High Throughput Detection of Pseudouridine: Caveats, Conundrums, and a Case for Open Science Maryam Zaringhalam
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SUPPLEMENTARY TABLE 1 Non-Destructive Characterisation Of
Electronic Supplementary Material (ESI) for Analyst. This journal is © The Royal Society of Chemistry 2016 SUPPLEMENTARY TABLE 1 Non-destructive characterisation of mesenchymal stem cell differentiation using LC-MS-based metabolite footprinting Amal Surrati 1, Rob Linforth 2, Ian Fisk 2, VirginieSottile1*, Dong-Hyun Kim 3*. 1Wolfson Centre for Stem Cells, Tissue, Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, CBS Building - University Park, Nottingham NG7 2RD (U.K.) 2Division of Food Sciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD (U.K.) 3Centre for Analytical Bioscience, Division of Molecular and Cellular Sciences, School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD (U.K.) *Correspondence to: Email: [email protected] Tel: +44 1158231235 Email: [email protected] Tel: +44 1157484697 Supplementary Table 1: Metabolites changed in MSC-conditioned medium compared to fresh medium (blank). ↑ indicates the metabolites that increased in all MSC-conditioned medium (control and OS) compared to their corresponding blanks, and ↓ indicates decreased metabolites. ID confidence: Metabolite identification level according to the metabolomics standards initiative 29,30 ; L1 – Level 1, L2 – Level 2. Change RT ID Identifier compared Exact mass Formula Putative metabolite (min) confidence (PubChem) to blank medium 179.0946 5.30 C10H13NO2 (-)-Salsolinol L2 91588 ↑ 358.1410 10.12 C20H22O6 (+)-Pinoresinol L2 7741 ↑ 148.0371 -
Investigation of Overhauser Effects Between Pseudouridine and Water Protons in RNA Helices
Investigation of Overhauser effects between pseudouridine and water protons in RNA helices Meredith I. Newby* and Nancy L. Greenbaum*†‡ *Department of Chemistry and Biochemistry and †Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390 Communicated by Michael Kasha, Florida State University, Tallahassee, FL, August 8, 2002 (received for review July 2, 2002) The inherent chemical properties of RNA molecules are expanded by posttranscriptional modification of specific nucleotides. Pseudouridine (), the most abundant of the modified bases, features an additional imino group, NH1, as compared with uri- dine. When forms a Watson–Crick base pair with adenine in an RNA helix, NH1 is positioned within the major groove. The pres- ence of often increases thermal stability of the helix or loop in which it is found [Hall, K. B. & McLaughlin, L. (1992) Nucleic Acids Res. 20, 1883–1889]. X-ray crystal structures of transfer RNAs [e.g., Arnez, J. & Steitz, T. (1994) Biochemistry 33, 7560–7567] have depicted water molecules bridging NH1 groups and nearby phos- phate oxygen atoms, but direct evidence for this interaction in solution has not been acquired. Toward this end, we have used a rotating-frame Overhauser effect spectroscopy-type NMR pulse sequence with a CLEAN chemical-exchange spectroscopy spin-lock pulse train [Hwang, T.-L., Mori, S., Shaka, A. J. & van Zijl, P. C. M. Fig. 1. Schematic structures of U and bases. R, ribose. The base is a uracil (1997) J. Am. Chem. Soc. 119, 6203–6204] to test for NH1–water rotated about the 3–6 ring axis, so that is has a COC base–sugar linkage and cross-relaxation effects within two RNA helices: (i) a complemen- an additional protonated ring nitrogen. -
The Human Ortholog of Archaeal Pus10 Produces Pseudouridine 54 in Select Trnas Where Its Recognition Sequence Contains a Modified Residue
Downloaded from rnajournal.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press The human ortholog of archaeal Pus10 produces pseudouridine 54 in select tRNAs where its recognition sequence contains a modified residue MANISHA DEOGHARIA,1 SHAONI MUKHOPADHYAY, ARCHI JOARDAR,2 and RAMESH GUPTA Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, Illinois 62901-4413, USA ABSTRACT The nearly conserved U54 of tRNA is mostly converted to a version of ribothymidine (T) in Bacteria and eukaryotes and to a version of pseudouridine (Ψ) in Archaea. Conserved U55 is nearly always modified to Ψ55 in all organisms. Orthologs of TrmA and TruB that produce T54 and Ψ55, respectively, in Bacteria and eukaryotes are absent in Archaea. Pus10 produces both Ψ54 and Ψ55 in Archaea. Pus10 orthologs are found in nearly all sequenced archaeal and most eukaryal genomes, but not in yeast and bacteria. This coincides with the presence of Ψ54 in most archaeal tRNAs and some animal tRNAs, but its absence from yeast and bacteria. Moreover, Ψ54 is found in several tRNAs that function as primers for retroviral DNA syn- thesis. Previously, no eukaryotic tRNA Ψ54 synthase had been identified. We show here that human Pus10 can produce Ψ54 in select tRNAs, including tRNALys3, the primer for HIV reverse transcriptase. This synthase activity of Pus10 is restrict- ed to the cytoplasm and is distinct from nuclear Pus10, which is known to be involved in apoptosis. The sequence GUUCAm1AAUC (m1A is 1-methyladenosine) at position 53–61 of tRNA along with a stable acceptor stem results in max- imum Ψ54 synthase activity. -
Pseudouridine Synthases Modify Human Pre-Mrna Co-Transcriptionally and Affect Splicing
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.29.273565; this version posted August 31, 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. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect splicing Authors: Nicole M. Martinez1, Amanda Su1, Julia K. Nussbacher2,3,4, Margaret C. Burns2,3,4, Cassandra Schaening5, Shashank Sathe2,3,4, Gene W. Yeo2,3,4* and Wendy V. Gilbert1* Authors and order TBD with final revision. Affiliations: 1Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA. 2Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA. 3Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA. 4Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA. 5Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. *Correspondence to: [email protected], [email protected] Abstract: Eukaryotic messenger RNAs are extensively decorated with modified nucleotides and the resulting epitranscriptome plays important regulatory roles in cells 1. Pseudouridine (Ψ) is a modified nucleotide that is prevalent in human mRNAs and can be dynamically regulated 2–5. However, it is unclear when in their life cycle RNAs become pseudouridylated and what the endogenous functions of mRNA pseudouridylation are. To determine if pseudouridine is added co-transcriptionally, we conducted pseudouridine profiling 2 on chromatin-associated RNA to reveal thousands of intronic pseudouridines in nascent pre-mRNA at locations that are significantly associated with alternatively spliced exons, enriched near splice sites, and overlap hundreds of binding sites for regulatory RNA binding proteins. -
Unveiling Structural and Functional Divergences Of
Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario Charles Bou-Nader, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, Djemel Hamdane To cite this version: Charles Bou-Nader, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, et al.. Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: per- spectives on the evolution scenario. Nucleic Acids Research, Oxford University Press, 2018, 46 (3), pp.1386-1394. 10.1093/nar/gkx1294. hal-01727508 HAL Id: hal-01727508 https://hal.sorbonne-universite.fr/hal-01727508 Submitted on 9 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. Distributed under a Creative Commons Attribution| 4.0 International License 1386–1394 Nucleic Acids Research, 2018, Vol. 46, No. 3 Published online 27 December 2017 doi: 10.1093/nar/gkx1294 Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario Charles -
N6-Methyladenosine (M6a) Is an Endogenous A3 Adenosine Receptor Ligand
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.21.391136; this version posted November 22, 2020. 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. N6-methyladenosine (m6A) is an endogenous A3 adenosine receptor ligand Akiko Ogawa,1, 2, 3 Chisae Nagiri,4, 13 Wataru Shihoya,4, 13 Asuka Inoue,5, 6, 7, 13 Kouki Kawakami,5 Suzune Hiratsuka,5 Junken Aoki,7, 8 Yasuhiro Ito,3 Takeo Suzuki,9 Tsutomu Suzuki,9 Toshihiro Inoue,3 Osamu Nureki,4 Hidenobu Tanihara,10 Kazuhito Tomizawa,2, 11 Fan-Yan Wei1, 2, 12, 14 1Department of Modomics Biology & Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai 980-8575, Japan. 2Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 3Department of Ophthalmology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 4Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.21.391136; this version posted November 22, 2020. 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. 5Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan. -
A Dissertation Entitled Ribonucleic Acids in Disease Etiology and Drug Discovery by Immaculate Sappy Submitted to the Graduate F
A Dissertation entitled Ribonucleic Acids in Disease Etiology and Drug Discovery by Immaculate Sappy Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Doctor of Philosophy Degree in Medicinal Chemistry ________________________________________ Amanda C. Bryant-Friedrich, Ph.D., Committee Chair ________________________________________ Zahoor A Shah, Ph.D., Committee Member ________________________________________ Steven M Peseckis, Ph.D., Committee Member ________________________________________ Caren Steinmiller, Ph.D., Committee Member ________________________________________ Amanda Bryant-Friedrich, PhD, Dean College of Graduate Studies The University of Toledo December 2019 Copyright 2019, Immaculate Sappy This document is copyrighted material. Under copyright law, no parts of this document may be reproduced without the expressed permission of the author. An Abstract of Ribonucleic Acids in Disease Etiology and Drug Discovery by Immaculate Sappy Submitted to the Graduate Faculty as partial fulfillment of the requirements for the Doctor of Philosophy Degree in Medicinal Chemistry The University of Toledo December 2019 Pseudouridine (Ψ), the 5-ribosyl isomer of uridine (U) is the most abundant nucleic acid modification found in all domains of life and all types of RNA. Studies have shown that, urinary levels of pseudouridine are higher in Alzheimer’s Disease (AD) patients and that RNA oxidation is a major component in the pathogenesis of Alzheimer’s Disease (AD) and other neurodegenerative disorders. Therefore, there is a potential correlation between higher urinary levels of pseudouridine in AD patients and oxidative stress. Hence, subjecting pseudouridine to oxidative conditions may provide some key information about the role of this nucleoside in RNA related processes and its role in disease etiology. Besides neurodegenerative disorders, antibiotic resistance is an additional threat to human health. -
Increased Excretion of Modified Adenine Nucleosides by Children with Adenosine Dearninase Deficiency
Pediatr. Res. 16: 362-369 (1982) Increased Excretion of Modified Adenine Nucleosides by Children with Adenosine Dearninase Deficiency ROCHELLE HIRSCHHORN,'"~ HOWARD RATECH, ARYE RUBINSTEIN, PHOTINI PAPAGEORGIOU, HERNANT KESARWALA, ERWIN GELFAND, AND VIVIEN ROEGNER-MANISCALCO Departments of Medicine and Pathology, New York University School of Medicine, New York, New York [R.H., H.R., and V.R.-M.];Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York [A.R.]; Department of Pediatrics, Rutgers University Medical ~chool,Piscataway, New Jersey [P.P., and H.K.]; and Department of Pediatrics, Hospital for Sick Children, Toronto, Ontario, Canada [E. G.] Summary tially in, and prevents proliferation of, irnmunocompetent cells, primarily of the T cell class (2, 5, 6, 23, 38, 49, 54). There is also We have identified seven adenine nucleosides in urines of un- in vivo and/or in vitro evidence for alternative mechanisms of treated adenosine deaminase (ADA) deficient patients, four of toxicity, which would operate via depletion of pyrimidine pools, which (adenosine, 2'-deoxyadenosine, 1-methyladenosine and N6- depletion of phosphoribosyl pyrophosphate and increases in cyclic methyladenosine) have been previously identified in urines of AMP or S-adenosyl homocysteine (16, 21, 24, 40, 46, 55). All of normals and/or ADA deficient patients. We confirm that ADA these mechanisms are dependent on accumulation of the substrates deficient patients excrete markedly increased amounts of 2'-deox- of ADA, adenosine and 2'-deoxyadenosine. yadenosine (582 k 363 versus normal of < 0.1 nmoles/mg creati- In addition to adenosine and 2'-deoxyadenosine, several other nine) and increased amounts of adenosine (29.4 & 5.7 versus modified adenine nucleosides occur naturally (17, 19) and are normal of 4.12 & 1.0 nmoles/mg creatinine). -
N4-Acetylcytidine and 5-Formylcytidine Are Present in Saccharomyces Cerevisiae Mrnas
bioRxiv preprint doi: https://doi.org/10.1101/327585; this version posted May 21, 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. N4-acetylcytidine and 5-formylcytidine are present in Saccharomyces cerevisiae mRNAs Mehmet Tardu1, Qishan Lin2, and Kristin S. Koutmou1* 1University of Michigan, Department of Chemistry, 930 N University, Ann Arbor, MI 48109, (734) 764-5650, [email protected], 2Mass Spectrometry Consortium for Epitranscriptomics, University at Albany, 1400 Washington Ave, Albany, NY 12222. Abstract Chemical modifications of RNAs have long been appreciated as key modulators of non-coding RNA structure and function. There is an emerging realization that chemical modification of protein-coding mRNAs also plays critical roles in the cell. Nonetheless, of the over 100 known RNA modifications found in biology only a handful have been identified in mRNAs. Here we use an ultra-high performance liquid chromatography- tandem mass spectrometry (UHPLC-MS/MS) method to identify and quantify modifications present in mRNAs of yeast cells. We detect the presence of four modified nucleosides in mRNAs at relatively high abundances: N7-methylguanosine, N6- methyladenosine, N4-acetylcytidine and 5-formylcytidine. Additionally, we investigate how the levels of mRNA modifications change in response to cellular stress. We find that the concentrations of nine mRNA modifications including N6-methyladenosine and N4- acetylcytidine change in response to heat stress, glucose starvation and/or oxidative stress. Our findings suggest that mRNA modification may provide a potential mechanism for cells to rapidly respond to environmental stressors. -
Modified Nucleosides, Nucleotides, and Nucleic
(19) TZZ ¥Z__T (11) EP 2 763 701 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: A61K 48/00 (2006.01) C07H 21/02 (2006.01) 19.12.2018 Bulletin 2018/51 C07H 21/04 (2006.01) (21) Application number: 12838676.0 (86) International application number: PCT/US2012/058519 (22) Date of filing: 03.10.2012 (87) International publication number: WO 2013/052523 (11.04.2013 Gazette 2013/15) (54) MODIFIED NUCLEOSIDES, NUCLEOTIDES, AND NUCLEIC ACIDS, AND USES THEREOF MODIFIZIERTE NUKLEOSIDE, NUKLEOTIDE UND NUKLEINSÄUREN UND VERWENDUNGEN DAVON NUCLÉOSIDES, NUCLÉOTIDES ET ACIDES NUCLÉIQUES MODIFIÉS, ET LEURS UTILISATIONS (84) Designated Contracting States: (74) Representative: Hoffmann Eitle AL AT BE BG CH CY CZ DE DK EE ES FI FR GB Patent- und Rechtsanwälte PartmbB GR HR HU IE IS IT LI LT LU LV MC MK MT NL NO Arabellastraße 30 PL PT RO RS SE SI SK SM TR 81925 München (DE) Designated Extension States: BA ME (56) References cited: WO-A2-2011/012316 US-A1- 2010 047 261 (30) Priority: 03.10.2011 US 201161542533 P US-A1- 2011 143 397 US-A1- 2012 251 618 (43) Date of publication of application: • KARIKÓ KATALIN ET AL: "Incorporation of 13.08.2014 Bulletin 2014/33 pseudouridine into mRNA yields superior nonimmunogenic vector with increased (73) Proprietor: Moderna Therapeutics, Inc. translational capacity and biological stability", Cambridge, Massachusetts 02141 (US) MOLECULAR THERAPY, NATURE PUBLISHING GROUP, GB, vol. 16, no. 11, 1 November 2008 (72) Inventors: (2008-11-01), pages 1833-1840, XP002598556, • DE FOUGEROLLES, Antonin ISSN: 1525-0024, DOI: 10.1038/MT.2008.200 Brookline, MA 02446 (US) [retrieved on 2008-09-16] •ROY,Atanu • LUIGI WARREN ET AL: "Highly efficient Stoneham, MA 02180 (US) reprogramming to pluripotency and directed • SCHRUM, Jason P. -
Pseudouridine-Mediated Translation Control of Mrna by Methionine Aminoacyl Trna Synthetase Ofri Levi and Yoav S
432–443 Nucleic Acids Research, 2021, Vol. 49, No. 1 Published online 10 December 2020 doi: 10.1093/nar/gkaa1178 Pseudouridine-mediated translation control of mRNA by methionine aminoacyl tRNA synthetase Ofri Levi and Yoav S. Arava * Faculty of Biology, Technion – Israel Institute of Technology, Haifa 3200003, Israel Received October 01, 2020; Revised November 06, 2020; Editorial Decision November 13, 2020; Accepted December 08, 2020 Downloaded from https://academic.oup.com/nar/article/49/1/432/6030234 by guest on 30 September 2021 ABSTRACT GRAPHICAL ABSTRACT Modification of nucleotides within an mRNA emerges as a key path for gene expression regulation. Pseu- douridine is one of the most common RNA modifica- tions; however, only a few mRNA modifiers have been identified to date, and no one mRNA pseudouridine reader is known. Here, we applied a novel genome- wide approach to identify mRNA regions that are bound by yeast methionine aminoacyl tRNAMet syn- thetase (MetRS). We found a clear enrichment to regions that were previously described to contain pseudouridine (). Follow-up in vitro and in vivo analyses on a prime target (position 1074 within YEF3 mRNA) demonstrated the importance of pseudouri- dine for MetRS binding. Furthermore, polysomal and INTRODUCTION protein analyses revealed that 1074 mediates trans- Over the past decades, >100 post-transcriptional RNA lation. Modification of this site occurs presumably by modifications have been identified in all kingdoms oflife(1). Pus6, a pseudouridine synthetase known to modify One of the most common RNA modifications in living cells MetRS cognate tRNA. Consistently, the deletion of is pseudouridine ()(2,3). The isomerization of uridine to Pus6 leads to a decrease in MetRS association with pseudouridine has a similar base pairing as uridine, yet it both tRNAMet and YEF3 mRNA. -
An Atlas of RNA Base Pairs Involving Modified Nucleobases with Optimal Geometries and Accurate Energies
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies Item Type Article Authors Chawla, Mohit; Oliva, R.; Bujnicki, J. M.; Cavallo, Luigi Citation An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies 2015 Nucleic Acids Research Eprint version Publisher's Version/PDF DOI 10.1093/nar/gkv606 Publisher Oxford University Press (OUP) Journal Nucleic Acids Research Rights This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Download date 26/09/2021 02:06:18 Link to Item http://hdl.handle.net/10754/558768 Nucleic Acids Research Advance Access published June 27, 2015 Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv606 An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies Mohit Chawla1, Romina Oliva2,*, Janusz M. Bujnicki3,4 and Luigi Cavallo1,* 1King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia, 2Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy, 3Laboratory of Bioinformatics and Protein Downloaded from Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland and 4Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland Received March 31, 2015; Revised May 27, 2015; Accepted May 28, 2015 http://nar.oxfordjournals.org/ ABSTRACT translational regulation, up to the tuning of cellular dif- ferentiation and development.