Functional Analysis of the Transcriptional Activator Encoded By
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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. -
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 Activator Protein-1 Transcription Factor in Respiratory Epithelium Carcinogenesis
Subject Review The Activator Protein-1 Transcription Factor in Respiratory Epithelium Carcinogenesis Michalis V. Karamouzis,1 Panagiotis A. Konstantinopoulos,1,2 and Athanasios G. Papavassiliou1 1Department of Biological Chemistry, Medical School, University of Athens, Athens, Greece and 2Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts Abstract Much of the current anticancer research effort is focused on Respiratory epithelium cancers are the leading cause cell-surface receptors and their cognate upstream molecules of cancer-related death worldwide. The multistep natural because they provide the easiest route for drugs to affect history of carcinogenesis can be considered as a cellular behavior, whereas agents acting at the level of gradual accumulation of genetic and epigenetic transcription need to invade the nucleus. However, the aberrations, resulting in the deregulation of cellular therapeutic effect of surface receptor manipulation might be homeostasis. Growing evidence suggests that cross- considered less than specific because their actions are talk between membrane and nuclear receptor signaling modulated by complex interacting downstream signal trans- pathways along with the activator protein-1 (AP-1) duction pathways. A pivotal transcription factor during cascade and its cofactor network represent a pivotal respiratory epithelium carcinogenesis is activator protein-1 molecular circuitry participating directly or indirectly in (AP-1). AP-1–regulated genes include important modulators of respiratory epithelium carcinogenesis. The crucial role invasion and metastasis, proliferation, differentiation, and of AP-1 transcription factor renders it an appealing survival as well as genes associated with hypoxia and target of future nuclear-directed anticancer therapeutic angiogenesis (7). Nuclear-directed therapeutic strategies might and chemoprevention approaches. -
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). -
Repressor to Activator Switch by Mutations in the First Zn Finger of The
Proc. Nat!. Acad. Sci. USA Vol. 88, pp. 7086-7090, August 1991 Biochemistry Repressor to activator switch by mutations in the first Zn finger of the glucocorticoid receptor: Is direct DNA binding necessary? (interleukin 1 indudbility/dexamethasone modulation/DNA-binding domain mutants/interleukin 6 and c-fos promoters) ANURADHA RAY, K. STEVEN LAFORGE, AND PRAVINKUMAR B. SEHGAL* The Rockefeller University, New York, NY 10021 Communicated by Igor Tamm, May 20, 1991 (receivedfor review March 15, 1991) ABSTRACT Transfection ofHeLa cells with cDNA vectors previous experiments in HeLa cells transfected with cDNA expressing the wild-type human glucocorticoid receptor (GR) vectors constitutively expressing the wild type (wt) but not enabled dexamethasone to strongly repress cytokine- and sec- the inactive carboxyl-terminal truncation mutants of GR, we ond messenger-induced expression of cotransfected chimeric observed that dexamethasone (Dex) strongly repressed the reporter genes containing transcription regulatory DNA ele- induction by interleukin 1 (IL-1), tumor necrosis factor, ments from the human interleukin 6 (IL-6) promoter. Deletion phorbol ester, or forskolin of IL-6-chloramphenicol acetyl- of the DNA-binding domain or of the second Zn finger or a transferase (CAT) constructs containing IL-6 DNA from point mutation in the Zn catenation site in the second finger -225 to +13. Dex also repressed induction of IL-6- blocked the ability of GR to mediate repression of the IL-6 thymidine kinase (TK)-CAT chimeric constructs containing promoter. -
MINIREVIEW Catabolite Gene Activator Protein Activation of Lac Transcription WILLIAM S
JOURNAL OF BACTERIOLOGY, Feb. 1992, p. 655-658 Vol. 174, No. 3 0021-9193/92/030655-04$02.00/0 Copyright © 1992, American Society for Microbiology MINIREVIEW Catabolite Gene Activator Protein Activation of lac Transcription WILLIAM S. REZNIKOFF Department of Biochemistry, College ofAgricultural and Life Sciences, University of Wisconsin-Madison, 420 Henry Mall, Madison, Wisconsin 53706 CAP ACTIVATION OF lac TRANSCRIPTION upon binding, and this could lead to contact of upstream DNA with RNA polymerase (21, 25). What is the mechanism by which genes are positively Finally, CAP acts as a repressor in some systems (18, 26). regulated? How can several unlinked genes encoding related Since the lac promoter region (and other regulatory regions functions be regulated by a common signal? These are two of such as gal) contains several promoterlike elements which the questions which can be addressed by studying the overlap the promoter (Fig. 1), it was thought that CAP could catabolite gene activator protein (CAP). CAP responds to activate transcription by limiting the access of nonproduc- differences in the availability and nature of carbon sources, tive competitive promoterlike elements to RNA polymerase via variations in the intracellular concentration of cyclic (16). AMP (cAMP). CAP, when complexed with cAMP, is a sequence-specific DNA-binding protein which activates sev- WHY DIRECT CAP-RNA POLYMERASE CONTACTS eral gene systems and represses others. It has been most ARE PROBABLY IMPORTANT FOR lac ACTIVATION extensively studied for Escherichia coli, although closely related proteins exist in other gram-negative bacteria. Several lines of evidence indicate that direct CAP-RNA CAP is an important paradigm for understanding the polymerase contacts play an important role in lac activation. -
Molecular Biology and Applied Genetics
MOLECULAR BIOLOGY AND APPLIED GENETICS FOR Medical Laboratory Technology Students Upgraded Lecture Note Series Mohammed Awole Adem Jimma University MOLECULAR BIOLOGY AND APPLIED GENETICS For Medical Laboratory Technician Students Lecture Note Series Mohammed Awole Adem Upgraded - 2006 In collaboration with The Carter Center (EPHTI) and The Federal Democratic Republic of Ethiopia Ministry of Education and Ministry of Health Jimma University PREFACE The problem faced today in the learning and teaching of Applied Genetics and Molecular Biology for laboratory technologists in universities, colleges andhealth institutions primarily from the unavailability of textbooks that focus on the needs of Ethiopian students. This lecture note has been prepared with the primary aim of alleviating the problems encountered in the teaching of Medical Applied Genetics and Molecular Biology course and in minimizing discrepancies prevailing among the different teaching and training health institutions. It can also be used in teaching any introductory course on medical Applied Genetics and Molecular Biology and as a reference material. This lecture note is specifically designed for medical laboratory technologists, and includes only those areas of molecular cell biology and Applied Genetics relevant to degree-level understanding of modern laboratory technology. Since genetics is prerequisite course to molecular biology, the lecture note starts with Genetics i followed by Molecular Biology. It provides students with molecular background to enable them to understand and critically analyze recent advances in laboratory sciences. Finally, it contains a glossary, which summarizes important terminologies used in the text. Each chapter begins by specific learning objectives and at the end of each chapter review questions are also included. -
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). -
Solutions for Practice Problems for Molecular Biology, Session 5
Solutions to Practice Problems for Molecular Biology, Session 5: Gene Regulation and the Lac Operon Question 1 a) How does lactose (allolactose) promote transcription of LacZ? 1) Lactose binds to the polymerase and increases efficiency. 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. 3) Lactose binds to an activator protein, which can then help the RNA polymerase bind to the promoter and begin transcription. 4) Lactose prevents premature termination of transcription by directly binding to and bending the DNA. Solution: 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. b) What molecule is used to signal low glucose levels to the Lac operon regulatory system? 1) Cyclic AMP 2) Calcium 3) Lactose 4) Pyruvate Solution: 1) Cyclic AMP. Question 2 You design a summer class where you recreate experiments studying the lac operon in E. coli (see schematic below). In your experiments, the activity of the enzyme b-galactosidase (β -gal) is measured by including X-gal and IPTG in the growth media. X-gal is a lactose analog that turns blue when metabolisize by b-gal, but it does not induce the lac operon. IPTG is an inducer of the lac operon but is not metabolized by b-gal. I O lacZ Plac Binding site for CAP Pi Gene encoding β-gal Promoter for activator protein Repressor (I) a) Which of the following would you expect to bind to β-galactosidase? Circle all that apply. -
Effects of Circadian Clock Genes and Health-Related
RESEARCH ARTICLE Effects of circadian clock genes and health- related behavior on metabolic syndrome in a Taiwanese population: Evidence from association and interaction analysis Eugene Lin1,2,3*, Po-Hsiu Kuo4, Yu-Li Liu5, Albert C. Yang6,7, Chung-Feng Kao8, Shih- Jen Tsai6,7* 1 Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan, 2 Vita Genomics, Inc., Taipei, Taiwan, 3 TickleFish Systems Corporation, Seattle, Western Australia, United States of America, a1111111111 4 Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan a1111111111 University, Taipei, Taiwan, 5 Center for Neuropsychiatric Research, National Health Research Institutes, a1111111111 Miaoli County, Taiwan, 6 Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan, 7 Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan, 8 Department of Agronomy, College a1111111111 of Agriculture & Natural Resources, National Chung Hsing University, Taichung, Taiwan a1111111111 * [email protected] (EL); [email protected] (SJT) Abstract OPEN ACCESS Citation: Lin E, Kuo P-H, Liu Y-L, Yang AC, Kao C- Increased risk of developing metabolic syndrome (MetS) has been associated with the cir- F, Tsai S-J (2017) Effects of circadian clock genes cadian clock genes. In this study, we assessed whether 29 circadian clock-related genes and health-related behavior on metabolic (including ADCYAP1, ARNTL, ARNTL2, BHLHE40, CLOCK, CRY1, CRY2, CSNK1D, syndrome in a Taiwanese population: Evidence from association and interaction analysis. PLoS CSNK1E, GSK3B, HCRTR2, KLF10, NFIL3, NPAS2, NR1D1, NR1D2, PER1, PER2, ONE 12(3): e0173861. https://doi.org/10.1371/ PER3, REV1, RORA, RORB, RORC, SENP3, SERPINE1, TIMELESS, TIPIN, VIP, and journal.pone.0173861 VIPR2) are associated with MetS and its individual components independently and/or Editor: Etienne Challet, CNRS, University of through complex interactions in a Taiwanese population. -
Tuning an Activator-Repressor Clock Employing Retroactivity
Tuning an Activator-Repressor Clock Employing Retroactivity Alexander Rosenberg∗, Shridhar Jayanthiy and Domitilla Del Vecchioz ∗Electrical Engineering Dept., University of Washington, Seattle WA 98195 yElectrical Engineering and Computer Science Dept., University of Michigan, Ann Arbor MI 48109 zDept. of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge MA 02139 Abstract— Activator-repressor systems have been shown to (a) Activator-Repressor Motif be capable of oscillations and are therefore an important clock motif in the field of Synthetic and Systems Biology. In this paper, we propose a method to regulate oscillatory behavior in such systems by the addition of DNA binding sites for the proteins involved in the clock network. We show that the retroactivity (b) Activator-Repressor with Activator Binding Sites effect caused by this addition can effectively change the relative timescales among the protein dynamics and impact the behavior of the clock. We also employ root locus analysis to obtain a graphical interpretation of the results. I. INTRODUCTION (c) Activator-Repressor with Repressor Binding Sites The design and analysis of oscillating modules is im- portant in the fields of Systems and Synthetic Biology as it enables the understanding of oscillator mechanisms that regulate essential natural processes, such as the cell cycle [1] or circadian clocks [2]. Oscillators are also a useful module in Synthetic Biology as they allow for synchroniza- Fig. 1. Diagram (a) illustrates the activator-repressor motif. Diagram (b) tion of different modules leading to more complex design and (c) illustrate the systems after the addition of DNA binding sites with affinity to the activator and the repressor respectively.