N4-Acetylcytidine and 5-Formylcytidine Are Present in Saccharomyces Cerevisiae Mrnas

Total Page:16

File Type:pdf, Size:1020Kb

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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Main text The presence of modified nucleosides was first reported in rRNAs and tRNAs over six decades ago1-2. To date over 100 RNA modifications have been identified across phylogeny3. These modifications are integral to biology and serve as crucial determinants of non-coding RNA structure and function4. There is a growing appreciation that RNA modifications are also found in coding messenger RNAs (mRNAs), and thus may potentially contribute to the stability and translation of mRNAs5-6. However, the specific 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. biological role, frequency and distribution of modified ribonucleosides in mRNAs is just being recognized. Although the list of chemical modifications present in mRNAs is growing, there are still fewer than 15 varieties7-8 of RNA chemical modifications known in mRNAs. Given the diversity of RNA chemical modifications found in non-coding RNA molecules, it is likely that the full catalog of RNA modifications present in mRNAs has not yet been uncovered. Recent advances in deep-sequencing technology unveiled the incorporation of a limited set of modifications in mRNAs including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A)9, and pseudouridine (Ψ)6, 10- 15. However, there is still some debate about the precise location and prevalence of several modifications; with m5C and m1A, in particular, being actively investigated. It is widely believed that mRNA modification is highly dynamic and likely serves as a gene regulation mechanism since the enzymatic incorporation of mRNA modifications has the potential to modulate mRNA stability and folding, protein-recruitment, and translation in a programmed manner3, 10, 16. However, much still remains to be understood about how the levels of modified mRNA nucleosides, resulting from either RNA damage or enzymatic incorporation, alter the stability, structure, function, and translatability of mRNAs. Here we seek to expand the variety of known nucleoside modifications present in mRNAs and to determine how the levels of specific mRNA modifications can be modulated. To accomplish this we examined the nucleoside modification profile of Sacchromyces cerevisiae mRNAs using high throughput ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)17 and quantified how the levels of modified mRNA nucleosides change in response to environmental stress. Our work reveals the presence of two chemical modifications previously not annotated in mRNAs, and evaluates if the levels of 12 mRNA modifications, identified by ourselves and others, are impacted by cellular stress. We find that the levels of nine modified nucleosides in mRNAs are altered under different environmental stress conditions, consistent with the idea that the mRNA epitranscriptome is not static. To determine the best conditions for purifying yeast mRNAs we tested four different purification schemes: single oligo-dT pull down, two oligo-dT bead pull-downs, single oligo-dT bead pull-down followed by a RiboZero rRNA depletion kit, and two oligo- dT pull downs followed by RiboZero depletion. Ultimately, we selected to use a two-step 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. protocol (oligo-dT pull-down followed by a RiboZero kit) because it yielded mRNAs of equal or greater purity than all other tested methods, and at a sufficient concentration for analysis. We first evaluated the quality and quantity of our mRNA samples by BioAnalyzer (Supplementary Figure S1). We then verified the purity of our isolated mRNA samples by qRT-PCR. Our qRT-PCR assays directly measured the levels of rRNAs (5S rRNA, 18S rRNA, 25S rRNA) and a diverse set of tRNAs mRNAs (tRNAArg,UCU, tRNAGlu,UUC, tRNASer,UGA). qRT-PCR data indicate that our mRNA samples lack rRNAs and are depleted of tRNAs (Figure 1 and Supplementary Table S1, Supporting Information). To further investigate the purity of our mRNA samples we used the results of our UPHLC-MS/MS assay, which contains many internal negative and positive controls. UHPLC-MS/MS is a powerful tool that allows us to simultaneously quantify the levels of multiple nucleosides with high accuracy, sensitivity and selectivity; quantifying modification levels down to attomolar concentrations (10-18 moles/L)17. We used this technique to measure the levels of 42 known RNA modifications simultaneously and assessed the levels of all modifications in mRNA samples relative to their levels in total RNA (level in mRNA/level in total RNA; Figure 1, Supplementary Table S2, and Supporting information). As positive controls we evaluated the levels of the widely accepted mRNA modifications N7-methylguanosine (m7G) and N6-methyladenosine (m6A). For comparison, we examined the levels of multiple modifications previously found in non-coding RNAs (e.g. N6-isopentyladenosine (i6A), 3-methyluridine (m3U), 5- methyluridine (m5U), 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine 1 3 2 1 (m acp Y), N2,N2-dimethylguanosine (m 2G), 1-methylguanosine (m G), dihydrouridine (D), andN2-dimethylguanosine (m2G)) (Supplementary Table S3). We find that m7G and m6A were retained at expected levels consistent with previous reports (40-90%), while the levels of the comparison non-coding RNA modifications are depleted below background (Figure 1 and Supporting Information). Since the distribution of modification levels is clearly bimodal, we can use a modification’s level to determine the likelihood that it is present in mRNA. The cut-off for considering modifications as in mRNA was based on modification retention in mRNAs, modification concentration, BioAnalyzer and qRT-PCR, as described in detail in the Supporting Information. Only three modifications previously identified as non-coding were retained in mRNAs at levels (80- 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. 90%) and concentrations comparable to m7G and m6A: formylcytidine (f5C), N4- acetylcytidine (ac4C) and 5-methylaminomethyluridine (mnm5U); these modifications are further scrutinized below (Figure 1 and Supplementary Table S2). We estimated the occurrence of each of the 42 modified nucleotides measured in our assay per mRNA (Supporting Information) and find that the most common modification in mRNAs is m7G (Supplementary Table S4). Our results indicate that m7G is incorporated roughly once per mRNA (~1.2-times per mRNA). This was not entirely unexpected because m7G recently been reported to be incorporated internally in mRNAs18. Similarly, the m6A prevalence we estimate, approximately once per every 1-2 mRNAs, is consistent with previous estimates based on transcriptome wide m6A mapping studies conducted in human cells9 (Supplementary Table S4). As mentioned above, we also found f5C, mnm5U and ac4C present every once every 1-10 mRNAs (Supplementary Table S4). Interestingly, both f5C and ac4C are conserved in all kingdoms of life, similar to 90% of the other mRNA modifications identified to date (Figure 2A). It is also clear how both modifications are made in cells; f5C is the oxidative product of m5C through 5-hydroxymethylcytidine (hm5C) 19 and ac4C is incorporated by the enzyme Rra120. In contrast, mnm5U has only been observed in bacteria and eukaryotes
Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Long Non-Coding RNA Epigenetics
    International Journal of Molecular Sciences Review Long Non-Coding RNA Epigenetics Marek Kazimierczyk and Jan Wrzesinski * Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Pozna´n,Poland; [email protected] * Correspondence: [email protected] Abstract: Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine–inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes. Keywords: lncRNA epigenetics; RNA modyfiing enzymes; detection modified nucleotides 1. General Remarks Citation: Kazimierczyk, M.; Although almost 80% of the human genome has been transcribed, only 2% of it Wrzesinski, J. Long Non-Coding RNA (mRNA) codes proteins [1,2]. All of the remaining RNAs belong to a vast group of noncod- Epigenetics. Int. J. Mol. Sci. 2021, 22, ing RNAs (ncRNAs). Based on their functions, ncRNAs can be classified as housekeeping 6166.
    [Show full text]
  • Ence of Pseudouridine (5-Ribosyluracil) and Uracil
    Journal of Clinical Investigation Vol. 41, No. 7, 1962 THE METABOLISM OF RING-LABELED OROTIC ACID IN MAN By S. M. WEISSMAN, A. Z. EISEN, H. FALLON, M. LEWIS AND M. KARON (From the Metabolism Service, Dermatology and Medicine Branches, National Cancer Institute, Bethesda, Md.) (Submitted for publication January 19, 1962; accepted March 29, 1962) Considerable knowledge concerning purine me- Total plasma and urine radioactivity was determined by tabolism has been obtained from chemical and first digesting the plasma or urine with an equal vol of isotopic studies of urinary uric acid. Correspond- 5 N KOH for 2 hours at 70° C, decolorizing with 1 to 2 drops of hydrogen peroxide, and counting 0.2 ml of this ing information in man is lacking for the closely digest in 20 ml of the toluene-methanol solution (8). In related field of pyrimidine metabolism. The avail- all cases counting efficiency was determined by the addi- ability of ring-labeled orotic acid as a specific tion of internal standards. pyrimidine precursor (1), together with the pres- Alternatively, radioactivity of urine was determined by ence of pseudouridine (5-ribosyluracil) and uracil, plating serial dilutions of each urine specimen on stainless steel cups, and extrapolating the count rates to infinite as specific end products of pyrimidine metabolism thinness. After the first 8 days, the count rate in total in man, in conveniently assayable amounts in urine was generally too low to be conveniently determined human urine (2-4), makes it possible to conduct directly. Extrapolations of total urine radioactivity were certain kinetic studies. In the present investiga- based on the assumption that total urine radioactivity had tion the metabolism of ring-labeled orotic acid and a constant ratio to urinary pseudouridine activity, since such parallelism was observed in days 3 through 8.
    [Show full text]
  • Characterization of UVA-Induced Alterations to Transfer RNA Sequences
    biomolecules Article Characterization of UVA-Induced Alterations to Transfer RNA Sequences Congliang Sun, Patrick A. Limbach and Balasubrahmanyam Addepalli * Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA; [email protected] (C.S.); [email protected] (P.A.L.) * Correspondence: [email protected] Received: 15 September 2020; Accepted: 5 November 2020; Published: 8 November 2020 Abstract: Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (tRNA) regions most vulnerable to photooxidation. Photooxidative damage to the anticodon and variable loop regions was consistently observed in both modified and unmodified sequences of tRNA upon UVA (λ 370 nm) exposure. The extent of oxidative damage measured in terms of oxidized guanosine, however, was higher in unmodified RNA compared to its modified version, suggesting an auxiliary role for nucleoside modifications. The type of oxidation product formed in the anticodon stem–loop region varied with the modification type, status, and whether the tRNA was inside or outside the cell during exposure. Oligonucleotide-based characterization of tRNA following UVA exposure also revealed the presence of novel photoproducts and stable intermediates not observed by nucleoside analysis alone. This approach provides sequence-specific information revealing potential hotspots for UVA-induced damage in tRNAs. Keywords: UVR; photooxidation; tRNA; post-transcriptional nucleoside modifications; cusativin; RNA modification mapping; RNA oxidation 1. Introduction Transfer RNAs (tRNAs) deliver amino acids to the site of ribosome-mediated protein synthesis while decoding the messenger RNA (mRNA).
    [Show full text]
  • Analysis of RNA Modifications by Second
    G C A T T A C G G C A T genes Review Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update Yuri Motorin 1,* and Virginie Marchand 2,* 1 Université de Lorraine, CNRS, IMoPA (UMR7365), F54000 Nancy, France 2 Université de Lorraine, CNRS, INSERM, IBSLor (UMS2008/US40), Epitranscriptomics and RNA Sequencing Core Facility, F54000 Nancy, France * Correspondence: [email protected] (Y.M.); [email protected] (V.M.); Tel.: +33-3-7274-6629 (Y.M.); +33-3-7274-6669 (V.M.) Abstract: The precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive m6A methylation in mRNAs, dozens of deep sequencing-based methods and protocols were proposed for the analysis of various RNA modifications, allowing us to considerably extend the list of detectable modified residues. Many of the currently used methods rely on the particular reverse transcription signatures left by RNA modifications in cDNA; these signatures may be naturally present or induced by an appropriate enzymatic or chemical treatment. The newest approaches also include labeling at RNA abasic sites that result from the selective removal of RNA modification or the enhanced cleavage of the RNA ribose-phosphate chain (perhaps also protection from cleavage), followed by specific adapter ligation. Classical affinity/immunoprecipitation-based protocols use either antibodies against modified RNA bases or proteins/enzymes, recognizing RNA modifications. In this survey, we review the most recent achievements in this highly dynamic field, including promising attempts to map RNA modifications by the direct single-molecule sequencing of RNA by nanopores.
    [Show full text]
  • FTO Levels Affect RNA Modification and the Transcriptome
    European Journal of Human Genetics (2013) 21, 317–323 & 2013 Macmillan Publishers Limited All rights reserved 1018-4813/13 www.nature.com/ejhg ARTICLE FTO levels affect RNA modification and the transcriptome Tea Berulava1, Matthias Ziehe2, Ludger Klein-Hitpass3, Emil Mladenov4,Ju¨rgen Thomale3, Ulrich Ru¨ther5 and Bernhard Horsthemke*,1 A block of single-nucleotide polymorphisms within intron 1 of the FTO (fat mass and obesity associated) gene is associated with variation in body weight. Previous works suggest that increased expression of FTO, which encodes a 2-oxoglutarate- dependent nucleic acid demethylase, leads to increased body weight, although the underlying mechanism has remained unclear. To elucidate the function of FTO, we examined the consequences of altered FTO levels in cultured cells and murine brain. Here we show that a knockdown of FTO in HEK293 cells affects the transcripts levels of genes involved in the response to starvation, whereas overexpression of FTO affects the transcript levels of genes related to RNA processing and metabolism. Subcellular localization of FTO further strengthens the latter notion. Using immunocytochemistry and confocal laser scanning microscopy, we detected FTO in nuclear speckles and – to a lesser and varying extent – in the nucleoplasm and nucleoli of HEK293, HeLa and MCF-7 cells. Moreover, RNA modification analyses revealed that loss of Fto affects the 3-methyluridine/ uridine and pseudouridine/uridine ratios in total brain RNA. We conclude that altered levels of FTO have multiple and diverse consequences on RNA modifications and the transcriptome. European Journal of Human Genetics (2013) 21, 317–323; doi:10.1038/ejhg.2012.168; published online 8 August 2012 Keywords: FTO; RNA modifications; nuclear speckles; transcriptome INTRODUCTION that FTO may modify rRNA.
    [Show full text]