DOCSLIB.ORG

Development of NMR Spectroscopic Methods for the Characterization of RNA

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Development of NMR Spectroscopic Methods for the Characterization of RNA Development of NMR spectroscopic methods for the characterization of RNA Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich Biochemie, Chemie und Pharmazie der Johann Wolfgang Goethe-Universität in Frankfurt am Main von Robbin Schnieders aus Baden/Schweiz Frankfurt am Main 2020 (D30) vom Fachbereich Biochemie, Chemie und Pharmazie der Johann Wolfgang Goethe- Universität als Dissertation angenommen Dekan: Prof. Dr. Clemens Glaubitz Erster Gutachter: Prof. Dr. Harald Schwalbe Zweiter Gutachter: Prof. Dr. Jens Wöhnert Datum der Disputation: Meiner Familie. TABLE OF CONTENTS Table of Contents SUMMARY 1 ZUSAMMENFASSUNG 5 LIST OF ABBREVIATIONS 11 CHAPTER I: GENERAL INTRODUCTION 13 1.1 NMR SPECTROSCOPY ON RNA – FROM MAJOR ACHIEVEMENTS TO CURRENT CHALLENGES 14 1.2 TOWARDS 13C-DETECTION 19 CHAPTER II: DEVELOPMENT OF 13C-DETECTED NMR EXPERIMENTS FOR AMINO GROUPS IN RNA 23 2.1 INTRODUCTION 24 2.1.1 FROM AMINO GROUP EXCHANGE AND ATTEMPTS TO REDUCE ITS EFFECTS 25 2.1.2 LEARNING FROM PROTEIN EXPERIMENTS 28 2.2 MATERIALS AND METHODS 30 2.2.1 THE RNAS UNDER STUDY 30 2.2.2 SAMPLE PREPARATION 30 2.2.3 NMR SPECTROSCOPY 32 2.2.4 STRUCTURE CALCULATION 32 2.3 RESULTS AND DISCUSSION 33 2.3.1 PULSE SEQUENCE ANALYSIS 33 2.3.2 OPTIMIZATION OF THE CN-TRANSFER DELAY 36 2.3.3 APPLICATION OF THE 13C-DETECTED C(N)H-HDQC EXPERIMENT 37 2.3.4 APPLICATION OF THE 13C-DETECTED “AMINO”-NOESY EXPERIMENT 43 2.4 CONCLUSION AND OUTLOOK 46 2.4.1 FROM DQ TO ZQ 48 2.4.2 THE C(N)H-HDQC EXPERIMENT FOR THE CHARACTERIZATION OF APO STATES 48 CHAPTER III: 15N-DETECTED H-N CORRELATION EXPERIMENTS FOR RNA 53 3.1 INTRODUCTION 54 3.1.1 TROSY IN AN N-H SPIN SYSTEM 55 3.2 MATERIALS AND METHODS 61 3.2.1 THE RNAS UNDER STUDY 61 3.2.2 SAMPLE PREPARATION 62 3.2.3 NMR SPECTROSCOPY 63 TABLE OF CONTENTS 3.3 RESULTS AND DISCUSSION 66 3.3.1 15N-DETECTED H-N CORRELATION EXPERIMENTS – WHICH ONE TO USE? 66 3.3.2 EFFECT OF MOLECULAR SIZE ON LINE WIDTHS 69 3.3.3 EFFECT OF MAGNETIC FIELD STRENGTH 73 3.4 CONCLUSIONS AND OUTLOOK 76 CHAPTER IV: STRUCTURAL CHARACTERIZATION OF RNA TETRALOOPS FOR FORCE FIELD CALIBRATION 79 4.1 INTRODUCTION 80 4.1.1 MD SIMULATIONS ON RNA 81 4.1.2 THE UUCG 14 NTS RNA STRUCTURES 81 4.1.3 NEW REFERENCE SYSTEMS – AN OVERVIEW 83 4.2 MATERIALS AND METHODS 86 4.2.1 THE RNAS UNDER STUDY 86 4.2.2 SAMPLE PREPARATION 86 4.2.3 NMR SPECTROSCOPY 90 4.2.4 STRUCTURE CALCULATION 90 4.3 RESULTS AND DISCUSSION 92 4.3.1 RESONANCE ASSIGNMENT OF THE 14 NTS RNA WITH GAAG TETRALOOP 92 4.3.2 RNA CONFORMATION – EXTERNAL INFLUENCES 96 4.3.3 DETERMINATION OF TORSION ANGLES IN RNA 100 4.3.4 ON THE WAY TO A THREE-DIMENSIONAL STRUCTURE – NOESY SPECTRA 107 4.3.5 THE STRUCTURE OF THE 14 NTS RNA WITH GAAG TETRALOOP 109 4.4 CONCLUSIONS AND OUTLOOK 111 REFERENCES 113 CHAPTER V: APPENDIX - SUPPORTING INFORMATION FOR 13C-DETECTION 123 5.1 DETAILED FIGURE CAPTIONS 126 5.1.1 EXPERIMENTAL PARAMETERS FOR SPECTRA IN FIGURE 19 126 5.1.2 EXPERIMENTAL PARAMETERS FOR SPECTRA IN FIGURE 25 127 5.2 34 NTS RNA – NEW NOE CONTACTS 128 5.3 PULSE PROGRAMS 128 5.3.1 13C-DETECTED AMINO-SELECTIVE CN-HSQC 128 5.3.2 13C-DETECTED C(N)H-HSQC EXPERIMENT 129 5.3.3 13C-DETECTED C(N)H-HDQC EXPERIMENT 131 5.3.4 13C-DETECTED “AMINO”-NOESY EXPERIMENT 132 CHAPTER VI: APPENDIX 2 - SUPPORTING INFORMATION FOR 15N-DETECTION 135 TABLE OF CONTENTS 6.1 DETAILED FIGURE CAPTIONS 137 6.1.1 EXPERIMENTAL PARAMETERS FOR SPECTRA IN FIGURE 34: 137 6.2 PULSE PROGRAMS 138 6.2.1 15N-DETECTED HSQC EXPERIMENT 138 6.2.2 15N-DETECTED TROSY EXPERIMENT 138 6.2.3 15N-DETECTED BEST-TROSY EXPERIMENT 140 CHAPTER VII: APPENDIX 3 - SUPPORTING INFORMATION FOR THE STRUCTURAL CHARACTERIZATION OF RNA TETRALOOPS 143 7.1 CHEMICAL SHIFT ASSIGNMENT OF THE 14 NTS RNA WITH GAAG TETRALOOP 143 7.1.1 EXPERIMENTAL DETAILS FOR EXPERIMENTS IN FIGURE 44 - FIGURE 46 143 7.1.2 RESONANCE OVERVIEW 144 7.2 TEMPERATURE-DEPENDENCE OF THE GAAG TETRALOOP 146 7.3 PULSE PROGRAMS 146 7.3.1 -HCNCH REFERENCE EXPERIMENT 146 7.3.2 -HCNCH CROSS EXPERIMENT 149 7.3.3 FORWARD DIRECTED HCC-TOCSY-CCH-E.COSY EXPERIMENT 151 7.3.4 2D -HCCH REFERENCE/ CROSS EXPERIMENT 153 7.4 COUPLING CONSTANTS AND CROSS-CORRELATED RELAXATION RATES 154 7.4.1 3J(H,H) COUPLING CONSTANTS 154 7.4.2 ΓCH, CHDD,DD CROSS-CORRELATED RELAXATION RATES 156 7.4.3 1J(C,H) COUPLING CONSTANTS 157 7.4.4 3J(C,P) AND 3J(H,P) COUPLING CONSTANTS 157 7.5 THE GAAG STRUCTURE 158 7.5.1 BASE PAIR PLANARITY AND HYDROGEN BOND RESTRAINTS 158 7.5.2 DIHEDRAL RESTRAINTS 159 7.5.3 NOESY PEAK LISTS 162 7.5.4 VIOLATIONS 171 ACKNOWLEDGEMENTS 173 PUBLICATIONS 175 CONFERENCE CONTRIBUTIONS 176 CURRICULUM VITAE 178 SUMMARY Summary This PhD thesis is dedicated to the extension of the portfolio of nuclear magnetic resonance (NMR) methods to characterize ribonucleic acids (RNAs). Only within the last few decades it has been realized that the cellular role of RNA goes well beyond the central dogma of molecular biology. In fact, RNA takes part in numerous cellular processes, executes numerous functions and acts either as a single player or in larger complexes, mostly RNA-protein complexes (RNPs) such as the ribosome or the spliceosome. This versatility in RNA function is coupled to a structural variety and the ability to adopt multiple long-lived and intricate conformations. Due to this high molecular complexity special demands are placed on the methods that are required for RNA structural characterization. With the ability to capture dynamics at atomic resolution and to measure under close to native conditions, NMR spectroscopy is undoubtedly a prime method for this purpose. A general introduction to the current state of research, selected achievements as well as challenges in the field of NMR spectroscopy on RNA is given in Chapter I. This thesis is further composed of three independent chapters covering the three separate projects, which form the main body of work within the course of this thesis. The imino group found in two of the four RNA nucleobases is generally considered to be the most powerful reporter group in the process of the NMR spectroscopic characterization of RNA. Its resonance assignment provides key information for a rapid determination of the RNA’s secondary structure. This is possible, since the imino proton can only be detected, if it is protected from rapid solvent exchange through hydrogen bonding interactions or, in rare cases, steric shielding. Consequently, information on flexible regions of RNA that are not protected against solvent exchange cannot be derived using this NMR spy. It is a key finding of the thesis that nucleobase interactions can also be mapped through the amino groups, as they similarly take part in base pairing or RNA- ligand interactions. Notably, solvent exchange of the amino protons is always slower compared to the imino proton. Thus, 1H,15N resonances of the amino group can be detected even for dynamic regions of RNA. Moreover, focusing on characterizing amino groups of RNA nucleobases increases the number of available reporters as amino groups are present in three out of four RNA nucleobases. However, there is a reason that up to work conducted in this thesis, amino groups have not been used for monitoring RNA nucleobases: the rate of the C-NH2 bond rotation is most often close to the chemical shift differences of the two non-identical amino proton resonances, in particular for guanosines and adenosines, amino resonances regularly remain elusive in NMR spectra. Therefore, we developed experiments that excite double 1 SUMMARY quantum (DQ) coherences of the two amino group protons and that further utilize 13C- detection. Results on these experiments are discussed in Chapter II and show that the rotational exchange can be avoided by evolving double quantum instead of single quantum (SQ) coherence in the indirect dimension of a 13C-detected C(N)H-HDQC experiment. The new experiment enables the detection of a full set of sharp amino resonances. The advantages of this experiment are immediately apparent when comparing the number of observable imino Figure I 1H,15N-HSQC vs. C(N)H-HDQC spectra. resonances in a classic 1H,15N-HSQC spectrum with the number of amino resonances obtained in the 13C-detected C(N)H- HDQC spectrum of the same RNA (Figure I). Furthermore, based on the newly available resonance assignment of amino groups, we developed a 13C-detected “amino”-NOESY experiment to obtain precious additional structural restraints. The 13C-detected “amino”-NOESY experiment enables the observation of NOE contacts that are not accessible using other 1H-detected NOESY experiment. Among these new NOE contacts are valuable, inter-residual correlations, which are otherwise scarce in RNA due to the proton deficiency of its nucleobases. We showed that the newly obtained NOE contacts are especially important in the structure determination of RNAs with only few NOE restraints. Under such circumstances, the inclusion of the newly obtained amino NOE contacts lead to a significant improvement in the root- mean-square deviation (RMSD) of the three-dimensional structure of the 34 nts GTP class II aptamer (Figure II). Together the novel 13C-detected NMR experiments developed within this PhD project provide a valuable alternative Figure II The impact of new amino NOE contacts.
Load more

Recommended publications
  • Life's Origins
    THE SEARCH FOR LIFE'S ORIGINS Progress and Future Directions in Planetary Biology and Chemical Evolution SPACE STUDIES BOARD Committee on Planetary Biology and Chemical Evolution Commission on Physical Sciences, Mathematics, and Applications National Research Council (NASA-CR-190929) THE SEARCH FCR N93-11603 LIFF'S nRIGINS: PROGRESS AND FUTURE DTR_CTI_NS IN PLANETARY biOLOgY AND CHEMICAL FVOLUTION (NAS-NRC) Unclas i59 p G3191 0125180 NATIONAL ACADEMY PRESS Washington, D.C. 1990 NATIONAL ACADEMY PRESS - 2101 Constitution Avenue, N.W. • Washington, D.C. 20418 NOTICE: The project that is the subject of this report was approved by the Governing Board of the National l_esearch Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special compe- tences and with regard for appropriate balance. This report has been reviewed by a group other than the authors according to procedures approved by a Report Review Committee consisting of members of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. Support for this project was provided by Contract NASW 4102 between the National Academy of Sciences and the National Aeronautics and Space Administration. Library of Congress Cataloging-in-Publication Data The Search for life's origins : progress and future directions in planetary biology and chemical evolution / Committee on Planetary Biology and Chemical Evolution. p. cm. Includes bibliographical references. Includes index. ISBN 0-309-04246-1 1. Life--Origin. 2. Space biology.
    [Show full text]
  • The Emerging Role of Ncrnas and RNA-Binding Proteins in Mitotic Apparatus Formation
    non-coding RNA Review The Emerging Role of ncRNAs and RNA-Binding Proteins in Mitotic Apparatus Formation Kei K. Ito, Koki Watanabe and Daiju Kitagawa * Department of Physiological Chemistry, Graduate School of Pharmaceutical Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan; [email protected] (K.K.I.); [email protected] (K.W.) * Correspondence: [email protected] Received: 11 November 2019; Accepted: 13 March 2020; Published: 20 March 2020 Abstract: Mounting experimental evidence shows that non-coding RNAs (ncRNAs) serve a wide variety of biological functions. Recent studies suggest that a part of ncRNAs are critically important for supporting the structure of subcellular architectures. Here, we summarize the current literature demonstrating the role of ncRNAs and RNA-binding proteins in regulating the assembly of mitotic apparatus, especially focusing on centrosomes, kinetochores, and mitotic spindles. Keywords: ncRNA; centrosome; kinetochore; mitotic spindle 1. Introduction Non-coding RNAs (ncRNAs) are defined as a class of RNA molecules that are transcribed from genomic DNA, but not translated into proteins. They are mainly classified into the following two categories according to their length—small RNA (<200 nt) and long non-coding RNA (lncRNA) (>200 nt). Small RNAs include traditional RNA molecules, such as transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), PIWI-interacting RNA (piRNA), and micro RNA (miRNA), and they have been studied extensively [1]. Research on lncRNA is behind that on small RNA despite that recent transcriptome analysis has revealed that more than 120,000 lncRNAs are generated from the human genome [2–4].
    [Show full text]
  • HERPESVIRAL MICRORNAS by SUNANTHA SETHURAMAN A
    DEREGULATION OF HUMAN LONG NONCODING RNAS BY ONCOGENIC GAMMA- HERPESVIRAL MICRORNAS By SUNANTHA SETHURAMAN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2017 © 2017 Sunantha Sethuraman To my parents, S Vijaya and K Sethuraman, and my brother S Srinivasan. ACKNOWLEDGMENTS I would like to acknowledge and thank all the people who have contributed directly and indirectly to my doctoral education and the work presented in this thesis. I would like to thank the members of the Renne laboratory, Dr. Rolf Renne, Dr. Peter Turner, Dr. Vaibhav Jain, Lauren Gay, Jackie Serfecz, Natalie Martinez and Merin Thomas, for making the lab an inspiring and fun environment. I am extremely thankful to my advisor Dr. Rolf Renne for being a mentor, a friend and a critique through the four years I have worked with him. I am also thankful to Dr. Peter Turner for carefully reviewing my manuscripts and this thesis. I would like to acknowledge the past members of the Renne laboratory, Dr. Irina Haecker and Dr. Hong Seok Choi. Dr. Irina Haecker is one of the most inspirational scientists I have met, who mentored me as a rotation student on the project that has now developed into my dissertation work. Dr. Hong Seok Choi, Dr. Vaibhav Jain and Lauren Gay have guided me with my experiments and made me a better scientist through the many scientific discussions. Jackie, Natalie and Merin have been amazing friends, and they make even a stressful day in the lab seem easy.
    [Show full text]
  • Ngs and Bioinformatics
    FÉDÉRER LA RECHERCHE ET L’INNOVATION MÉDICALE EN CANCÉROLOGIE NGS AND BIOINFORMATICS Yannick BOURSIN Jean-Charles CADORET Marc DELOGER M’Boyba DIOP Pierre GESTRAUD www.canceropole-idf.fr Jean-François OUIMETTE NGS & Cancer : Analyses RNA-Seq Nicolas SERVANT 7, 8, 9 novembre 2018 2 Outline 1- INTRODUCTION a) Sequencing technologies b) Sequencing library technologies c) Bioinformatics part of sequencing projects d) The RNA world e) RNA-seq usage in oncology 2- QUALITY CONTROLS ON RAW READS a) Raw reads formats b) Quality controls 3- SHORT READS ALIGNMENT AND QUALITY CONTROL a) Reads alignment b) Alignment formats c) Quality controls on aligned data d) And then ? NGS & Cancer : Analyses RNA-Seq 7, 8, 9 novembre 2018 A short introduction SEQUENCING TECHNOLOGIES NGS & Cancer : Analyses RNA-Seq 7, 8, 9 novembre 2018 4 NGS technologies S. Baulande, I. Curie NGS & Cancer : Analyses RNA-Seq 7, 8, 9 novembre 2018 5 Hiseq, Pacbio, PGM, … What does that mean ? Platform Provider Reads Max Reads Size Throughput Time Number (bp) (Gb) Novaseq Illumina 20000 M 2x150 6000 <3 days Hiseq X Illumina 6000 M 2x150 1800 <3 days Hiseq Illumina 5000 M 2x150 1500 <7 days NextSeq Illumina 400 M 2x150 120 <2days S5 Ion Torrent 80 M 200 15 2-4 hours MiSeq Illumina 25 M 2x300 15 40 hours MiniSeq Illumina 25 M 2x150 7.5 24 hours S5 Ion Torrent 12 M 600 4.5 2-4 hours PGM 318 Ion Torrent 4 M 400 >1 2-4 hours PGM 316 Ion Torrent 2 M 400 >0.1 2-4 hours PGM 314 Ion Torrent 0.5 M 400 >0.01 2-4 hours Sequel Pacific 385 K – 6M 20000 8 – 128 <6 hours Bioscience (1-16 cells) (1-16 cells) NGS & Cancer : Analyses RNA-Seq 7, 8, 9 novembre 2018 6 NGS Market (2013) http://enseqlopedia.com/ngs-mapped/ S.
    [Show full text]
  • RNA at the Heart of Gene Expression: Special Issue of BMB Reports 2017
    BMB Rep. 2017; 50(4): 157 BMB www.bmbreports.org Reports Editorial RNA at the heart of gene expression: Special issue of BMB Reports 2017 Over the past several decades, our knowledge of RNAs has discovered that transcripts harboring nonsense mutation are increased dramatically. In particular, the recent advances in degraded on mRNAs bound by a nuclear cap-binding complex next-generation sequencing, combined with crosslinking im- (CBC). Because NMD is tightly coupled to a translation event, munoprecipitation or other variants, has led to the expansion this observation indicates that CBC can direct mRNA trans- of a list of RNAs including long noncoding RNAs (lncRNAs) lation. The details for CBC-dependent translation and the and small regulatory RNAs such as microRNAs, short differences in regulatory mechanisms between CBC and interfering RNAs, and Piwi-interacting RNAs. Although only a eIF4E-dependent translations are reviewed by Dr. Incheol Ryu small number of previously unappreciated RNA roles have from Korea University in Korea, and myself. In addition, the begun to be revealed, it is a good time to introduce the recent efficiency of eIF4E-dependent translation is dynamically con- RNA advances and their related functions to readers. This trolled by 3’-untranslated region (3’UTR). Prof. Akio Yamashita special issue on RNA invites three perspectives, five mini- from Yokohama City University School of Medicine and Prof. reviews, and four research articles. The topics covered in this Osamu Takeuchi from Kyoto University in Japan introduce a special issue include microRNA-mediated gene silencing, the variety of regulatory mechanisms for eIF4E-dependent trans- molecular mechanism of nonsense-mediated mRNA decay lation by 3’UTR-binding proteins.
    [Show full text]
  • Phase Separations Driven by RNA Scaffolds and Protein Sequestration in FXTAS
    bioRxiv preprint doi: https://doi.org/10.1101/298943; this version posted May 15, 2018. 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. Teresa Botta-Orfila et al. Phase Separations Driven by RNA Scaffolds and Protein Sequestration in FXTAS Teresa Botta-Orfila1,2, Fernando Cid-Samper1,2, Mariona Gelabert-Baldrich1,2, Benjamin Lang1,2, Nieves Lorenzo-Gotor1,2, Riccardo Delli Ponti1,2, Lies-Anne WFM Severijnen3, Benedetta Bolognesi1,2, Ellen Gelpi4,5, Renate K. Hukema3 and Gian Gaetano Tartaglia1,2,6 1 Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain 2 Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain 3 Department of Clinical Genetics, Erasmus MC, 3000 CA Rotterdam, The Netherlands 4 Neurological Tissue Bank of the Biobanc-Hospital Clinic-IDIBAPS, Barcelona, Spain 5 Institute of Neurology, Medical University of Vienna, Vienna, Austria 6 Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Passeig Lluís Companys, 08010 Barcelona, Spain * To whom correspondence should be addressed. Tel: +34 93 316 01 16; Fax: +34 93 396 99 83; Email: [email protected] Keywords Scaffolding RNA, CGG repeat expansion, FMR1 premutation, Fragile-X associated tremor ataxia syndrome (FXTAS), RNA aggregates, RNA binding proteins (RBP), TRA2A splicing regulator, Neurodegeneration 1 bioRxiv preprint doi: https://doi.org/10.1101/298943; this version posted May 15, 2018. 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.
    [Show full text]
  • Regulation of Microrna Biogenesis and Turnover by Animals and Their Viruses
    Edinburgh Research Explorer Regulation of microRNA biogenesis and turnover by animals and their viruses Citation for published version: Buck, A, Libri, V, Miesen, P & van Rij, RP 2013, 'Regulation of microRNA biogenesis and turnover by animals and their viruses', Cellular and Molecular Life Sciences. https://doi.org/10.1007/s00018-012-1257-1 Digital Object Identifier (DOI): 10.1007/s00018-012-1257-1 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Cellular and Molecular Life Sciences Publisher Rights Statement: Gold Open Access paid General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 05. Oct. 2021 Cell. Mol. Life Sci. DOI 10.1007/s00018-012-1257-1 Cellular and Molecular Life Sciences REVIEW Regulation of microRNA biogenesis and turnover by animals and their viruses Valentina Libri • Pascal Miesen • Ronald P. van Rij • Amy H. Buck Received: 22 November 2012 / Revised: 27 December 2012 / Accepted: 27 December 2012 Ó The Author(s) 2013.
    [Show full text]
  • Small RNA-Mediated Regulation of Gene Expression in Escherichia Coli
    TILL MIN FAMILJ List of Publications Publications I-III This thesis is based on the following papers, which are referred to in the text as Paper I-III. I *Darfeuille, F., *Unoson, C., Vogel, J., and Wagner, E.G.H. (2007) An antisense RNA inhibits translation by competing with standby ribosomes. Molecular Cell, 26, 381-392 II Unoson, C., and Wagner, E.G.H. (2008) A small SOS-induced toxin is targeted against the inner membrane in Escherichia coli. Molecular Microbiology, 70(1), 258-270 III *Holmqvist, E., *Unoson, C., Reimegård, J., and Wagner, E.G.H. (2010) The small RNA MicF targets its own regulator Lrp and promotes a positive feedback loop. Manuscript *Shared first authorship Reprints were made with permission from the publishers. Some of the results presented in this thesis are not included in the publications listed above Additional publications Unoson, C., and Wagner, E.G.H. (2007) Dealing with stable structures at ribosome binding sites. RNA biology, 4:3, 113-117 (point of view) Contents Introduction................................................................................................... 11 A historical view of gene regulation and RNA research ......................... 11 Small RNAs in Escherichia coli .............................................................. 13 Antisense mechanisms ............................................................................. 14 Translation inhibition by targeting the TIR ............................................. 15 Degradation versus translation inhibition ...............................................
    [Show full text]
  • To Be Or Not to Be: Circular Rnas Or Mrnas from Circular Dnas? Frontiers in Genetics, 10, [940]
    To Be or Not to Be Circular RNAs or mRNAs From Circular DNAs? Iparraguirre, Leire; Prada-Luengo, Iñigo; Regenberg, Birgitte; Otaegui, David Published in: Frontiers in Genetics DOI: 10.3389/fgene.2019.00940 Publication date: 2019 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Iparraguirre, L., Prada-Luengo, I., Regenberg, B., & Otaegui, D. (2019). To Be or Not to Be: Circular RNAs or mRNAs From Circular DNAs? Frontiers in Genetics, 10, [940]. https://doi.org/10.3389/fgene.2019.00940 Download date: 27. sep.. 2021 PERSPECTIVE published: 11 October 2019 doi: 10.3389/fgene.2019.00940 To Be or Not to Be: Circular RNAs or mRNAs From Circular DNAs? Leire Iparraguirre 1†, Iñigo Prada-Luengo 2†, Birgitte Regenberg 2 and David Otaegui 1* 1 Neurosciences Area, Biodonostia Health Research Institute, San Sebastián, Spain, 2 Department of Biology, University of Copenhagen, Copenhagen, Denmark In recent years, there has been a growing interest in circular RNAs (circRNAs) since they are involved in a wide spectrum of cellular functions that might have a large impact on phenotype and disease. CircRNAs are mainly recorded by RNA-Seq and computational methods focused on the detection of back-splicing junction sequences considered the diagnostic feature of circRNAs. While some protocols remove linear RNA prior to sequencing, many have characterized circRNAs by sorting through total RNA sequencing data without excluding the possibility that some linear RNA can provide the same signal as a circRNA. Recent studies have revealed that circular DNAs of chromosomal origin are common in eukaryotic genomes and that they can be transcribed.
    [Show full text]
  • Definition and Identification of Small RNA Sponges: Focus on Mirna Sequestration Mélodie Migault, Emmanuelle Donnou-Fournet, Marie-Dominique Galibert, David Gilot
    Definition and identification of small RNA sponges: Focus on miRNA sequestration Mélodie Migault, Emmanuelle Donnou-Fournet, Marie-Dominique Galibert, David Gilot To cite this version: Mélodie Migault, Emmanuelle Donnou-Fournet, Marie-Dominique Galibert, David Gilot. Definition and identification of small RNA sponges: Focus on miRNA sequestration. Methods, Elsevier, 2017, 117, pp.35-47. 10.1016/j.ymeth.2016.11.012. hal-01502131 HAL Id: hal-01502131 https://hal-univ-rennes1.archives-ouvertes.fr/hal-01502131 Submitted on 5 Apr 2017 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. Definition and identification of small RNA sponges: focus on miRNA sequestration Mélodie Migaulta,b,c,‡, Emmanuelle Donnou-Fourneta,b,c,‡, Marie-Dominique Galiberta,b,c,d,* & David Gilota,b,c,* aCentre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 6290, Institut de Génétique et Développement de Rennes, France bUniversité de Rennes 1, Rennes, France c Cancer Research Association (ARC) Labelled Team dDepartment of Medical Genomic, Rennes University Hospital, Rennes, France. ‡Co-first authors *Address: CNRS UMR6290, IGDR, Université de Rennes 1, 2 avenue Pr Léon Bernard, 35043, Rennes, France. Fax: +33 (0) 223234478 E-mail addresses: [email protected] or [email protected] ABSTRACT Targeting RNAs appears as an important opportunity to modulate biological processes.
    [Show full text]
  • Synergistic Roles of Eukaryotic Translation Elongation Factors 1Bγ
    University of Kentucky UKnowledge Plant Pathology Faculty Publications Plant Pathology 12-15-2011 Synergistic roles of eukaryotic translation elongation factors 1Bγ and 1A in stimulation of tombusvirus minus-strand synthesis Zsuzsanna Sasvari University of Kentucky, [email protected] Lara Izotova University of Medicine and Dentistry of New Jersey Terri Goss Kinzy University of Medicine and Dentistry of New Jersey Peter D. Nagy University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits oy u. Follow this and additional works at: https://uknowledge.uky.edu/plantpath_facpub Part of the Plant Pathology Commons Repository Citation Sasvari, Zsuzsanna; Izotova, Lara; Kinzy, Terri Goss; and Nagy, Peter D., "Synergistic roles of eukaryotic translation elongation factors 1Bγ and 1A in stimulation of tombusvirus minus-strand synthesis" (2011). Plant Pathology Faculty Publications. 8. https://uknowledge.uky.edu/plantpath_facpub/8 This Article is brought to you for free and open access by the Plant Pathology at UKnowledge. It has been accepted for inclusion in Plant Pathology Faculty Publications by an authorized administrator of UKnowledge. For more information, please contact [email protected]. Synergistic roles of eukaryotic translation elongation factors 1Bγ and 1A in stimulation of tombusvirus minus- strand synthesis Notes/Citation Information Published in PLoS Pathogens, v. 7, no. 12, e1002438. © 2011 Sasvari et al. This is an open-access article distributed
    [Show full text]
  • This Thesis Has Been Submitted in Fulfilment of the Requirements for a Postgraduate Degree (E.G
    This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Identifying novel targets for the snoRNA class of stable non-coding RNAs Rosie Peters Thesis presented for the degree of Doctor of Philosophy University of Edinburgh 2018 1 DECLARATION I declare that this thesis was composed by myself. The research in this thesis is my own, unless otherwise stated, and has not been submitted for any other degree or professional qualification. Rosie Peters 2 ACKNOWLEDGEMENTS I would first like to thank my supervisor, David, for his help and guidance throughout the PhD project. Many thanks to Tanya, for her supervision in the lab and her advice throughout, and also to Hywel, for all of his work and assistance in bioinformatics. I’d like to thank everyone in the Tollervey lab - past and present - for their advice, and whose work provided the foundation on which to develop my research.
    [Show full text]