessary and sufficient to reliably govern bab2 expression in distinct morphogenetic fields.
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Grubbs N, Leach M, Su X, Petrisko T, Rosario JB, Mahaffey JW. New components of Drosophila leg development identified through genome wide association studies. PLoS One 2013; 8:e60261. [PMID: 23560084 PMCID: PMC3613359 DOI: 10.1371/journal.pone.0060261] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/24/2013] [Indexed: 11/29/2022] Open
Abstract
The adult Drosophila melanogaster body develops from imaginal discs, groups of cells set-aside during embryogenesis and expanded in number during larval stages. Specification and development of Drosophila imaginal discs have been studied for many years as models of morphogenesis. These studies are often based on mutations with large developmental effects, mutations that are often lethal in embryos when homozygous. Such forward genetic screens can be limited by factors such as early lethality and genetic redundancy. To identify additional genes and genetic pathways involved in leg imaginal disc development, we employed a Genome Wide Association Study utilizing the natural genetic variation in leg proportionality found in the Drosophila Genetic Reference Panel fly lines. In addition to identifying genes already known to be involved in leg development, we identified several genes involved in pathways that had not previously been linked with leg development. Several of the genes appear to be involved in signaling activities, while others have no known roles at this time. Many of these uncharacterized genes are conserved in mammals, so we can now begin to place these genes into developmental contexts. Interestingly, we identified five genes which, when their function is reduced by RNAi, cause an antenna-to-leg transformation. Our results demonstrate the utility of this approach, integrating the tools of quantitative and molecular genetics to study developmental processes, and provide new insights into the pathways and networks involved in Drosophila leg development.
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Affiliation(s)
- Nathaniel Grubbs
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Megan Leach
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Xin Su
- Transgenics Department, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | | | - Juan B. Rosario
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
| | - James W. Mahaffey
- Department of Genetics, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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Devi TR, Amruthavalli C, Shyamala B. Evolution of sex comb from the primitive bristle pattern indrosophilais associated with modification in the developmental regulatory protein dachshund. Genesis 2013. [DOI: 10.1002/dvg.22361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Ing T, Tseng A, Sustar A, Schubiger G. Sp1 modifies leg-to-wing transdetermination in Drosophila. Dev Biol 2013; 373:290-9. [PMID: 23165292 DOI: 10.1016/j.ydbio.2012.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 10/20/2012] [Accepted: 11/09/2012] [Indexed: 10/27/2022]
Abstract
During Drosophila development, the transcription factor Sp1 is necessary for proper leg growth and also to repress wing development. Here we test the role of Sp1 during imaginal disc regeneration. Ubiquitous expression of wg induces a regeneration blastema in the dorsal aspect of the leg disc. Within this outgrowth, the wing selector gene vg is activated in some cells, changing their fate to wing identity in a process known as transdetermination. In this report we demonstrate that reducing the gene copy number of Sp1 significantly increases both the frequency and the area of transdetermination in regenerating leg discs. By examining the expression of known Sp1 target genes, we also show that the proximo-distal patterning gene dachshund is downregulated dorsally, leading to a break in its normal ring-shaped expression pattern. We further report that transdetermination, as evidenced by Vg expression, is only observed when there is a broken ring of Dachshund expression. Combined, these studies establish a role for Sp1 in leg-to-wing transdetermination.
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Affiliation(s)
- Thomas Ing
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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Mendes CS, Bartos I, Akay T, Márka S, Mann RS. Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster. eLife 2013. [PMID: 23326642 DOI: 10.7554/elife.00231.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Coordinated walking in vertebrates and multi-legged invertebrates [corrected] such as Drosophila melanogaster requires a complex neural network coupled to sensory feedback. An understanding of this network will benefit from systems such as Drosophila that have the ability to genetically manipulate neural activities. However, the fly's small size makes it challenging to analyze walking in this system. In order to overcome this limitation, we developed an optical method coupled with high-speed imaging that allows the tracking and quantification of gait parameters in freely walking flies with high temporal and spatial resolution. Using this method, we present a comprehensive description of many locomotion parameters, such as gait, tarsal positioning, and intersegmental and left-right coordination for wild type fruit flies. Surprisingly, we find that inactivation of sensory neurons in the fly's legs, to block proprioceptive feedback, led to deficient step precision, but interleg coordination and the ability to execute a tripod gait were unaffected.DOI:http://dx.doi.org/10.7554/eLife.00231.001.
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Affiliation(s)
- César S Mendes
- Department of Biochemistry and Molecular Biophysics , Columbia University , New York , USA
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31
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Mendes CS, Bartos I, Akay T, Márka S, Mann RS. Quantification of gait parameters in freely walking wild type and sensory deprived Drosophila melanogaster. eLife 2013; 2:e00231. [PMID: 23326642 PMCID: PMC3545443 DOI: 10.7554/elife.00231] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/26/2012] [Indexed: 11/13/2022] Open
Abstract
Coordinated walking in vertebrates and multi-legged invertebrates such as Drosophila melanogaster requires a complex neural network coupled to sensory feedback. An understanding of this network will benefit from systems such as Drosophila that have the ability to genetically manipulate neural activities. However, the fly's small size makes it challenging to analyze walking in this system. In order to overcome this limitation, we developed an optical method coupled with high-speed imaging that allows the tracking and quantification of gait parameters in freely walking flies with high temporal and spatial resolution. Using this method, we present a comprehensive description of many locomotion parameters, such as gait, tarsal positioning, and intersegmental and left-right coordination for wild type fruit flies. Surprisingly, we find that inactivation of sensory neurons in the fly's legs, to block proprioceptive feedback, led to deficient step precision, but interleg coordination and the ability to execute a tripod gait were unaffected. DOI:http://dx.doi.org/10.7554/eLife.00231.001 Most animals need to be able to move to survive. Animals without limbs, such as snakes, move by generating by wave-like contractions along their bodies, whereas limbed animals, such as vertebrates and arthropods, walk by coordinating the movements of multi-jointed arms and legs. Locomotion in limbed animals involves bending each joint within each arm or leg in a coordinated manner, while also ensuring that the movements of all the limbs are coordinated with each other. In bipeds such as humans, for example, it is critical that one leg is in the stance phase when the other leg is in the swing phase. The rules that govern the coordination of limbs also depend on the gait, so the rules for walking are not the same as the rules for running. The nervous systems of bipeds and other animals that walk solve these problems by using complex neural circuits that coordinate the firing of the relevant motor neurons. Two general mechanisms are used to coordinate the firing of motor neurons. In one mechanism, local interneurons within the central nervous system coordinate motor neuron activities: in vertebrates these interneurons are found in the spinal cord. A second mechanism, termed proprioception, relies on sensory neurons that report the load and joint angles from the arms and legs back to the central nervous system, and thereby influence the firing of the motor neurons. Remarkably, both of these mechanisms, and also the types of neurons that comprise motor neuron circuits, are conserved from arthropods to vertebrates. Mendes et al. describe a new approach that can be used to analyze how the fruit fly, D. melanogaster, walks on surfaces. They use a combination of an optical touch sensor and high-speed video imaging to follow the body of the fly as it walks, and also to record when and where it places each of its six feet on the surface as it moves. Then, using a software package called FlyWalker, they are able to extract a large of number of parameters that can be used to describe locomotion in adult fruit flies with high temporal and spatial resolution. Many of these parameters have never been measured or studied before. Mendes et al. show that fruit flies do not display the abrupt transitions in gait that are typically observed in vertebrates. However, they do modify their neural circuits depending on their speed: indeed it appears that flies use subtly different neural circuitry for walking at slow, medium and fast speeds. Moreover, when genetic methods are used to block sensory feedback, the fly is still able to walk, albeit with reduced coordination and precision. Further, the data suggest that proprioception is less important when flies walk faster compared to when they walk more slowly. The next step in this research will be to combine this new method for analyzing locomotion in flies with the wide range of genetic tools that are available for the study of Drosophila: this will allow researchers to explore in greater detail the components of the motor neuron circuitry and their role in coordinated walking. DOI:http://dx.doi.org/10.7554/eLife.00231.002
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Affiliation(s)
- César S Mendes
- Department of Biochemistry and Molecular Biophysics , Columbia University , New York , USA
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Grossmann D, Prpic NM. Egfr signaling regulates distal as well as medial fate in the embryonic leg of Tribolium castaneum. Dev Biol 2012; 370:264-72. [DOI: 10.1016/j.ydbio.2012.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 07/18/2012] [Accepted: 08/10/2012] [Indexed: 11/30/2022]
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Estella C, Voutev R, Mann RS. A dynamic network of morphogens and transcription factors patterns the fly leg. Curr Top Dev Biol 2012; 98:173-98. [PMID: 22305163 DOI: 10.1016/b978-0-12-386499-4.00007-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Animal appendages require a proximodistal (PD) axis, which forms orthogonally from the two main body axes, anteroposterior and dorsoventral. In this review, we discuss recent advances that begin to provide insights into the molecular mechanisms controlling PD axis formation in the Drosophila leg. In this case, two morphogens, Wingless (Wg) and Decapentaplegic (Dpp), initiate a genetic cascade that, together with growth of the leg imaginal disc, establishes the PD axis. The analysis of cis-regulatory modules (CRMs) that control the expression of genes at different positions along the PD axis has been particularly valuable in dissecting this complex process. From these experiments, it appears that only one concentration of Wg and Dpp are required to initiate PD axis formation by inducing the expression of Distal-less (Dll), a homeodomain-encoding gene that is required for leg development. Once Dll is turned on, it activates the medially expressed gene dachshund (dac). Cross-regulation between Dll and dac, together with cell proliferation in the growing leg imaginal disc, results in the formation of a rudimentary PD axis. Wg and Dpp also initiate the expression of ligands for the EGFR pathway, which in turn induces the expression of a series of target genes that pattern the distal-most portion of the leg.
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Affiliation(s)
- Carlos Estella
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
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Progressive tarsal patterning in the Drosophila by temporally dynamic regulation of transcription factor genes. Dev Biol 2012; 361:450-62. [DOI: 10.1016/j.ydbio.2011.10.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Revised: 10/24/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
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