Transcriptomic Data from Panarthropods Shed New Light on the Evolution of Insulator Binding Proteins in Insects
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bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted March 26, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: Evolution of the D. melanogaster chromatin landscape and its associated proteins Authors and affiliations: Elise Parey(1, 2) and Anton Crombach*(1,3) (1) Center for Interdisciplinary Research in Biology (CIRB), Collè!e de France, C#RS, IN$ERM, P$& Uni(ersit) Paris, 75005 Paris, France (2) (c-rrent address) Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, P$& Uni(ersit) Paris, 75005 Paris, France (3) (current address) Inria, Antenne Lyon La Doua, 69603 Villeurbanne, France Author for Correspondence (*): Anton Crombach, Center for Interdisciplinary Research in Biology (CIRB), Collè!e de France, CNRS, I#$ERM, P$& Uni(ersit) Paris, 75005 Paris, "rance, anton.crombach@colle!e0de-france.fr Keywords: phylogenomics, chromatin-associated proteins, chromatin types, histone modi1cations, centromere dri(e, D. melanogaster. 1 of 46 bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted March 26, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract (221w, max 250w) In the nucleus of eukaryotic cells, !enomic 3#A associates 4ith numerous protein comple5es and RNAs, forming the chromatin landscape. -
Evolution of the D. Melanogaster Chromatin Landscape and Its Associated Proteins
bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted January 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: Evolution of the D. melanogaster chromatin landscape and its associated proteins Authors and affiliations: Elise Parey(1, 2) and Anton Crombach*(1,3,4) (1) Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Université Paris, 75005 Paris, France (2) (current address) Institut de Biologie de l’Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France (3) (current address) Inria, Antenne Lyon La Doua, 69603 Villeurbanne, France (4) Université de Lyon, INSA-Lyon, LIRIS, UMR 5205, 69621 Villeurbanne, France Author for Correspondence (*): Anton Crombach, Inria, Antenne Lyon La Doua, 69603 Villeurbanne, France, [email protected] 1 of 49 bioRxiv preprint doi: https://doi.org/10.1101/284828; this version posted January 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract (240w, max 250w) In the nucleus of eukaryotic cells, genomic DNA associates with numerous protein complexes and RNAs, forming the chromatin landscape. Through a genome-wide study of chromatin- associated proteins in Drosophila cells, five major chromatin types were identified as a refinement of the traditional binary division into hetero- and euchromatin. -
1 Title: Loss of Function Mutations in a Glutathione-S-Transferase Suppress
Genetics: Published Articles Ahead of Print, published on September 2, 2005 as 10.1534/genetics.105.044669 Title: Loss of function mutations in a glutathione-S-transferase suppress the prune-Killer of prune lethal interaction. Authors: Elayne Provost, Grafton Hersperger, Lisa Timmons, Wen Qi Ho, Evelyn Hersperger, Rosa Alcazar, and Allen Shearn ABSTRACT The prune gene of Drosophila melanogaster is predicted to encode a phosphodiesterase. Null alleles of prune are viable but cause an eye color phenotype. The abnormal wing discs gene encodes a nucleoside diphosphate kinase. Killer of prune is a missense mutation in the abnormal wing discs gene. Although it has no phenotype by itself even when homozygous, Killer of prune when heterozygous causes lethality in the absence of prune gene function. A screen for suppressors of transgenic Killer of prune led to the recovery of three mutations all of which are in the same gene. As heterozygotes these mutations are dominant suppressors of the prune-Killer of prune lethal interaction; as homozygotes these mutations cause early larval lethality and the absence of imaginal discs. These alleles are loss of function mutations in CG10065, a gene that is predicted to encode a protein with several zinc finger domains and glutathione S transferase activity. INTRODUCTION The prune (pn) gene was identified by viable mutations that cause a brownish purple eye color phenotype (Beadle and Ephrussi, 1936). The pn gene encodes a single 1.8 KB transcript that is predicted to be translated into a 44.5 kDa protein (Frolov et al., 1994). Nucleotide sequence analysis of pn mutants suggested that many of them are null alleles (Timmons and Shearn, 1996). -
IISER Pune Annual Report 2015-16 Chairperson Pune, India Prof
dm{f©H$ à{VdoXZ Annual Report 2015-16 ¼ããäÌãÓ¾ã ãä¶ã¹ã¥ã †Ìãâ Êãà¾ã „ÞÞã¦ã½ã ½ãÖ¦Ìã ‡ãŠñ †‡ãŠ †ñÔãñ Ìãõ—ãããä¶ã‡ãŠ ÔãâÔ©ãã¶ã ‡ãŠãè Ô©ãã¹ã¶ãã ãä•ãÔã½ãò ‚㦾ãã£ãìãä¶ã‡ãŠ ‚ã¶ãìÔãâ£ãã¶ã Ôããä֦㠂㣾ãã¹ã¶ã †Ìãâ ãäÍãàã¥ã ‡ãŠã ¹ãî¥ãùã Ôãñ †‡ãŠãè‡ãŠÀ¥ã Öãñý ãä•ã—ããÔãã ¦ã©ãã ÀÞã¶ã㦽ã‡ãЦãã Ôãñ ¾ãì§ãŠ ÔãÌããó§ã½ã Ôã½ãã‡ãŠÊã¶ã㦽ã‡ãŠ ‚㣾ãã¹ã¶ã ‡ãñŠ ½ã㣾ã½ã Ôãñ ½ããõãäÊã‡ãŠ ãäÌã—ãã¶ã ‡ãŠãñ ÀãñÞã‡ãŠ ºã¶ãã¶ããý ÊãÞããèÊãñ †Ìãâ Ôããè½ããÀãäÖ¦ã / ‚ãÔããè½ã ¹ã㟿ã‰ãŠ½ã ¦ã©ãã ‚ã¶ãìÔãâ£ãã¶ã ¹ããäÀ¾ããñ•ã¶ãã‚ããò ‡ãñŠ ½ã㣾ã½ã Ôãñ œãñ›ãè ‚ãã¾ãì ½ãò Öãè ‚ã¶ãìÔãâ£ãã¶ã àãñ¨ã ½ãò ¹ãÆÌãñÍãý Vision & Mission Establish scientific institution of the highest caliber where teaching and education are totally integrated with state-of-the- art research Make learning of basic sciences exciting through excellent integrative teaching driven by curiosity and creativity Entry into research at an early age through a flexible borderless curriculum and research projects Annual Report 2015-16 Governance Correct Citation Board of Governors IISER Pune Annual Report 2015-16 Chairperson Pune, India Prof. T.V. Ramakrishnan (till 03/12/2015) Emeritus Professor of Physics, DAE Homi Bhabha Professor, Department of Physics, Indian Institute of Science, Bengaluru Published by Dr. K. Venkataramanan (from 04/12/2015) Director and President (Engineering and Construction Projects), Dr. -
Computational Investigation of Thiol-Based Redox Modifications in Proteins: Redox-Active Disulfides, Zn2+ Sites and Their Associations
THESIS SUBMITTED IN TOTAL FULFILLMENT OF THE REQUIREMENTS OF THE DEGREE OF DOCTOR OF PHILOSOPHY Computational investigation of thiol‐based redox modifications in proteins: redox‐active disulfides, 2+ Zn sites and their associations Application of tools of bioinformatics in health and disease Dhakshinari Vihara Kumari Hulugalle March 2013 Victor Chang Cardiac Research Institute School of Medical Sciences, Faculty of Medicine, University of New South Wales PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: HULUGALLE First name: DHAKSHINARI Other name/s: VIHARA KUMARI PhD Abbreviation for degree as given in the University calendar: School: SCHOOL OF MEDICAL SCIENCES Faculty: MEDICINE Title: Computational investigation of thiol-based redox modifications in proteins: redox-active disulfides, Zn2+ sites and their associations Abstract 350 words maximum: (PLEASE TYPE) Thiol based redox signalling is an emerging area of research in protein science. Reversible disulfide bonding and Zn2+ expulsion are two important but less explored oxidative thiol modifications associated with redox signalling. They have numerous implications in health and disease. Three computational methods have previously been developed to predict redox-active disulfides in proteins: redox pair protein (RP) method, ‘forbidden disulfides’ (FD) method and torsional energy (TE) method. These methods and other tools of bioinformatics are used in my study to investigate redox-active disulfides, Zn2+ sites and the association between FDs and Zn fingers in protein structures. The first objective of my study was to apply the RP method to predict novel proteins containing likely redox-active disulfides. Over 300 novel RP proteins were found during this study. Significant conformational changes associated with disulfide redox activity in RP protein structures were also identified. -
The Drosophila Speciation Factor HMR Localizes to Genomic Insulator Sites
Aus dem Biomedizinischen Centrum der Ludwig-Maximilians-Universität München Medizinische Fakultät Lehrstuhl für Molekularbiologie Vorstand: Prof. Dr. rer. nat. Peter B. Becker The Drosophila speciation factor HMR localizes to genomic insulator sites Dissertation zum Erwerb des Doktorgrades der Naturwissenschaften an der Medizinischen Fakultät der Ludwig-Maximilians-Universität München vorgelegt von Thomas Andreas Gerland aus München Jahr 2017 Gedruckt mit Genehmigung der Medizinischen Fakultät der Ludwig-Maximilians-Universität München Betreuer: Prof. Dr. rer. nat. Axel Imhof Zweitgutachter: Prof. Dr. André Brändli Dekan: Prof. Dr. med. dent. Reinhard Hickel Tag der mündlichen Prüfung: 14.11.2017 Eidesstattliche Versicherung Gerland, Thomas Andreas Ich erkläre hiermit an Eides statt, dass ich die vorliegende Dissertation mit dem Thema “The Drosophila speciation factor HMR localizes to genomic insulator sites” selbständig verfasst, mich außer der angegebenen keiner weiteren Hilfsmittel bedient und alle Erkenntnisse, die aus dem Schrifttum ganz oder annähernd übernommen sind, als solche kenntlich gemacht und nach ihrer Herkunft unter Bezeichnung der Fundstelle einzeln nachgewiesen habe. Ich erkläre des Weiteren, dass die hier vorgelegte Dissertation nicht in gleicher oder in ähnlicher Form bei einer anderen Stelle zur Erlangung eines akademischen Grades eingereicht wurde. _________________________________ _________________________________ Ort, Datum Unterschrift Doktorandin/Doktorand Wesentliche Teile dieser Arbeit sind veröffentlicht in: PLoS ONE, 2017 February 16, doi:10.1371/journal.pone.0171798 The Drosophila speciation factor HMR localizes to genomic insulator sites Gerland T. A., Sun B., Smialowski P., Lukacs A., Thomae A. W., Imhof A. Mitwirkungen: Bioinformatische und statistische Datenanalyse durchgeführt in Zusammenarbeit mit Bo Sun, Dr. Pawel Smialowski und Dr. Tobias Straub Next Generation Sequencing durchgeführt in Zusammenarbeit mit Dr. -
Structure, Function, and Evolution of a Signal-Regulated Enhancer
Structure, Function, and Evolution of a Signal-Regulated Enhancer by Christina Ione Swanson A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Cell and Developmental Biology) in the University of Michigan 2010 Doctoral Committee: Assistant Professor Scott E. Barolo, Chair Professor J. Douglas Engel Associate Professor Kenneth M. Cadigan Associate Professor Billy Tsai Assistant Professor Patricia J. Wittkopp To my family, for your truly unconditional love and support. And to Mike - the best thing that happened to me in grad school. ii TABLE OF CONTENTS DEDICATION .................................................................................................................. ii LIST OF FIGURES ............................................................................................................ v CHAPTER I: INTRODUCTION ....................................................................................... 1 What do enhancers look like? ................................................................................ 2 Mechanisms of enhancer function ......................................................................... 3 Enhancer structure and organization ...................................................................... 6 Unanswered questions in the field ....................................................................... 10 The D-Pax2 sparkling enhancer .......................................................................... 12 CHAPTER II: STRUCTURAL RULES -
Promoter-Proximal Chromatin Domain Insulator Protein Beaf Mediates
Louisiana State University LSU Digital Commons Faculty Publications Department of Biological Sciences 5-1-2020 Promoter-proximal chromatin domain insulator protein BeaF mediates local and long-range communication with a transcription factor and directly activates a housekeeping promoter in Drosophila Yuankai Dong Louisiana State University S. V. Satya Prakash Avva Louisiana State University Mukesh Maharjan Louisiana State University Janice Jacobi Tulane University Craig M. Hart Louisiana State University Follow this and additional works at: https://digitalcommons.lsu.edu/biosci_pubs Recommended Citation Dong, Y., Satya Prakash Avva, S., Maharjan, M., Jacobi, J., & Hart, C. (2020). Promoter-proximal chromatin domain insulator protein BeaF mediates local and long-range communication with a transcription factor and directly activates a housekeeping promoter in Drosophila. Genetics, 215 (1), 89-101. https://doi.org/ 10.1534/genetics.120.303144 This Article is brought to you for free and open access by the Department of Biological Sciences at LSU Digital Commons. It has been accepted for inclusion in Faculty Publications by an authorized administrator of LSU Digital Commons. For more information, please contact [email protected]. | INVESTIGATION Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Downloaded from https://academic.oup.com/genetics/article/215/1/89/5930442 by LSU Health Sciences Ctr user on 05 August 2021 Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila -
Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Facto
Genetics: Early Online, published on March 17, 2020 as 10.1534/genetics.120.303144 Promoter-proximal chromatin domain insulator protein BEAF mediates local and long- range communication with a transcription factor and directly activates a housekeeping promoter in Drosophila Yuankai Dong,* S. V. Satya Prakash Avva,* Mukesh Maharjan,*,1 Janice Jacobi,† and Craig M. Hart*,2 *Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803 †Hayward Genetics Center, Tulane University, New Orleans, Louisiana 70112 1Present address: Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030 0 Copyright 2020. Running title: Transcriptional effects of BEAF insulator proteins Key words: BEAF; Insulators; Chromatin domains; Gene regulation; Enhancer-promoter looping; Drosophila 2Corresponding author: Department of Biological Sciences, Louisiana State University, 202 Life Sciences Bldg, Baton Rouge, Louisiana, 70803 E-mail: [email protected] 1 ABSTRACT BEAF (Boundary Element-Associated Factor) was originally identified as a Drosophila melanogaster chromatin domain insulator binding protein, suggesting a role in gene regulation through chromatin organization and dynamics. Genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, suggesting a role in promoter function. This would be a nontraditional role for an insulator binding protein. To gain insight into molecular mechanisms of BEAF function, we identified interacting proteins using yeast 2-hybrid assays. Here we focus on the transcription factor Sry-δ. Interactions were confirmed in pull- down experiments using bacterially expressed proteins, by bimolecular fluorescence complementation, and in a genetic assay in transgenic flies. Sry-δ interacted with promoter- proximal BEAF both when bound to DNA adjacent to BEAF or over 2 kb upstream to activate a reporter gene in transient transfection experiments. -
Gene Duplication, Lineage-Specific Expansion, And
INVESTIGATION Gene Duplication, Lineage-Specific Expansion, and Subfunctionalization in the MADF-BESS Family Patterns the Drosophila Wing Hinge Vallari Shukla, Farhat Habib, Apurv Kulkarni, and Girish S. Ratnaparkhi1 Indian Institute of Science Education and Research, Pune, Maharashtra, India 411008 ABSTRACT Gene duplication, expansion, and subsequent diversification are features of the evolutionary process. Duplicated genes can be lost, modified, or altered to generate novel functions over evolutionary timescales. These features make gene duplication a powerful engine of evolutionary change. In this study, we explore these features in the MADF-BESS family of transcriptional regulators. In Drosophila melanogaster, the family contains 16 similar members, each containing an N-terminal, DNA-binding MADF domain and a C-terminal, protein-interacting, BESS domain. Phylogenetic analysis shows that members of the MADF-BESS family are expanded in the Drosophila lineage. Three members, which we name hinge1, hinge2, and hinge3 are required for wing development, with a critical role in the wing hinge. hinge1 is a negative regulator of Winglesss expression and interacts with core wing-hinge patterning genes such as teashirt, homothorax, and jing. Double knockdowns along with heterologous rescue experiments are used to demonstrate that members of the MADF-BESS family retain function in the wing hinge, in spite of expansion and diversification for over 40 million years. The wing hinge connects the blade to the thorax and has critical roles in fluttering during flight. MADF-BESS family genes appear to retain redundant functions to shape and form elements of the wing hinge in a robust and fail-safe manner. HE MADF-BESS gene family in Drosophila melanogaster in a broader sense a subgroup of the individual, indepen- Tconsists of 16 transcriptional regulators (Figure 1A), dent MADF and BESS family genes, where both MADF and coded by 16 discrete genes. -
Transcriptome Analysis of the Whitefly, Bemisia Tabaci MEAM1 During
Kaur et al. BMC Genomics (2017) 18:370 DOI 10.1186/s12864-017-3751-1 RESEARCH ARTICLE Open Access Transcriptome analysis of the whitefly, Bemisia tabaci MEAM1 during feeding on tomato infected with the crinivirus, Tomato chlorosis virus, identifies a temporal shift in gene expression and differential regulation of novel orphan genes Navneet Kaur1, Wenbo Chen2, Yi Zheng2, Daniel K. Hasegawa3, Kai-Shu Ling3, Zhangjun Fei2 and William M. Wintermantel1* Abstract Background: Whiteflies threaten agricultural crop production worldwide, are polyphagous in nature, and transmit hundreds of plant viruses. Little is known how whitefly gene expression is altered due to feeding on plants infected with a semipersistently transmitted virus. Tomato chlorosis virus (ToCV; genus Crinivirus, family Closteroviridae) is transmitted by the whitefly (Bemisia tabaci) in a semipersistent manner and infects several globally important agricultural and ornamental crops, including tomato. Results: To determine changes in global gene regulation in whiteflies after feeding on tomato plants infected with a crinivirus (ToCV), comparative transcriptomic analysis was performed using RNA-Seq on whitefly (Bemisia tabaci MEAM1) populations after 24, 48, and 72 h acquisition access periods on either ToCV-infected or uninfected tomatoes. Significant differences in gene expression were detected between whiteflies fed on ToCV-infected tomato and those fed on uninfected tomato among the three feeding time periods: 447 up-regulated and 542 down-regulated at 24 h, 4 up-regulated and 7 down-regulated at 48 h, and 50 up-regulated and 160 down-regulated at 72 h. Analysis revealed differential regulation of genes associated with metabolic pathways, signal transduction, transport and catabolism, receptors, glucose transporters, α-glucosidases, and the uric acid pathway in whiteflies fed on ToCV-infected tomatoes, as well as an abundance of differentially regulated novel orphan genes. -
Insect Transcription Factors: a Landscape of Their Structures and Biological Functions in Drosophila and Beyond
International Journal of Molecular Sciences Review Insect Transcription Factors: A Landscape of Their Structures and Biological Functions in Drosophila and beyond Zhaojiang Guo 1,† , Jianying Qin 1,2,†, Xiaomao Zhou 2 and Youjun Zhang 1,* 1 Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; [email protected] (Z.G.); [email protected] (J.Q.) 2 Longping Branch, Graduate School of Hunan University, Changsha 410125, China; [email protected] * Correspondence: [email protected]; Tel.: +86-10-82109518 † These authors contributed equally to this work. Received: 23 October 2018; Accepted: 16 November 2018; Published: 21 November 2018 Abstract: Transcription factors (TFs) play essential roles in the transcriptional regulation of functional genes, and are involved in diverse physiological processes in living organisms. The fruit fly Drosophila melanogaster, a simple and easily manipulated organismal model, has been extensively applied to study the biological functions of TFs and their related transcriptional regulation mechanisms. It is noteworthy that with the development of genetic tools such as CRISPR/Cas9 and the next-generation genome sequencing techniques in recent years, identification and dissection the complex genetic regulatory networks of TFs have also made great progress in other insects beyond Drosophila. However, unfortunately, there is no comprehensive review that systematically summarizes the structures and biological functions of TFs in both model and non-model insects. Here, we spend extensive effort in collecting vast related studies, and attempt to provide an impartial overview of the progress of the structure and biological functions of current documented TFs in insects, as well as the classical and emerging research methods for studying their regulatory functions.