3,759
Views
20
CrossRef citations to date
0
Altmetric
Review

Detection of nucleic acid modifications by chemical reagents

&
Pages 1166-1174 | Received 19 Sep 2016, Accepted 11 Nov 2016, Published online: 24 Dec 2016

References

  • Bakin A, Ofengand J. Four newly located pseudouridylate residues in Escherichia coli 23S ribosomal RNA are all at the peptidyltransferase center: analysis by the application of a new sequencing technique. Biochemistry 1993; 32(37):9754-62. Epub 1993/09/21; PMID:8373778; http://dx.doi.org/10.1021/bi00088a030
  • Li X, Zhu P, Ma S, Song J, Bai J, Sun F, Yi C. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat Chem Biol 2015; 11(8):592-7; PMID:26075521; http://dx.doi.org/10.1038/nchembio.1836
  • Durairaj A, Limbach PA. Improving CMC-derivatization of pseudouridine in RNA for mass spectrometric detection. Analytica Chimica Acta 2008; 612(2):173-81; PMID:18358863; http://dx.doi.org/10.1016/j.aca.2008.02.026
  • Carlile TM, Rojas-Duran MF, Zinshteyn B, Shin H, Bartoli KM, Gilbert WV. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 2014; 515(7525):143-6; PMID:25192136; http://dx.doi.org/10.1038/nature13802
  • Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, Leon-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 2014; 159(1):148-62; PMID:25219674; http://dx.doi.org/10.1016/j.cell.2014.08.028
  • Lovejoy AF, Riordan DP, Brown PO. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 2014; 9(10):e110799; http://dx.doi.org/10.1371/journal.pone.0110799
  • Schaefer M, Pollex T, Hanna K, Lyko F. RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Res 2009; 37(2):e12. Epub 2008/12/09; PMID:19059995; http://dx.doi.org/10.1093/nar/gkn954
  • Behm-Ansmant I, Helm M, Motorin Y. Use of specific chemical reagents for detection of modified nucleotides in RNA. J Nucleic Acids 2011; 2011:408053; PMID:21716696; http://dx.doi.org/10.4061/2011/408053
  • Watson BS, Hazlett TL, Eccleston JF, Davis C, Jameson DM, Johnson AE. Macromolecular arrangement in the aminoacyl-tRNA.elongation factor Tu.GTP ternary complex. A fluorescence energy transfer study. Biochemistry 1995; 34(24):7904-12. Epub 1995/06/20; PMID:7794902; http://dx.doi.org/10.1021/bi00024a015
  • Caron M, Dugas H. Specific spin-labeling of transfer ribonucleic acid molecules. Nucleic Acids Res 1976; 3(1):19-34. Epub 1976/01/01; PMID:175353; http://dx.doi.org/10.1093/nar/3.1.19
  • Yang CH, Soll D. Covalent attachment of a fluorescent group to 4-thiouridine in transfer RNA. J Biochem 1973; 73(6):1243-7. Epub 1973/06/01; PMID:4579541
  • Umemoto T, Okamoto A. Synthesis and characterization of the 5-methyl-2′-deoxycytidine glycol-dioxoosmium-bipyridine ternary complex in DNA. Org Biomol Chem 2008; 6(2):269-71; PMID:18174995; http://dx.doi.org/10.1039/B716400A
  • Tserovski L, Helm M. Diastereoselectivity of 5-Methyluridine Osmylation Is Inverted inside an RNA Chain. Bioconjug Chem 2016; 27(9):2188-97; PMID:27540864; http://dx.doi.org/10.1021/acs.bioconjchem.6b00403
  • Gornicki P, Judek M, Wolanski A, Krzyzosiak WJ. Hypermodified nucleoside carboxyl group as a target site for specific tRNA modification. Eur J Biochem 1986; 155(2):371-5; PMID:3956493; http://dx.doi.org/10.1111/j.1432-1033.1986.tb09500.x
  • Pingoud A, Kownatzki R, Maass G. Fluoresceinylthiocarbamyl-tRNATyr: a useful derivative of tRNATyr (E.coli) for physicochemical studies. Nucleic Acids Res 1977; 4(2):327-38. Epub 1977/02/01; PMID:14327; http://dx.doi.org/10.1093/nar/4.2.327
  • Plumbridge JA, Baumert HG, Ehrenberg M, Rigler R. Characterisation of a new, fully active fluorescent derivative of E. coli tRNA Phe. Nucleic Acids Res 1980; 8(4):827-43; PMID:6776491
  • Schiller PW, Schechter AN. Covalent attachment of fluorescent probes to the X-base of Escherichia coli phenylalanine transfer ribonucleic acid. Nucleic Acids Res 1977; 4(7):2161-7; PMID:333386; http://dx.doi.org/10.1093/nar/4.7.2161
  • Friedman S, Li HJ, Nakanishi K, Van Lear G. 3-(3-amino-3-carboxy-n-propyl)uridine. The structure of the nucleoside in Escherichia coli transfer ribonucleic acid that reacts with phenoxyacetoxysuccinimide. Biochemistry 1974; 13(14):2932-7; PMID:4601538; http://dx.doi.org/10.1021/bi00711a024
  • McIntosh AR, Caron M, Dugas H. A specific spin labeling of the anticodon of E. coli tRNA-Glu. Biochem Biophys Res Commun 1973; 55(4):1356-63; PMID:4358937; http://dx.doi.org/10.1016/S0006-291X(73)80043-9
  • Ho NW, Gilham PT. Reaction of pseudouridine and inosine with N-cyclohexyl-N';-beta-(4-methylmorpholinium)ethylcarbodiimide. Biochemistry 1971; 10(20):3651-7; PMID:4328867; http://dx.doi.org/10.1021/bi00796a002
  • Naylor R, Ho NW, Gilham PT. Selective chemical modifications of uridine and pseudouridine in polynucleotides and their effect on the specificities of ribonuclease and phosphodiesterases. J Am Chem Soc 1965; 87(18):4209-10; PMID:4284810; http://dx.doi.org/10.1021/ja01096a050
  • Mengel-Jorgensen J, Kirpekar F. Detection of pseudouridine and other modifications in tRNA by cyanoethylation and MALDI mass spectrometry. Nucleic Acids Res 2002; 30(23):e135. Epub 2002/12/06; PMID:12466567; http://dx.doi.org/10.1093/nar/gnf135
  • Emmerechts G, Herdewijn P, Rozenski J. Pseudouridine detection improvement by derivatization with methyl vinyl sulfone and capillary HPLC-mass spectrometry. J Chromatography B, Analytical technologies in the biomedical and life sciences 2005; 825(2):233-8. Epub 2005/07/21; PMID:16029966; http://dx.doi.org/10.1016/j.jchromb.2005.06.041
  • Sakurai M, Yano T, Kawabata H, Ueda H, Suzuki T. Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol 2010; 6(10):733-40; PMID:20835228; http://dx.doi.org/10.1038/nchembio.434
  • Yang C, Soll D. Covalent attachment of fluorescent groups to transfer ribonucleic acid. Reactions with 4-bromomethyl-7-methoxy-2-oxo-2H-benzopyran. Biochemistry 1974; 13(17):3615-21. Epub 1974/08/13; PMID:4367729; http://dx.doi.org/10.1021/bi00714a033
  • Kellner S, Seidu-Larry S, Burhenne J, Motorin Y, Helm M. A multifunctional bioconjugate module for versatile photoaffinity labeling and click chemistry of RNA. Nucleic Acids Res 2011; 39(16):7348-60; PMID:21646334; http://dx.doi.org/10.1093/nar/gkr449
  • Wilkinson KA, Merino EJ, Weeks KM. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 2006; 1(3):1610-6; PMID:17406453; http://dx.doi.org/10.1038/nprot.2006.249
  • Hayatsu H. Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis–a personal account. Proc Japan Academy Series B, Physical and Biol Sci 2008; 84(8):321-30. Epub 2008/10/23; PMID:18941305; http://dx.doi.org/10.2183/pjab.84.321
  • Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 2012; 40(11):5023-33; PMID:22344696; http://dx.doi.org/10.1093/nar/gks144
  • Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R. Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet 2013; 9(6):e1003602; PMID:23825970; http://dx.doi.org/10.1371/journal.pgen.1003602
  • Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, et al. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep 2013; 4(2):255-61; PMID:23871666; http://dx.doi.org/10.1016/j.celrep.2013.06.029
  • Burgess AL, David R, Searle IR. Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae. BMC Plant Biol 2015; 15:199; PMID:26268215; http://dx.doi.org/10.1186/s12870-015-0580-8
  • Fukuzawa S, Takahashi S, Tachibana K, Tajima S, Suetake I. Simple and accurate single base resolution analysis of 5-hydroxymethylcytosine by catalytic oxidative bisulfite sequencing using micelle incarcerated oxidants. Bioorg Med Chem 2016; 24(18):4254-62; PMID:27460669; http://dx.doi.org/10.1016/j.bmc.2016.07.016
  • Song CX, Szulwach KE, Dai Q, Fu Y, Mao SQ, Lin L, Street C, Li Y, Poidevin M, Wu H, et al. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell 2013; 153(3):678-91; PMID:23602153; http://dx.doi.org/10.1016/j.cell.2013.04.001
  • Van Haute L, Dietmann S, Kremer L, Hussain S, Pearce SF, Powell CA, Rorbach J, Lantaff R, Blanco S, Sauer S, et al. Deficient methylation and formylation of mt-tRNA(Met) wobble cytosine in a patient carrying mutations in NSUN3. Nat Commun 2016; 7:12039; PMID:27356879; http://dx.doi.org/10.1038/ncomms12039
  • Haag S, Sloan KE, Ranjan N, Warda AS, Kretschmer J, Blessing C, Hübner B, Seikowski J, Dennerlein S, Rehling P, et al. NSUN3 and ABH1 modify the wobble position of mt-tRNAMet to expand codon recognition in mitochondrial translation. EMBO J 2016; 35(19):2104-19; PMID:27497299; http://dx.doi.org/10.15252/embj.201694885
  • Neri F, Incarnato D, Krepelova A, Parlato C, Oliviero S. Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis. Nat Protoc 2016; 11(7):1191-205; PMID:27281647; http://dx.doi.org/10.1038/nprot.2016.063
  • Cozen AE, Quartley E, Holmes AD, Hrabeta-Robinson E, Phizicky EM, Lowe TM. ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments. Nat Methods 2015; 12(9):879-84; PMID:26237225; http://dx.doi.org/10.1038/nmeth.3508
  • Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T. Efficient and quantitative high-throughput TRNA sequencing. Nat Methods 2015; 12(9):835-7; PMID:26214130; http://dx.doi.org/10.1038/nmeth.3478
  • Macon JB, Wolfenden R. 1-Methyladenosine. Dimroth rearrangement and reversible reduction. Biochemistry 1968; 7(10):3453-8; PMID:5681457; http://dx.doi.org/10.1021/bi00850a021
  • Dominissini D, Nachtergaele S, Moshitch-Moshkovitz S, Peer E, Kol N, Ben-Haim MS, Dai Q, Di Segni A, Salmon-Divon M, Clark WC, et al. The dynamic N(1)-methyladenosine methylome in eukaryotic messenger RNA. Nature 2016; 530(7591):441-6; PMID:26863196; http://dx.doi.org/10.1038/nature16998
  • Wintermeyer W, Zachau HG. A specific chemical chain scission of tRNA at 7-methylguanosine. FEBS Lett 1970; 11(3):160-4; PMID:11945476; http://dx.doi.org/10.1016/0014-5793(70)80518-X
  • Igo-Kemenes T, Zachau HG. On the specificity of the reduction of transfer ribonucleic acids with sodium borohydride. Eur J Biochem 1969; 10(3):549-56; PMID:4899928; http://dx.doi.org/10.1111/j.1432-1033.1969.tb00723.x
  • Peattie DA. Direct chemical method for sequencing RNA. Proc Natl Acad Sci U S A 1979; 76(4):1760-4; PMID:377283; http://dx.doi.org/10.1073/pnas.76.4.1760
  • Duh JL, Punzalan RR, Pless RC. Reactivity of pyrimidine nucleosides under the conditions of the pyrimidine sequencing reactions of Maxam and Gilbert. Anal Biochem 1988; 168(2):231-8; PMID:3364724; http://dx.doi.org/10.1016/0003-2697(88)90312-0
  • Marchand V, Blanloeil-Oillo F, Helm M, Motorin Y. Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA. Nucleic Acids Res 2016; 44(16):e135; PMID:27302133; http://dx.doi.org/10.1093/nar/gkw547
  • Krogh N, Jansson MD, Hafner SJ, Tehler D, Birkedal U, Christensen-Dalsgaard M, Lund AH, Nielsen H. Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Res 2016; 44(16):7884-95; PMID:27257078; http://dx.doi.org/10.1093/nar/gkw482
  • Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angew Chem Int Ed Engl 2015; 54(2):451-5; PMID:25417815; http://dx.doi.org/10.1002/anie.201408362
  • Thiebe R, Zachau HG. A specific modification next to the anticodon of phenylalanine transfer ribonucleic acid. Eur J Biochem 1968; 5(4):546-55; PMID:5698615; http://dx.doi.org/10.1111/j.1432-1033.1968.tb00404.x
  • Melvin WT, Milne HB, Slater AA, Allen HJ, Keir HM. Incorporation of 6-thioguanosine and 4-thiouridine into RNA. Application to isolation of newly synthesised RNA by affinity chromatography. Eur J Biochem 1978; 92(2):373-9; PMID:570106; http://dx.doi.org/10.1111/j.1432-1033.1978.tb12756.x
  • Reeve AE, Smith MM, Pigiet V, Huang RC. Incorporation of purine nucleoside 5′-[gamma-S]triphosphates as affinity probes for initiation of RNA synthesis in vitro. Biochemistry 1977; 16(20):4464-70; PMID:334243; http://dx.doi.org/10.1021/bi00639a021
  • Ching WM, Stadtman TC. Selenium-containing tRNAGlu from Clostridium sticklandii: correlation of aminoacylation with selenium content. Proc Natl Acad Sci U S A 1982; 79(2):374-7; PMID:6176991; http://dx.doi.org/10.1073/pnas.79.2.374
  • Woodford TA, Schlegel R, Pardee AB. Selective isolation of newly synthesized mammalian mRNA after in vivo labeling with 4-thiouridine or 6-thioguanosine. Anal Biochem 1988; 171(1):166-72; PMID:3407913; http://dx.doi.org/10.1016/0003-2697(88)90138-8
  • Igloi GL. Interaction of tRNAs and of phosphorothioate-substituted nucleic acids with an organomercurial. Probing the chemical environment of thiolated residues by affinity electrophoresis. Biochemistry 1988; 27(10):3842-9; PMID:3044450; http://dx.doi.org/10.1021/bi00410a048
  • Biondi E, Burke DH. Separating and analyzing sulfur-containing RNAs with organomercury gels. Methods Mol Biol 2012; 883:111-20; PMID:22589128; http://dx.doi.org/10.1007/978-1-61779-839-9_8
  • Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M. Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature 2009; 458(7235):228-32; PMID:19145231; http://dx.doi.org/10.1038/nature07643
  • Delaunay S, Rapino F, Tharun L, Zhou Z, Heukamp L, Termathe M, Shostak K, Klevernic I, Florin A, Desmecht H, et al. Elp3 links tRNA modification to IRES-dependent translation of LEF1 to sustain metastasis in breast cancer. J Exp Med 2016; 213(11):2503-2523; PMID:27811057; http://dx.doi.org/10.1084/jem.20160397
  • Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Mol Cell 2015; 59(5):858-66; PMID:26340425; http://dx.doi.org/10.1016/j.molcel.2015.07.023
  • Igloi GL, Kossel H. Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid. Nucleic Acids Res 1985; 13(19):6881-98; PMID:2414733; http://dx.doi.org/10.1093/nar/13.19.6881
  • Zaborske JM, DuMont VL, Wallace EW, Pan T, Aquadro CF, Drummond DA. A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. PLoS Biol 2014; 12(12):e1002015; PMID:25489848; http://dx.doi.org/10.1371/journal.pbio.1002015
  • Cahova H, Winz ML, Hofer K, Nubel G, Jaschke A. NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs. Nature 2015; 519(7543):374-7; PMID:25533955; http://dx.doi.org/10.1038/nature14020
  • Nubel G, Sorgenfrei FA, Jaschke A. Boronate affinity electrophoresis for the purification and analysis of cofactor-modified RNAs. Methods 2016; S1046-2023(16)30246-8; PMID:27645507; http://dx.doi.org/10.1016/j.ymeth.2016.09.008