Hedgehog Signaling Regulates Transcription Through Cubitus Interruptus, a Sequence-Specific DNA Binding Protein
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Hedgehog Signaling Is Evolutionarily Conserved Cilium-Independent
Downloaded from genesdev.cshlp.org on August 14, 2009 - Published by Cold Spring Harbor Laboratory Press Cilium-independent regulation of Gli protein function by Sufu in Hedgehog signaling is evolutionarily conserved Miao-Hsueh Chen, Christopher W. Wilson, Ya-Jun Li, et al. Genes Dev. 2009 23: 1910-1928 Access the most recent version at doi:10.1101/gad.1794109 Supplemental http://genesdev.cshlp.org/content/suppl/2009/07/23/23.16.1910.DC1.html Material References This article cites 97 articles, 47 of which can be accessed free at: http://genesdev.cshlp.org/content/23/16/1910.full.html#ref-list-1 Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here To subscribe to Genes & Development go to: http://genesdev.cshlp.org/subscriptions Copyright © 2009 by Cold Spring Harbor Laboratory Press Downloaded from genesdev.cshlp.org on August 14, 2009 - Published by Cold Spring Harbor Laboratory Press Cilium-independent regulation of Gli protein function by Sufu in Hedgehog signaling is evolutionarily conserved Miao-Hsueh Chen,1,3 Christopher W. Wilson,1,3 Ya-Jun Li,1 Kelvin King Lo Law,2 Chi-Sheng Lu,1 Rhodora Gacayan,1 Xiaoyun Zhang,2 Chi-chung Hui,2 and Pao-Tien Chuang1,4 1Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158, USA; 2Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada A central question in Hedgehog (Hh) signaling is how evolutionarily conserved components of the pathway might use the primary cilium in mammals but not fly. -
Functional Analysis of the Homeobox Gene Tur-2 During Mouse Embryogenesis
Functional Analysis of The Homeobox Gene Tur-2 During Mouse Embryogenesis Shao Jun Tang A thesis submitted in conformity with the requirements for the Degree of Doctor of Philosophy Graduate Department of Molecular and Medical Genetics University of Toronto March, 1998 Copyright by Shao Jun Tang (1998) National Library Bibriothèque nationale du Canada Acquisitions and Acquisitions et Bibiiographic Services seMces bibliographiques 395 Wellington Street 395, rue Weifington OtbawaON K1AW OttawaON KYAON4 Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive licence alIowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distri%uteor sell reproduire, prêter' distribuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/nlm, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fkom it Ni la thèse ni des extraits substantiels may be printed or otherwise de celle-ci ne doivent être imprimés reproduced without the author's ou autrement reproduits sans son permission. autorisation. Functional Analysis of The Homeobox Gene TLr-2 During Mouse Embryogenesis Doctor of Philosophy (1998) Shao Jun Tang Graduate Department of Moiecular and Medicd Genetics University of Toronto Abstract This thesis describes the clonhg of the TLx-2 homeobox gene, the determination of its developmental expression, the characterization of its fiuiction in mouse mesodem and penpheral nervous system (PNS) developrnent, the regulation of nx-2 expression in the early mouse embryo by BMP signalling, and the modulation of the function of nX-2 protein by the 14-3-3 signalling protein during neural development. -
The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
The Mechanisms of Hedgehog Signal Transduction
Markku Varjosalo The Mechanisms of Hedgehog Signal Transduction Publications of the National Public Health Institute A 12/2008 Department of Molecular Medicine National Public Health Institute and Institute of Biomedicine, University of Helsinki, Finland Helsinki, Finland 2008 Markku Varjosalo THE MECHANISMS OF HEDGEHOG SIGNAL TRANSDUCTION ACADEMIC DISSERTATION To be publicly discussed with the permission of the Faculty of Medicine, University of Helsinki, in Lecture Hall 2, Biomedicum Helsinki, on 2nd May 2008, at noon. National Public Health Institute, Helsinki, Finland and Institute of Biomedicine, University of Helsinki, Finland Helsinki 2008 Publications of the National Public Health Institute KTL A12 / 2008 Copyright National Public Health Institute Julkaisija-Utgivare-Publisher Kansanterveyslaitos (KTL) Mannerheimintie 166 00300 Helsinki Puh. vaihde (09) 474 41, telefax (09) 4744 8408 Folkhälsoinstitutet Mannerheimvägen 166 00300 Helsingfors Tel. växel (09) 474 41, telefax (09) 4744 8408 National Public Health Institute Mannerheimintie 166 FIN-00300 Helsinki, Finland Telephone +358 9 474 41, telefax +358 9 4744 8408 ISBN 978-951-740-805-9 ISSN 0359-3584 ISBN 978-951-740-806-6 (pdf) ISSN 1458-6290 (pdf) Kannen kuva - cover graphic: Yliopistopaino Helsinki 2008 Supervised by Academy Professor Jussi Taipale Genome-Scale Biology Program Institute of Biomedicine, University of Helsinki Department of Molecular Medicine National Public Health Institute (KTL) Helsinki, Finland Reviewed by Professor Tomi Mäkelä Genome-Scale Biology Program -
Dynamics of Maternal Morphogen Gradients in Drosophila Stanislav Y Shvartsman1, Mathieu Coppey1 and Alexander M Berezhkovskii2
COGEDE-512; NO OF PAGES 6 Available online at www.sciencedirect.com Dynamics of maternal morphogen gradients in Drosophila Stanislav Y Shvartsman1, Mathieu Coppey1 and Alexander M Berezhkovskii2 The first direct studies of morphogen gradients were done in ified genes [1]. Since most of these studies were done the end of 1980s, in the early Drosophila embryo, which is with fixed embryos, maternal gradients were viewed as patterned under the action of four maternally determined relatively static signals. Several recent studies report morphogens. Since the early studies of maternal morphogens quantitative measurements of the anterior, dorsoventral, were done with fixed embryos, they were viewed as relatively and terminal gradients and propose biophysical models static signals. Several recent studies analyze dynamics of the for their formation and interpretation. We review these anterior, dorsoventral, and terminal patterning signals. The studies and discuss how their conclusions affect our view results of these quantitative studies provide critical tests of of dynamics in one of the most extensively studied classical models and reveal new modes of morphogen patterning systems. regulation and readout in one of the most extensively studied patterning systems. Bicoid gradient: diffusion and reversible Addresses trapping of a stable protein? 1 Department of Chemical Engineering and Lewis-Sigler Institute for In the end of 1980s, studies of the distribution and Integrative Genomics, Princeton University, New Jersey, United States transcriptional effects of the Bicoid (Bcd) protein in 2 Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National the Drosophila embryo provided the first molecularly Institutes of Health, Bethesda, MD 20892, United States defined example of a morphogen gradient [2–4]. -
Differentiating Mesoderm and Muscle Cell Lineages During Drosophila Embryogenesis BRENDA LILLY, SAMUEL GALEWSKY, ANTHONY B
Proc. Nati. Acad. Sci. USA Vol. 91, pp. 5662-5666, June 1994 Developmental Biology D-MEF2: A MADS box transcription factor expressed in differentiating mesoderm and muscle cell lineages during Drosophila embryogenesis BRENDA LILLY, SAMUEL GALEWSKY, ANTHONY B. FIRULLI, ROBERT A. SCHULZ, AND ERIC N. OLSON* Department of Biochemistry and Molecular Biology, Box 117, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030 Communicated by Thomas P. Maniatis, January 21, 1994 ABSTRACT The myocyte enhancer factor (MEF) 2 family cle-specific genes (13). The recent cloning of MEF2 has oftranscription factors has been Implicated In the regultion of revealed that it belongs to the MADS (MCM1, Agamous, musle tansription in vertebrates. We have cloned a protein Deficiens, and serum-response factor) family oftranscription fromDrosophia, termed D-MEF2, that shares extensive amino factors. Four MEF2 genes, designated MEF2A, -B, -C, and acid homology with the MADS (MCM1, Agamous, Defdcens, -D, have been cloned from vertebrates (10, 14-19). The and serum-response factor) d of the vertebrate MEF2 proteins encoded by these genes are highly homologous proteins. D-mef2 gene expression Is first detected dring within the 55-amino-acid MADS domain at their amino Drosophila embryogenesis within mesodermal precursor cells termini and within an adjacent MEF2-specific region of 27 prior to spcation of the somatic and visceral muscle lin- residues, but they diverge outside of these regions. eages. Expression of D-mef2 Is dependent on the mesodermal We have cloned aDrosophila homologue ofMEF2, termed determinants twist and snail but independent ofthe homeobox- D-MEF2,t which, to our knowledge, is the first MADS containng gene dtnman, which is required for visceral muscle protein to be identified in Drosophila. -
Analysis of Cubitus Interruptus Regulation in Drosophila Embryos and Imaginal Disks
Development 121, 1625-1635 (1995) 1625 Printed in Great Britain © The Company of Biologists Limited 1995 Analysis of cubitus interruptus regulation in Drosophila embryos and imaginal disks Carol Schwartz1, John Locke2, Craig Nishida1 and Thomas B. Kornberg1 1Department of Biochemistry and Biophysics, University of California, San Francisco, California 94143, USA 2Department of Biological Sciences, University of Alberta, Alberta, Canada SUMMARY The cubitus interruptus (ci) gene of Drosophila is expressed expression. Evidence that the engrailed protein normally in all anterior compartment cells in both embryos and represses ci in posterior compartments includes the imaginal disks where it encodes a putative zinc-finger expansion of ci expression into posterior compartment cells protein related to the vertebrate Gli and C. elegans Tra-1 that lack engrailed function, diminution of ci expression proteins. Using ci/lacZ fusions, we located regulatory upon overexpression of engrailed protein in anterior com- sequences responsible for the normal pattern of ci partment cells, and the ability of engrailed protein to bind expression, and obtained evidence that separate elements to the ci regulatory region in vivo and in vitro. We suggest regulate its expression in embryos and imaginal disks. that engrailed protein directly represses ci expression in Mutants that delete a portion of this regulatory region posterior compartment cells. express ci ectopically in the posterior compartments of their wing imaginal disks and have wings with malformed posterior compartments. Similar deletions of ci/lacZ fusion Key words: Drosophila, developmental regulation, compartments, constructs also result in ectopic posterior compartment engrailed, cubitus interruptus, imaginal disk, segment polarity gene INTRODUCTION have been isolated; these cause defects predominantly in the wings (Locke and Tartof, 1994; Slusarski et al., 1995). -
Dynamics of the Dorsal Morphogen Gradient
Dynamics of the Dorsal morphogen gradient Jitendra S. Kanodiaa, Richa Rikhyb, Yoosik Kima, Viktor K. Lundc, Robert DeLottoc, Jennifer Lippincott-Schwartzb,1, and Stanislav Y. Shvartsmana,1 aDepartment of Chemical Engineering and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, NJ 08544; bCell Biology and Metabolism Branch, NIH, Building 32, 18 Library Drive, Bethesda, MD 20892; and cDepartment of Molecular Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark Contributed by Jennifer Lippincott-Schwartz, October 28, 2009 (sent for review September 6, 2009) The dorsoventral (DV) patterning of the Drosophila embryo depends several minutes (16). Nuclei change in volume and undergo five on the nuclear localization gradient of Dorsal (Dl), a protein related to synchronous divisions (15, 17). To explore how these processes the mammalian NF-B transcription factors. Current understanding of contribute to the formation of the Dl gradient, we formulated a how the Dl gradient works has been derived from studies of its mathematical model that accounts for the nuclear import and transcriptional interpretation, but the gradient itself has not been export of Dl, its interaction with Cact, and the dynamics of nuclear quantified. In particular, it is not known whether the Dl gradient is density and volumes in the syncytial blastoderm. Based on the stable or dynamic during the DV patterning of the embryo. To address computational analysis of this model and a number of our model- this question, we developed a mathematical model of the Dl gradient based experiments, we argue that the Dl gradient is dynamic and, and constrained its parameters by experimental data. -
The Physical Mechanisms of Drosophila Gastrulation: Mesoderm and Endoderm Invagination
| FLYBOOK DEVELOPMENT AND GROWTH The Physical Mechanisms of Drosophila Gastrulation: Mesoderm and Endoderm Invagination Adam C. Martin1 Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142 ORCID ID: 0000-0001-8060-2607 (A.C.M.) ABSTRACT A critical juncture in early development is the partitioning of cells that will adopt different fates into three germ layers: the ectoderm, the mesoderm, and the endoderm. This step is achieved through the internalization of specified cells from the outermost surface layer, through a process called gastrulation. In Drosophila, gastrulation is achieved through cell shape changes (i.e., apical constriction) that change tissue curvature and lead to the folding of a surface epithelium. Folding of embryonic tissue results in mesoderm and endoderm invagination, not as individual cells, but as collective tissue units. The tractability of Drosophila as a model system is best exemplified by how much we know about Drosophila gastrulation, from the signals that pattern the embryo to the molecular components that generate force, and how these components are organized to promote cell and tissue shape changes. For mesoderm invagination, graded signaling by the morphogen, Spätzle, sets up a gradient in transcriptional activity that leads to the expression of a secreted ligand (Folded gastrulation) and a transmembrane protein (T48). Together with the GPCR Mist, which is expressed in the mesoderm, and the GPCR Smog, which is expressed uniformly, these signals activate heterotrimeric G-protein and small Rho-family G-protein signaling to promote apical contractility and changes in cell and tissue shape. A notable feature of this signaling pathway is its intricate organization in both space and time. -
Computational Studies of Gene Regulatory Networks: in Numero Molecular Biology
REVIEWS COMPUTATIONAL STUDIES OF GENE REGULATORY NETWORKS: IN NUMERO MOLECULAR BIOLOGY Jeff Hasty, David McMillen, Farren Isaacs and James J. Collins Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques. NONLINEAR DYNAMICS An important theme in post-genomic research will description of gene regulation. If this were a complex In a system governed by probably be the dissection and analysis of the complex electrical circuit, there would be an accompanying set nonlinear dynamics, the rate dynamical interactions involved in gene regulation. of equations that would faithfully describe its func- of change of any variable Although the concepts of protein–DNA feedback loops tionality. This description would be built from a cannot be written as a linear function of the other variables. and network complexity are not new, experimental knowledge of the properties of the individual compo- Most real systems are nonlinear advances are inducing a resurgence of interest in the nents (resistors, capacitors, inductors and so on) and and show interesting quantitative description of gene regulation. These provide a framework for predicting behaviour that behaviours not seen in advances are beginning to allow a ‘modular’ description results from modification of the circuit. -
Drosophila Embryo and the Mechanisms That Generate Tissue-Specific Outputs of Hedgehog Signaling Brian Biehs, Katerina Kechris*, Songmei Liu and Thomas B
RESEARCH ARTICLE 3887 Development 137, 3887-3898 (2010) doi:10.1242/dev.055871 © 2010. Published by The Company of Biologists Ltd Hedgehog targets in the Drosophila embryo and the mechanisms that generate tissue-specific outputs of Hedgehog signaling Brian Biehs, Katerina Kechris*, SongMei Liu and Thomas B. Kornberg† SUMMARY Paracrine Hedgehog (Hh) signaling regulates growth and patterning in many Drosophila organs. We mapped chromatin binding sites for Cubitus interruptus (Ci), the transcription factor that mediates outputs of Hh signal transduction, and we analyzed transcription profiles of control and mutant embryos to identify genes that are regulated by Hh. Putative targets that we identified included several Hh pathway components, mostly previously identified targets, and many targets that are novel. Every Hh target we analyzed that is not a pathway component appeared to be regulated by Hh in a tissue-specific manner; analysis of expression patterns of pathway components and target genes provided evidence of autocrine Hh signaling in the optic primordium of the embryo. We present evidence that tissue specificity of Hh targets depends on transcription factors that are Hh- independent, suggesting that ‘pre-patterns’ of transcription factors partner with Ci to make Hh-dependent gene expression position specific. KEY WORDS: Drosophila, Hedgehog, Cubitus interruptus INTRODUCTION Pleiotropic phenotypes result from loss or inactivation of Hh Hedgehog (Hh) is a secreted signaling protein that regulates the pathway components, suggesting that the pathway is similarly growth and patterning of many organs. First identified because of constituted in the affected tissues (reviewed by McMahon et al., its roles in Drosophila embryonic and imaginal disc development, 2003). -
S41467-018-04754-Z.Pdf
ARTICLE DOI: 10.1038/s41467-018-04754-z OPEN Guided morphogenesis through optogenetic activation of Rho signalling during early Drosophila embryogenesis Emiliano Izquierdo 1, Theresa Quinkler1 & Stefano De Renzis 1 During organismal development, cells undergo complex changes in shape whose causal relationship to individual morphogenetic processes remains unclear. The modular nature of 1234567890():,; such processes suggests that it should be possible to isolate individual modules, determine the minimum set of requirements sufficient to drive tissue remodeling, and re-construct morphogenesis. Here we use optogenetics to reconstitute epithelial folding in embryonic Drosophila tissues that otherwise would not undergo invagination. We show that precise spatial and temporal activation of Rho signaling is sufficient to trigger apical constriction and tissue folding. Induced furrows can occur at any position along the dorsal–ventral or anterior–posterior embryo axis in response to the spatial pattern and level of optogenetic activation. Thus, epithelial folding is a direct function of the spatio-temporal organization and strength of Rho signaling that on its own is sufficient to drive tissue internalization independently of any pre-determined condition or differentiation program associated with endogenous invagination processes. 1 EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany. Correspondence and requests for materials should be addressed to S.D.R. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:2366 | DOI: 10.1038/s41467-018-04754-z | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-04754-z raditional genetic approaches have played a pivotal role in Results establishing the requirement of individual gene activities RhoGEF2 plasma membrane recruitment and tissue responses.