DOCSLIB.ORG

University of Veterinary Medicine Hannover THESIS DOCTOR OF

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
University of Veterinary Medicine Hannover THESIS DOCTOR OF University of Veterinary Medicine Hannover Institute for Experimental Infection Research TWINCORE, Center for Experimental and Clinical Infection Research, GmbH MicroRNAs as biomarkers in the host response to influenza A virus infection in humans and animals THESIS Submitted in partial fulfilment of the requirements for the degree DOCTOR OF PHILOSOPHY (PhD) Awarded by the University of Veterinary Medicine Hannover By Mohamed Samir Ahmed Mohamed Zagazig, El-Sharkia province, Egypt Hannover, Germany (2016) Supervisor: PD Dr. med. Frank Pessler Supervision Group: Prof. Dr. med. vet. Silke Rautenschlein Prof. Dr. rer. nat. Klaus Schughart 1st evaluation: PD Dr. med. Frank Pessler Institute for experimental Infection Research,TWINCORE, Center for Experimental and Clinical Infection Research Hannover, Germany Prof. Dr. med. vet. Silke Rautenschlein Head, Clinic for Poultry, University of Veterinary Medicine Hannover Hannover, Germany Prof. Dr. rer. nat. Klaus Schughart Department of Infection Genetics Helmholtz Center for Infection Research Braunschweig, Germany Memphis, Tennessee, United States. 2nd evaluation: Prof. Dr. med. vet. Martin Beer FLIFLI, of Insel Tennessee Riems Health Science Center Institute of Viral Diagnostics Greifswald, Insel Riems, Germany Date of final exam: 18.03.2016 Parts of this thesis that have been submitted/accepted for publication: Manuscript I: In preparation Manuscript II: In revision for “Frontiers in Veterinary Science” Manuscript III: In revision for “Archives of Virology” Manuscript IV: In preparation Manuscript V: In preparation Sponsorship statement: Financial support of this study was from the German Egyptian Research Long-term Scholarship (GERLS), a joint program between the German Academic Exchange Service (DAAD) and the Egyptian Ministry of Higher Education and Scientific Research (grant ID: A/11/92510). Additional funds came from iMed, the Helmholtz Association’s Initiative on Personalized Medicine. To my parents, sisters and wife Table of contents Summary (English version) …………….......................…………………………….7 Zusammenfassung (German version)……………....................……….………....10 1. Introduction 1.1. Influenza A Virus (IAV)………..………………...................….……..14 1.1.1. Epidemiology and significance of IAVs …………………….….….14 1.1.2. Morphology of IAVs…………………………………………...….....15 1.1.3. IAV replication cycle …………………………………………….…..16 1.1.4. Host factors involved in IAV infection ………………………...…...18 1.1.4.1. Chemokines ……………………………………….…….18 1.1.4.2. Cytokines ………………………………………………...19 1.1.5. Host range of IAVs ………………………………………………….20 1.2. MicroRNAs (miRNAs)…………………………………………….……21 1.2.1. Nomenclature of miRNA………………………...………….……....22 1.2.2. MiRNA biogenesis and mechanism of action ……………....……22 1.2.3. Potential roles of miRNA as diagnostic and prognostic biomarkers……………………………….…..………………….……23 1.2.4. MiRNAs in IAV infection……………………………………..……...24 2. Objectives………………………………………………………...………......... 26 3. Results 3.1. Manuscript I: Host-encoded microRNA associated with viral infectious diseases of veterinary importance: general aspects and role in pathobiology…………………………………………..…….28 3.2. Manuscript II: Small non-coding RNAs associated with viral infectious diseases of veterinary importance: potential clinical applications……….………….………………………..…….……….…..83 3.3. Manuscript III: Pandemic 2009 H1N1 variants and toll-like receptor (TLR) ligands induce cell- and virus-specific miRNA expression in A549 and dTHP-1 cells………………..…...…….……125 3.4. Manuscript IV: A previously uncharacterized Egyptian strain of highly pathogenic avian influenza virus (H5N1) emerged in clade 2.2.1.2 and is highly pathogenic in an experimentally infected domestic duck breed ……..……………………….……….…….…...158 3.5. Manuscript V: Highly pathogenic influenza A virus (H5N1) induces tissue-specific differential expression of small non-coding RNAs in experimentally infected duck……………….…….…..……...….…190 3.6. Own contributions to the manuscripts….………….…………….246 4. Unpublished Data 4.1. Differential miRNA expression in genetically diverse H1N1-infected mouse strains………..……..…………………….......247 4.2. Establishment of human lung tissue explants (HLTE) to study miRNAs expression in response to 2009 swine-origin influenza viruses (S-OIVs) of differential virulence……………….………...….259 5. Discussion……………………………………………………………………..278 6. Conclusions and outlook ……………………………………………………287 7. References …………………………………………………………………….289 8. Affidavit…………………………………………………………………………298 9. Acknowledgements………………………..………………………….……...299 10. Curriculum Vitae………………………………………………..………....….301 Summary “MicroRNAs as biomarkers in the host response to influenza A virus infection in humans and animals” Mohamed Samir Ahmed Mohamed Influenza A virus (IAV) is a negative sense, single-stranded RNA virus that belongs to the family of Orthomyxoviridae. In addition to the seasonal epidemics, it caused three human pandemics in the last century (1918 A/H1N1, 1957 A/H2N2, and 1968 A/H3N2). In 2009, the world was confronted with the fourth pandemic caused by a triple reassortant H1N1 virus. The highly pathogenic avian influenza (HPAI) viruses of the subtype H5N1 are unique in that they are highly lethal to birds and are able to cross the species barrier and infect humans. MicroRNAs (miRNAs) are small non- coding RNAs (sncRNAs) that are able to fine-tune gene expression. The modulation of miRNAs under pathological conditions raises the possibilities of utilizing them as host biomarkers to pinpoint the disease in question and track its progress. This applies similarly to IAV at the farm level, where these small molecules might aid sensing the very early cases before the outbreaks spread widely. The objectives of my thesis were to investigate the importance of miRNAs as components of the host response to IAVs in humans and animals and to identify candidate miRNAs that might be used as future biomarkers. Before starting the experiments, I performed a literature search with the aim to review the up-to-date known roles of host-encoded miRNAs in infectious viral diseases of veterinary importance and the potential of using small non-coding RNAs to limit and/or prevent infectious viral diseases in livestock of veterinary importance. This resulted in two review articles (Manuscript I and II). In the first part of the experimental work (section 4.1 in Unpublished Data), I used reverse transcriptase real-time PCR (RT-qPCR) to validate the results of next generation sequencing (NGS; specifically, small RNA sequencing, small RNA-seq) with regard to the relative expression levels of a set of miRNAs. Those miRNAs have been previously identified by Dr. Matthias Preuße (Helmholtz Center for Infection 7 Research) to be associated with susceptibility to PR8 H1N1 in murine system. As a result, both approaches agreed to a high degree, indicating that RT-qPCR is a valid method to confirm the results of RNA-seq. In the second part (Manuscript III), I established in vitro assays comprising human cell lines to study the cell type-specific expression of miRNAs following stimulation with toll-like receptor (TLR) agonists and after infection with 2009 swine-origin influenza virus wild type (S-OIV wt) and S-OIV NS PR8, a reassortant variant of it that carries the NS segment of the PR8 H1N1 virus. The findings indicated that S- OIV NS PR8 triggered a cell-dependent alteration of certain miRNA (e.g. miR-223 and miR-155) as compared to the S-OIV wt. The data also show that while the infection with both viruses caused higher expression of miRNAs in human lung epithelial (A549) than in macrophage-like (dTHP-1) cell lines, the TLR agonists (LPS and R848) displayed the reverse pattern. In the third part of my thesis (Manuscripts IV and V), I aimed to analyze the miRNA responses to the HPAI virus H5N1 in a natural host. Therefore, a native duck breed (derived from Anas platyrhynchos) was experimentally infected with A/chicken/Faquos/amn12/2011(H5N1) virus, an Egyptian isolate that, according to my phylogenetic analyses, belongs to the recently emerging clade 2.2.1.2. The initial viral characterization revealed that brain, compared to other organs notably lung, exhibited much lower viral transcription, growth rate and associated tissue- pathology. As these results suggested an organ-specific host response to HPAI H5N1 virus infection, small RNA-seq. was employed to test the hypothesis if there is a unique miRNA response in these organs. As a result, the overall degree of miRNA reprogramming was higher and manifested earlier in lung than in brain. In both organs, the magnitude of the miRNA response reached the peak during the late infection stage (72-120 hpi), following the peak of viral transcription, arguing that the miRNA reprogramming is part of the host tissue response to viral transcription and, consequently, replication. I also identified common and organ-specific miRNAs that have a characteristic clustering pattern, including miR-183, miR-194, miR-205 and miR-215. Generally, gene ontologies such as T-helper cell differentiation and Positive regulation of JUN kinase activity were commonly enriched in both organs. Although certain pathways were enriched in both organs such as MAPK and Jak- 8 STAT signaling pathways, their enrichment degree was higher in lung than in brain. Considered together, these results propose the involvement of miRNAs in the organ- specific response to HPAI H5N1 and that their regulatory roles might shape the replication of the virus in different duck tissues. Furthermore, this study suggests possibilities
Load more

Recommended publications
  • Role of Cajal Bodies and Nucleolus in the Maturation of the U1 Snrnp in Arabidopsis
    CORE Metadata, citation and similar papers at core.ac.uk Provided by PubMed Central Role of Cajal Bodies and Nucleolus in the Maturation of the U1 snRNP in Arabidopsis Zdravko J. Lorkovic´*, Andrea Barta Max F. Perutz Laboratories, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria Abstract Background: The biogenesis of spliceosomal snRNPs takes place in both the cytoplasm where Sm core proteins are added and snRNAs are modified at the 59 and 39 termini and in the nucleus where snRNP-specific proteins associate. U1 snRNP consists of U1 snRNA, seven Sm proteins and three snRNP-specific proteins, U1-70K, U1A, and U1C. It has been shown previously that after import to the nucleus U2 and U4/U6 snRNP-specific proteins first appear in Cajal bodies (CB) and then in splicing speckles. In addition, in cells grown under normal conditions U2, U4, U5, and U6 snRNAs/snRNPs are abundant in CBs. Therefore, it has been proposed that the final assembly of these spliceosomal snRNPs takes place in this nuclear compartment. In contrast, U1 snRNA in both animal and plant cells has rarely been found in this nuclear compartment. Methodology/Principal Findings: Here, we analysed the subnuclear distribution of Arabidopsis U1 snRNP-specific proteins fused to GFP or mRFP in transiently transformed Arabidopsis protoplasts. Irrespective of the tag used, U1-70K was exclusively found in the nucleus, whereas U1A and U1C were equally distributed between the nucleus and the cytoplasm. In the nucleus all three proteins localised to CBs and nucleoli although to different extent. Interestingly, we also found that the appearance of the three proteins in nuclear speckles differ significantly.
    [Show full text]
  • The Reaction Mechanism of Cellular U Snrnp Assembly
    The Reaction Mechanism of Cellular U snRNP Assembly Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Ashwin Chari Aus Bangalore (Indien) Würzburg 2009 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. M. Müller 1. Gutachter: Prof. Dr. U. Fischer 2. Gutachter: Prof. Dr. U. Scheer Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Erklärung Erklärung gemäss §4 Absatz 3 der Promotionsordnung der Fakultät für Biologie der Bayerischen Julius-Maximilians-Universität Würzburg vom 15. März 1999 1. Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die angegebenen Quellen und Hilfsmittel benutzt habe. 2. Ich erkläre, dass die vorliegende Dissertation weder in gleicher noch in ähnlicher Form bereits in einem Prüfungsverfahren vorgelegen hat. 3. Ich erkläre, dass ich ausser den mit dem Zulassungsantrag urkundlich vorgelegten Graden keine weiteren akademischen Grade erworben oder zu erwerben versucht habe. Würzburg, 2009 Ashwin Chari Table of Contents 1. Summary 1 2. Zusammenfassung 5 3. Introduction 9 3.1 Principles Governing Macromolecular Complex Assembly in Vivo 9 3.2 Pre-mRNA Splicing 12 3.3 Architecture of Spliceosomal U snRNPs 14 3.4 The Cell Biology of U snRNP Biogenesis 16 3.5 U snRNP Assembly in Vivo is an Active, Factor-Mediated Process 19 3.6 References 22 4. Goals of this Thesis 29 5. Results 31 5.1 Taking an Inventory of the Subunits of the Human SMN-Complex 31 5.2 Definition of the Basic Architecture of the Human SMN-Complex 49 5.3 Mechanistic Aspects of Cellular U snRNP Assembly 65 5.4 Evolution of the SMN-Complex 115 6.
    [Show full text]
  • RNA-Protein Interactions of a Kink
    Florida State University Libraries Electronic Theses, Treatises and Dissertations The Graduate School 2005 Biophysical and Biochemical Investigation of an Archaeal Box C/D SRNP: RNA- Protein Interactions of a Kink Turn RNA within the Functional Enzyme Terrie Luong Moore Follow this and additional works at the FSU Digital Library. For more information, please contact [email protected] THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES BIOPHYSICAL AND BIOCHEMICAL INVESTIGATION OF AN ARCHAEAL BOX C/D SRNP: RNA-PROTEIN INTERACTIONS OF A KINK TURN RNA WITHIN THE FUNCTIONAL ENZYME By TERRIE LUONG MOORE A Dissertation submitted to the Department of Chemistry and Biochemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy Degree Awarded: Summer Semester, 2005 The members of the Committee approve the dissertation of Terrie Luong Moore defended on May 3, 2005. ________________________________ Hong Li Professor Directing Dissertation ________________________________ Lloyd M. Epstein Outside Committee Member ________________________________ Timothy M. Logan Committee Member ________________________________ John G. Dorsey Committee Member Approved: ___________________________________________________ Naresh Dalal, Chair, Department of Chemistry and Biochemistry The Office of Graduate Studies has verified and approved the above named committee members. ii I dedicate this work to my husband, Michael, for being there every step of the way and always giving me hope about the future. Without your love and support, this work would not have been possible. iii ACKNOWLEDGEMENTS I would like to thank my mentor, Dr. Hong Li, first and foremost for taking me into her lab and allowing me to grow intellectually. I would like to thank all of my committee members, Dr.
    [Show full text]
  • Snorna Guide Activities – Real and Ambiguous Svetlana Deryusheva, Gaëlle JS Talross
    Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Deryusheva, Talross and Gall SnoRNA guide activities – real and ambiguous Svetlana Deryusheva, Gaëlle J.S. Talross 1, Joseph G. Gall Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA 1 Present address: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06510, USA Corresponding authors: e-mail [email protected] [email protected] Running title: Testing snoRNA activities Keywords: modification guide RNA activity, 2’-O-methylation, pseudouridylation, Pus7p, snoRNA 1 Downloaded from rnajournal.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Deryusheva, Talross and Gall ABSTRACT In eukaryotes, rRNAs and spliceosomal snRNAs are heavily modified posttranscriptionally. Pseudouridylation and 2’-O-methylation are the most abundant types of RNA modifications. They are mediated by modification guide RNAs, also known as small nucleolar (sno)RNAs and small Cajal body-specific (sca)RNAs. We used yeast and vertebrate cells to test guide activities predicted for a number of snoRNAs, based on their regions of complementarity with rRNAs. We showed that human SNORA24 is a genuine guide RNA for 18S-Ψ609, despite some non- canonical base-pairing with its target. At the same time, we found quite a few snoRNAs that have the ability to base-pair with rRNAs and can induce predicted modifications in artificial substrate RNAs, but do not modify the same target sequence within endogenous rRNA molecules. Furthermore, certain fragments of rRNAs can be modified by the endogenous yeast modification machinery when inserted into an artificial backbone RNA, even though the same sequences are not modified in endogenous yeast rRNAs.
    [Show full text]
  • Guide Rnas with 5 Caps and Novel Box C/D Snorna-Like Domains For
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Current Biology, Vol. 14, 1985–1995, November 23, 2004, 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.cub.2004.11.003 Guide RNAs with 5؅ Caps and Novel Box C/D snoRNA-like Domains for Modification of snRNAs in Metazoa Kazimierz T. Tycowski, Alar Aab, duced by small nucleolar RNP particles (snoRNPs). Box and Joan A. Steitz* C/D snoRNPs direct 2Ј-O-methylation, while box H/ACA Department of Molecular Biophysics particles are involved in pseudouridylation (reviewed in and Biochemistry [4]). The RNA components of the snoRNPs select the Howard Hughes Medical Institute sites for modification by engaging in extensive base Yale University School of Medicine pairing interactions with the substrate RNA, while meth- 295 Congress Avenue ylation and pseudouridylation are believed to be carried New Haven, Connecticut 06536 out by a snoRNP core protein specific to each particle class. Box C/D snoRNPs are composed of a small RNA mole- Summary cule, typically 70–90 nt long in vertebrates, and a set of at least four proteins: fibrillarin, which is the methyltrans- Background: Spliceosomal snRNAs and ribosomal ferase [5, 6], Nop56, Nop58, and 15.5 kDa (reviewed RNAs in metazoans contain numerous modified resi- in [4]). All box C/D snoRNAs contain four conserved Ј dues that are functionally important. The most common sequence elements: boxes C and D close to the 5 and Ј modifications are site-specific 2Ј-O-methylation and 3 termini, respectively, and internal copies of each box Ј Ј pseudouridylation, both directed by small ribonucleo- referred to as C and D .
    [Show full text]
  • RNA Promotes the Formation of Spatial Compartments in the Nucleus
    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.25.267435; this version posted August 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. RNA promotes the formation of spatial compartments in the nucleus 1 1,2,5 1,5 1,5 Sofia A. Quinodoz , Prashant Bhat , Noah Ollikainen , Joanna W. Jachowicz , Abhik K. Banerjee1,3, Peter Chovanec1, Mario R. Blanco1, Amy Chow1, Yolanda Markaki4, Kathrin Plath4, and Mitchell Guttman1* (1) Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA (2) David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA (3) Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA (4) Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA (5) These authors contributed equally to this work. * To whom correspondence should be addressed. [email protected] (MG) bioRxiv preprint doi: https://doi.org/10.1101/2020.08.25.267435; this version posted August 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 SUMMARY 2 The nucleus is a highly organized arrangement of RNA, DNA, and protein molecules that are 3 compartmentalized within three-dimensional (3D) structures involved in shared functional and regulatory 4 processes. Although RNA has long been proposed to play a global role in organizing nuclear structure, 5 exploring the role of RNA in shaping nuclear structure has remained a challenge because no existing 6 methods can simultaneously measure RNA-RNA, RNA-DNA, and DNA-DNA contacts within 3D 7 structures.
    [Show full text]
  • A Minimal SMN Complex Facilitates Formation of Usnrnps in Drosophila Melanogaster
    Evolution of an RNP assembly system: A minimal SMN complex facilitates formation of UsnRNPs in Drosophila melanogaster Matthias Kroiss*, Jo¨ rg Schultz†, Julia Wiesner‡, Ashwin Chari*, Albert Sickmann‡, and Utz Fischer*§ Departments of *Biochemistry and †Bioinformatics, Theodor Boveri Institute, Biocenter, Am Hubland, 97074 Wu¨rzburg, Germany; and ‡Functional Genomics Group, Rudolf Virchow Center, Versbacher Strasse 9, 97078 Wu¨rzburg, Germany Edited by Kay E. Davies, University of Oxford, Oxford, United Kingdom, and accepted by the Editorial Board April 25, 2008 (received for review March 8, 2008) In vertebrates, assembly of spliceosomal uridine-rich small nuclear The SMN complex not only functions in the assembly of the ribonucleoproteins (UsnRNPs) is mediated by the SMN complex, a Sm core domain, but also influences additional steps in the macromolecular entity composed of the proteins SMN and Gemins biogenesis pathway of UsnRNPs. One such step is the nuclear 2–8. Here we have studied the evolution of this machinery using import of the assembled UsnRNP, which is mediated by the complete genome assemblies of multiple model organisms. The SMN complex (or parts thereof) in conjunction with the import SMN complex has gained complexity in evolution by a blockwise factor importin ␤ (9). In addition, specific UsnRNP proteins addition of Gemins onto an ancestral core complex composed of and the cap hypermethylase Tgs1 have been found in associa- SMN and Gemin2. In contrast to this overall evolutionary trend to tion of the SMN complex (10). This observation indicates that more complexity in metazoans, orthologs of most Gemins are the SMN complex coordinates various events during UsnRNP missing in dipterans.
    [Show full text]
  • Characterization of the RNA Exosome in Insect Cells
    Characterization of the RNA Exosome in Insect Cells Role in mRNA Surveillance Viktoria Hessle Doctoral Thesis Stockholm, 2011 Department of Molecular Biology and Functional Genomics Stockholm University, Sweden The cover picture shows an immunolabeling experiment with an antibody against the core exosome protein Rrp4 in a salivary gland cell of Chironomus tentans. Viktoria Hessle, 2011 ISBN 978-91-7447-208-0 Printed in Sweden by Universitetsservice US-AB Stockholm 2011 Distributor: Stockholm University Library 1 To my family 2 Table of Contents ABSTRACT ..............................................................................................................................4 LIST OF ARTICLES INCLUDED IN THIS THESIS ......................................................... 5 LIST OF ABBREVIATIONS.................................................................................................. 6 INTRODUCTION.................................................................................................................... 7 NUCLEAR ORGANIZATION IN EUKARYOTIC CELLS............................................... 7 The nuclear envelope, chromatin and the nucleolus ......................................................... 7 Subnuclear compartments ...............................................................................................10 EXPRESSION OF PROTEIN-CODING GENES IN EUKARYOTIC CELLS .............. 15 Co-transcriptional mRNA processing ............................................................................. 16 Coupling
    [Show full text]
  • The Role of Histone Modifications in the Regulation of Alternative Splicing During Epithelial-To-Mesenchymal Transition Alexandre Segelle
    The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition Alexandre Segelle To cite this version: Alexandre Segelle. The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition. Agricultural sciences. Université Montpellier, 2020. English. NNT : 2020MONTT017. tel-03137009 HAL Id: tel-03137009 https://tel.archives-ouvertes.fr/tel-03137009 Submitted on 10 Feb 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Biologie Moléculaire et Cellulaire École doctorale Sciences Chimiques et Biologiques pour la Santé (ED CBS2 168) Unité de recherche UMR9002 CNRS-UM – Institut de Génétique Humaine (IGH) The role of histone modifications in the regulation of alternative splicing during the epithelial-to-mesenchymal transition Présentée par Alexandre Segelle Le 28 Septembre 2020 Sous la direction de Reini Fernandez de Luco Devant le jury composé de Anne-Marie MARTINEZ,
    [Show full text]
  • Étude Des Dérégulations De L'épissage Alternatif Du Pré-ARN
    Étude des dérégulations de l’épissage alternatif du pré-ARN messager de la troponine T cardiaque humaine associées aux dystrophies myotoniques de types 1 et 2 et des caractéristiques du facteur d’épissage MBNL1 impliqué dans ces pathologies Audrey Vautrin To cite this version: Audrey Vautrin. Étude des dérégulations de l’épissage alternatif du pré-ARN messager de la troponine T cardiaque humaine associées aux dystrophies myotoniques de types 1 et 2 et des caractéristiques du facteur d’épissage MBNL1 impliqué dans ces pathologies. Médecine humaine et pathologie. Université Henri Poincaré - Nancy 1, 2011. Français. NNT : 2011NAN10141. tel-01746306 HAL Id: tel-01746306 https://hal.univ-lorraine.fr/tel-01746306 Submitted on 29 Mar 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. AVERTISSEMENT Ce document est le fruit d'un long travail approuvé par le jury de soutenance et mis à disposition de l'ensemble de la communauté universitaire élargie. Il est soumis à la propriété intellectuelle de l'auteur. Ceci implique une obligation de citation et de référencement lors de l’utilisation de ce document. D’autre part, toute contrefaçon, plagiat, reproduction illicite encourt une poursuite pénale.
    [Show full text]
  • NON-CODING Rnas
    CHAPTER 1 NON-CODING RNAs Alexander Donatha, Sven Findeißa, Jana Hertela, Manja Marza, Wolfgang Ottoa, Christine Schulzc, Peter F Stadlera,b,c,d, and Stefan Wirtha aBioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, H¨artelstrasse 16-18, D-01407, Leipzig, Germany bInstitute for Theoretical Chemistry, University of Vienna, W¨ahringerstraße 17, A-1090 Wien, Austria cFraunhofer Institute for Cell Therapy und Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany d Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA 1.1 INTRODUCTION The advent of high-throughput techniques that allow comprehensive unbiased studies of transcription has lead to a dramatic change in our understanding of genome organization. A decade ago, the genome was seen as a linear arrangement of separated individual genes which are predominantly protein-coding, with a small set of ancient non-coding “house- keeping” RNAs such as tRNA and rRNA dating all the way back to an RNA-World. How- ever, in contrast to this simple views more recent studies reveal a much more complex genomic picture. The ENCODE Pilot Project [239], the mouse cDNA project FANTOM [151], and a series of other large scale transcriptome studies, e.g. [202], leave no doubt that the mammalian transcriptome is characterized by a complex mosaic of overlapping, bi-directional transcripts and a plethora of non-protein coding transcripts arising from the same locus, Fig. 1.1. This newly discovered complexity is not unique to mammals. Similar high-throughput studies in invertebrate animals [152, 93] and plants [135] demonstrate the generality of the mammalian genome organization among higher eukaryotes.
    [Show full text]
  • RNA 2 -O-Methylation (Nm) Modification in Human Diseases
    G C A T T A C G G C A T genes Review RNA 20-O-Methylation (Nm) Modification in Human Diseases Dilyana G. Dimitrova, Laure Teysset and Clément Carré * Sorbonne Université, Institut de Biologie Paris Seine, Centre National de la Recherche Scientifique, Transgenerational Epigenetics & Small RNA Biology, Laboratoire de Biologie du Développement, 75005 Paris, France; [email protected] (D.G.D.); [email protected] (L.T.) * Correspondence: [email protected] Received: 17 December 2018; Accepted: 30 January 2019; Published: 5 February 2019 Abstract: Nm (20-O-methylation) is one of the most common modifications in the RNA world. It has the potential to influence the RNA molecules in multiple ways, such as structure, stability, and interactions, and to play a role in various cellular processes from epigenetic gene regulation, through translation to self versus non-self recognition. Yet, building scientific knowledge on the Nm matter has been hampered for a long time by the challenges in detecting and mapping this modification. Today, with the latest advancements in the area, more and more Nm sites are discovered on RNAs (tRNA, rRNA, mRNA, and small non-coding RNA) and linked to normal or pathological conditions. This review aims to synthesize the Nm-associated human diseases known to date and to tackle potential indirect links to some other biological defects. Keywords: RNA modifications; 20-O-methylation (Nm); human diseases; epitranscriptomics 1. Introduction 1.1. What is Nm/20-O-Methylation? 20-O-methylation (or Nm, where N stands for any nucleotide) is a co- or post-transcriptional 0 modification of RNA, where a methyl group (–CH3) is added to the 2 hydroxyl (–OH) of the ribose moiety (Figure1).
    [Show full text]