Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague Czech Republic

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Breitbart M, Rohwer F. 2005. Here a virus, there a virus, everywhere the same virus? Trends Microbiol 13:278–284. doi:10.1016/j.tim.2005.04.003. PubMed DOI

Baltimore D. 1971. Expression of animal virus genomes. Bacteriol Rev 35:235–241. doi:10.1128/MMBR.35.3.235-241.1971. PubMed DOI PMC

King AMQ, Lefkowitz E, Adams MJ, Carstens EB. 2011. Virus taxonomy. Elsevier, Amsterdam, the Netherlands.

Walsh D, Mathews MB, Mohr I. 2013. Tinkering with translation: protein synthesis in virus-infected cells. Cold Spring Harb Perspect Biol 5:a012351. doi:10.1101/cshperspect.a012351. PubMed DOI PMC

Bushell M, Sarnow P. 2002. Hijacking the translation apparatus by RNA viruses. J Cell Biol 158:395–399. doi:10.1083/jcb.200205044. PubMed DOI PMC

López-Lastra M, Ramdohr P, Letelier A, Vallejos M, Vera-Otarola J, Valiente-Echeverrkía F. 2010. Translation initiation of viral mRNAs. Rev Med Virol 20:177–195. doi:10.1002/rmv.649. PubMed DOI PMC

Nicholson BL, White KA. 2015. Exploring the architecture of viral RNA genomes. Curr Opin Virol 12:66–74. doi:10.1016/j.coviro.2015.03.018. PubMed DOI

Cross ST, Michalski D, Miller MR, Wilusz J. 2019. RNA regulatory processes in RNA virus biology. Wiley Interdiscip Rev RNA 10:e1536. doi:10.1002/wrna.1536. PubMed DOI PMC

Limbach PA, Crain PF, McCloskey JA. 1994. Summary: the modified nucleosides of RNA. Nucleic Acids Res 22:2183–2196. doi:10.1093/nar/22.12.2183. PubMed DOI PMC

Davis FF, Allen FW. 1957. Ribonucleic acids from yeast which contain a fifth nucleotide. J Biol Chem 227:907–915. PubMed

Roundtree IA, Evans ME, Pan T, He C. 2017. Dynamic RNA modifications in gene expression regulation. Cell 169:1187–1200. doi:10.1016/j.cell.2017.05.045. PubMed DOI PMC

Baudin-Baillieu A, Fabret C, Liang XH, Piekna-Przybylska D, Fournier MJ, Rousset JP. 2009. Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy. Nucleic Acids Res 37:7665–7677. doi:10.1093/nar/gkp816. PubMed DOI PMC

Boccaletto P, MacHnicka MA, Purta E, Pitkowski P, Baginski B, Wirecki TK, De Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM. 2018. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. PubMed PMC

Helm M, Alfonzo JD. 2014. Posttranscriptional RNA modifications: playing metabolic games in a cell’s chemical legoland. Chem Biol 21:174–185. doi:10.1016/j.chembiol.2013.10.015. PubMed DOI PMC

Phizicky EM, Alfonzo JD. 2010. Do all modifications benefit all tRNAs? FEBS Lett 584:265–271. doi:10.1016/j.febslet.2009.11.049. PubMed DOI PMC

Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE. 2012. The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol 13:175. doi:10.1186/gb-2012-13-10-175. PubMed DOI PMC

Li S, Mason CE. 2014. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet 15:127–150. doi:10.1146/annurev-genom-090413-025405. PubMed DOI

Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. 2012. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149:1635–1646. doi:10.1016/j.cell.2012.05.003. PubMed DOI PMC

Finka A, Sood V, Quadroni M, De Los Rios PDL, Goloubinoff P. 2015. Quantitative proteomics of heat-treated human cells show an across-the-board mild depletion of housekeeping proteins to massively accumulate few HSPs. Cell Stress Chaperones 20:605–620. doi:10.1007/s12192-015-0583-2. PubMed DOI PMC

Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, Cesarkas K, Jacob-Hirsch J, Amariglio N, Kupiec M, Sorek R, Rechavi G. 2012. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485:201–206. doi:10.1038/nature11112. PubMed DOI

Potapov V, Fu X, Dai N, Corrêa IR, Tanner NA, Ong JL. 2018. Base modifications affecting RNA polymerase and reverse transcriptase fidelity. Nucleic Acids Res 46:5753–5763. doi:10.1093/nar/gky341. PubMed DOI PMC

Šimonová A, Svojanovská B, Trylčová J, Hubálek M, Moravčík O, Zavřel M, Pávová M, Hodek J, Weber J, Cvačka J, Pačes J, Cahová H. 2019. LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion. Sci Rep 9:8697. doi:10.1038/s41598-019-45079-1. PubMed DOI PMC

Batista PJ. 2017. The RNA modification N6-methyladenosine and its implications in human disease. Genomics Proteomics Bioinformatics 15:154–163. doi:10.1016/j.gpb.2017.03.002. PubMed DOI PMC

Netzband R, Pager CT. 2019. Epitranscriptomic marks: emerging modulators of RNA virus gene expression. Wiley Interdiscip Rev RNA 11:e1576. doi:10.1002/wrna.1576. PubMed DOI PMC

Riquelme-Barrios S, Pereira-Montecinos C, Valiente-Echeverría F, Soto-Rifo R. 2018. Emerging roles of N6-methyladenosine on HIV-1 RNA metabolism and viral replication. Front Microbiol 9:576. doi:10.3389/fmicb.2018.00576. PubMed DOI PMC

Gokhale NS, Horner SM. 2017. RNA modifications go viral. PLoS Pathog 13:e1006188. doi:10.1371/journal.ppat.1006188. PubMed DOI PMC

Kennedy EM, Courtney DG, Tsai K, Cullen BR. 2017. Viral epitranscriptomics. J Virol 91:e02263-16. doi:10.1128/JVI.02263-16. PubMed DOI PMC

Pereira-Montecinos C, Valiente-Echeverría F, Soto-Rifo R. 2017. Epitranscriptomic regulation of viral replication. Biochim Biophys Acta Gene Regul Mech 1860:460–471. doi:10.1016/j.bbagrm.2017.02.002. PubMed DOI

Yang J, Wang H, Zhang W. 2019. Regulation of virus replication and T cell homeostasis by N 6 -methyladenosine. Virol Sin 34:22–29. doi:10.1007/s12250-018-0075-5. PubMed DOI PMC

Manners O, Baquero-Perez B, Whitehouse A. 2019. m6A: widespread regulatory control in virus replication. Biochim Biophys Acta Gene Regul Mech 1862:370–381. doi:10.1016/j.bbagrm.2018.10.015. PubMed DOI PMC

Tan B, Gao SJ. 2018. RNA epitranscriptomics: regulation of infection of RNA and DNA viruses by N6-methyladenosine (m6A). Rev Med Virol 28:e1983. doi:10.1002/rmv.1983. PubMed DOI PMC

Tan B, Gao S-J. 2018. The RNA epitranscriptome of DNA viruses. J Virol 92:e00696-18. doi:10.1128/JVI.00696-18. PubMed DOI PMC

Dang W, Xie Y, Cao P, Xin S, Wang J, Li S, Li Y, Lu J. 2019. N6-methyladenosine and viral infection. Front Microbiol 10:417. doi:10.3389/fmicb.2019.00417. PubMed DOI PMC

Williams GD, Gokhale NS, Horner SM. 2019. Regulation of viral infection by the RNA modification N6-methyladenosine. Annu Rev Virol 6:235–253. doi:10.1146/annurev-virology-092818-015559. PubMed DOI PMC

Wu F, Cheng W, Zhao F, Tang M, Diao Y, Xu R. 2019. Association of N6-methyladenosine with viruses and related diseases. Virol J 16:133. doi:10.1186/s12985-019-1236-3. PubMed DOI PMC

Zhao BS, Roundtree IA, He C. 2017. Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol 18:31–42. doi:10.1038/nrm.2016.132. PubMed DOI PMC

Nichols JL. 1979. N6-methyladenosine in maize poly(A)-containing RNA. Plant Sci Lett 15:357–361. doi:10.1016/0304-4211(79)90141-X. DOI

Perry RP, Kelley DE. 1974. Existence of methylated messenger RNA in mouse L cells. Cell 1:37–42. doi:10.1016/0092-8674(74)90153-6. DOI

Deng X, Chen K, Luo GZ, Weng X, Ji Q, Zhou T, He C. 2015. Widespread occurrence of N6-methyladenosine in bacterial mRNA. Nucleic Acids Res 43:6557–6567. doi:10.1093/nar/gkv596. PubMed DOI PMC

Kowalak JA, Dalluge JJ, McCloskey JA, Stetter KO. 1994. The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry 33:7869–7876. doi:10.1021/bi00191a014. PubMed DOI

Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A. 2014. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5’ sites. Cell Rep 8:284–296. doi:10.1016/j.celrep.2014.05.048. PubMed DOI PMC

Zhang X, Wei L-H, Wang Y, Xiao Y, Liu J, Zhang W, Yan N, Amu G, Tang X, Zhang L, Jia G. 2019. Structural insights into FTO’s catalytic mechanism for the demethylation of multiple RNA substrates. Proc Natl Acad Sci U S A 116:2919–2924. doi:10.1073/pnas.1820574116. PubMed DOI PMC

Wang X, Zhao BS, Roundtree IA, Lu Z, Han D, Ma H, Weng X, Chen K, Shi H, He C. 2015. N6-methyladenosine modulates messenger RNA translation efficiency. Cell 161:1388–1399. doi:10.1016/j.cell.2015.05.014. PubMed DOI PMC

Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, Fu Y, Parisien M, Dai Q, Jia G, Ren B, Pan T, He C. 2014. N 6-methyladenosine-dependent regulation of messenger RNA stability. Nature 505:117–120. doi:10.1038/nature12730. PubMed DOI PMC

Liu N, Dai Q, Zheng G, He C, Parisien M, Pan T. 2015. N6 -methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518:560–564. doi:10.1038/nature14234. PubMed DOI PMC

Kandimalla R, Gao F, Li Y, Huang H, Ke J, Deng X, Zhao L, Zhou S, Goel A, Wang X. 2019. RNAMethyPro: a biologically conserved signature of N6-methyladenosine regulators for predicting survival at pan-cancer level. NPJ Precis Oncol 3:13. doi:10.1038/s41698-019-0085-2. PubMed DOI PMC

Shi H, Wang X, Lu Z, Zhao BS, Ma H, Hsu PJ, Liu C, He C. 2017. YTHDF3 facilitates translation and decay of N 6-methyladenosine-modified RNA. Cell Res 27:315–328. doi:10.1038/cr.2017.15. PubMed DOI PMC

Du H, Zhao Y, He J, Zhang Y, Xi H, Liu M, Ma J, Wu L. 2016. YTHDF2 destabilizes m 6 A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex. Nat Commun 7:12626. doi:10.1038/ncomms12626. PubMed DOI PMC

Kennedy EM, Bogerd HP, Kornepati AVR, Kang D, Ghoshal D, Marshall JB, Poling BC, Tsai K, Gokhale NS, Horner SM, Cullen BR. 2016. Posttranscriptional m6A editing of HIV-1 mRNAs enhances viral gene expression. Cell Host Microbe 22:830. doi:10.1016/j.chom.2017.11.010. PubMed DOI PMC

Lu W, Tirumuru N, Gelais CS, Koneru Pc Liu C, Kvaratskhelia M, He C, Wu L. 2018. N 6 –Methyladenosine-binding proteins suppress HIV-1 infectivity and viral production. J Biol Chem 293:12992–13005. doi:10.1074/jbc.RA118.004215. PubMed DOI PMC

Lichinchi G, Gao S, Saletore Y, Gonzalez GM, Bansal V, Wang Y, Mason CE, Rana TM. 2016. Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells. Nat Microbiol 1:16011. doi:10.1038/nmicrobiol.2016.11. PubMed DOI PMC

Tirumuru N, Zhao BS, Lu W, Lu Z, He C, Wu L. 2016. N(6)-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression. Elife 5:e15528. doi:10.7554/eLife.15528. PubMed DOI PMC

Chu C-C, Liu B, Plangger R, Kreutz C, Al-Hashimi HM. 2019. m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB. PLoS One 14:e0224850. doi:10.1371/journal.pone.0224850. PubMed DOI PMC

Sherpa C, Grice SL. 2020. Structural fluidity of the human immunodeficiency virus Rev response element. Viruses 12:86. doi:10.3390/v12010086. PubMed DOI PMC

Tirumuru N, Wu L. 2019. HIV-1 envelope proteins up-regulate N 6 -methyladenosine levels of cellular RNA independently of viral replication. J Biol Chem 294:3249–3260. doi:10.1074/jbc.RA118.005608. PubMed DOI PMC

Bradrick SS. 2017. Causes and consequences of flavivirus RNA methylation. Front Microbiol 8:2374. doi:10.3389/fmicb.2017.02374. PubMed DOI PMC

Gokhale NS, McIntyre ABR, McFadden MJ, Roder AE, Kennedy EM, Gandara JA, Hopcraft SE, Quicke KM, Vazquez C, Willer J, Ilkayeva OR, Law BA, Holley CL, Garcia-Blanco MA, Evans MJ, Suthar MS, Bradrick SS, Mason CE, Horner SM. 2016. N6-methyladenosine in Flaviviridae viral RNA genomes regulates infection. Cell Host Microbe 20:654–665. doi:10.1016/j.chom.2016.09.015. PubMed DOI PMC

Lichinchi G, Zhao BS, Wu Y, Lu Z, Qin Y, He C, Rana TM. 2016. Dynamics of human and viral RNA methylation during Zika virus infection. Cell Host Microbe 20:666–673. doi:10.1016/j.chom.2016.10.002. PubMed DOI PMC

Hotchkiss RD. 1948. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem 175:315–332. PubMed

Dubin DT, Stollar V. 1975. Methylation of sindbis virus “26S” messenger RNA. Biochem Biophys Res Commun 66:1373–1379. doi:10.1016/0006-291x(75)90511-2. PubMed DOI

Dubin DT, Stollar V, Hsuchen CC, Timko K, Guild GM. 1977. Sindbis virus messenger RNA: the 5′-termini and methylated residues of 26 and 42 S RNA. Virology 77:457–470. doi:10.1016/0042-6822(77)90471-8. PubMed DOI

Durbin AF, Wang C, Marcotrigiano J, Gehrke L. 2016. RNAs containing modified nucleotides fail to trigger RIG-I conformational changes for innate immune signaling. mBio 7:e00833-16. doi:10.1128/mBio.00833-16. PubMed DOI PMC

Di Serio F, Torchetti EM, Daròs JA, Navarro B. 2019. Reassessment of viroid RNA cytosine methylation status at the single nucleotide level. Viruses 11:357. doi:10.3390/v11040357. PubMed DOI PMC

Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T. 2012. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 40:5023–5033. doi:10.1093/nar/gks144. PubMed DOI PMC

Courtney D, Tsai K, Bogerd HP, Kennedy EM, Law BA, Emery A, Swanstrom R, Holley CL, Cullen BR. 2019. Epitranscriptomic addition of m5C to HIV-1 transcripts regulates viral gene expression. Cell Host Microbe 26:217–227.e6. doi:10.1016/j.chom.2019.07.005. PubMed DOI PMC

Courtney DG, Chalem A, Bogerd HP, Law BA, Kennedy EM, Holley CL, Cullen BR. 2019. Extensive epitranscriptomic methylation of A and C residues on murine leukemia virus transcripts enhances viral gene expression. mBio 10:e01209-19. doi:10.1128/mBio.01209-19. PubMed DOI PMC

Kim D, Lee J-Y, Yang J-S, Kim JW, Kim VN, Chang H. 2020. The architecture of SARS-CoV-2 transcriptome. Cell 181:914–921. doi:10.1016/j.cell.2020.04.011. PubMed DOI PMC

Zinshteyn B, Nishikura K. 2009. Adenosine-to-inosine RNA editing. Wiley Interdiscip Rev Syst Biol Med 1:202–209. doi:10.1002/wsbm.10. PubMed DOI PMC

Nishikura K. 2010. Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321–349. doi:10.1146/annurev-biochem-060208-105251. PubMed DOI PMC

Jayan GC, Casey JL. 2002. Increased RNA editing and inhibition of hepatitis delta virus replication by high-level expression of ADAR1 and ADAR2. J Virol 76:3819–3827. doi:10.1128/jvi.76.8.3819-3827.2002. PubMed DOI PMC

Gandy SZ, Linnstaedt SD, Muralidhar S, Cashman KA, Rosenthal LJ, Casey JL. 2007. RNA editing of the human herpesvirus 8 kaposin transcript eliminates its transforming activity and is induced during lytic replication. J Virol 81:13544–13551. doi:10.1128/JVI.01521-07. PubMed DOI PMC

Liao JY, Thakur SA, Zalinger ZB, Gerrish KE, Imani F. 2011. Inosine-containing RNA is a novel innate immune recognition element and reduces RSV infection. PLoS One 6:e26463. doi:10.1371/journal.pone.0026463. PubMed DOI PMC

Nie Y, Hammond GL, Yang J-H. 2007. Double-stranded RNA deaminase ADAR1 increases host susceptibility to virus infection. J Virol 81:917–923. doi:10.1128/JVI.01527-06. PubMed DOI PMC

Doria M, Neri F, Gallo A, Farace MG, Michienzi A. 2009. Editing of HIV-1 RNA by the double-stranded RNA deaminase ADAR1 stimulates viral infection. Nucleic Acids Res 37:5848–5858. doi:10.1093/nar/gkp604. PubMed DOI PMC

George CX, Samuel CE. 1999. Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible. Proc Natl Acad Sci U S A 96:4621–4626. doi:10.1073/pnas.96.8.4621. PubMed DOI PMC

Toth AM, Li Z, Cattaneo R, Samuel CE. 2009. RNA-specific adenosine deaminase ADAR1 suppresses measles virus-induced apoptosis and activation of protein kinase PKR. J Biol Chem 284:29350–29356. doi:10.1074/jbc.M109.045146. PubMed DOI PMC

Orecchini E, Federico M, Doria M, Arenaccio C, Giuliani E, Ciafrè SA, Michienzi A. 2015. The ADAR1 editing enzyme is encapsidated into HIV-1 virions. Virology 485:475–480. doi:10.1016/j.virol.2015.07.027. PubMed DOI

Sarvestani ST, Tate MD, Moffat JM, Jacobi AM, Behlke MA, Miller AR, Beckham SA, McCoy CE, Chen W, Mintern JD, O’Keeffe M, John M, Williams BRG, Gantier MP. 2014. Inosine-mediated modulation of RNA sensing by Toll-like receptor 7 (TLR7) and TLR8. J Virol 88:799–810. doi:10.1128/JVI.01571-13. PubMed DOI PMC

Rizzetto M, Hoyer B, Canese MG, Shih JW, Purcell RH, Gerin JL. 1980. δ agent: association of δ antigen with hepatitis B surface antigen and RNA in serum of δ-infected chimpanzees. Proc Natl Acad Sci U S A 77:6124–6128. doi:10.1073/pnas.77.10.6124. PubMed DOI PMC

Weiner AJ, Choo QL, Wang KS, Govindarajan S, Redeker AG, Gerin JL, Houghton M. 1988. A single antigenomic open reading frame of the hepatitis delta virus encodes the epitope(s) of both hepatitis delta antigen polypeptides p24 delta and p27 delta. J Virol 62:594–599. doi:10.1128/JVI.62.2.594-599.1988. PubMed DOI PMC

Polson AG, Bass BL, Casey JL. 1996. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature 381:346–346. doi:10.1038/381346a0. PubMed DOI

Sato S, Wong SK, Lazinski DW. 2001. Hepatitis delta virus minimal substrates competent for editing by ADAR1 and ADAR2. J Virol 75:8547–8555. doi:10.1128/jvi.75.18.8547-8555.2001. PubMed DOI PMC

Jones JW, Robins RK. 1963. Purine nucleosides. III. Methylation studies of certain naturally occurring purine nucleosides. J Am Chem Soc 85:193–201. doi:10.1021/ja00885a019. DOI

Hall RH. 1964. On the 2’-O-methylribonucleoside content of ribonucleic acids. Biochemistry 3:876–880. doi:10.1021/bi00895a001. PubMed DOI

Werner M, Purta E, Kaminska KH, Cymerman IA, Campbell DA, Mittra B, Zamudio JR, Sturm NR, Jaworski J, Bujnicki JM. 2011. 2′-O-ribose methylation of cap2 in human: function and evolution in a horizontally mobile family. Nucleic Acids Res 39:4756–4768. doi:10.1093/nar/gkr038. PubMed DOI PMC

Byszewska M, Mietański M, Purta E, Bujnicki JM. 2014. RNA methyltransferases involved in 5′ cap biosynthesis. RNA Biol 11:1597–1607. doi:10.1080/15476286.2015.1004955. PubMed DOI PMC

Smietanski M, Werner M, Purta E, Kaminska KH, Stepinski J, Darzynkiewicz E, Nowotny M, Bujnicki JM. 2014. Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation. Nat Commun 5:3004. doi:10.1038/ncomms4004. PubMed DOI PMC

Picard-Jean F, Brand C, Tremblay-Létourneau M, Allaire A, Beaudoin MC, Boudreault S, Duval C, Rainville-Sirois J, Robert F, Pelletier J, Geiss BJ, Bisaillon M. 2018. 2’-O-methylation of the mRNA cap protects RNAs from decapping and degradation by DXO. PLoS One 13:e0193804. doi:10.1371/journal.pone.0193804. PubMed DOI PMC

Koonin EV, Moss B. 2010. Viruses know more than one way to don a cap. Proc Natl Acad Sci U S A 107:3283–3284. doi:10.1073/pnas.0915061107. PubMed DOI PMC

Decroly E, Ferron F, Lescar J, Canard B. 2012. Conventional and unconventional mechanisms for capping viral mRNA. Nat Rev Microbiol 10:51–65. doi:10.1038/nrmicro2675. PubMed DOI PMC

Bamming D, Horvath CM. 2009. Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. J Biol Chem 284:9700–9712. doi:10.1074/jbc.M807365200. PubMed DOI PMC

Züst R, Cervantes-Barragan L, Habjan M, Maier R, Neuman BW, Ziebuhr J, Szretter KJ, Baker SC, Barchet W, Diamond MS, Siddell SG, Ludewig B, Thiel V. 2011. Ribose 2’-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5. Nat Immunol 12:137–143. doi:10.1038/ni.1979. PubMed DOI PMC

Reikine S, Nguyen JB, Modis Y. 2014. Pattern recognition and signaling mechanisms of RIG-I and MDA5. Front Immunol 5:342. doi:10.3389/fimmu.2014.00342. PubMed DOI PMC

Fang R, Jiang Q, Zhou X, Wang C, Guan Y, Tao J, Xi J, Feng JM, Jiang Z. 2017. MAVS activates TBK1 and IKKε through TRAFs in NEMO dependent and independent manner. PLoS Pathog 13:e1006720. doi:10.1371/journal.ppat.1006720. PubMed DOI PMC

Jacobs JL, Coyne CB. 2013. Mechanisms of MAVS regulation at the mitochondrial membrane. J Mol Biol 425:5009–5019. doi:10.1016/j.jmb.2013.10.007. PubMed DOI PMC

Dias Junior AG, Sampaio NG, Rehwinkel J. 2019. A balancing act: MDA5 in antiviral immunity and autoinflammation. Trends Microbiol 27:75–85. doi:10.1016/j.tim.2018.08.007. PubMed DOI PMC

Brisse M, Ly H. 2019. Comparative structure and function analysis of the RIG-I-like receptors: RIG-I and MDA5. Front Immunol 10:1586. doi:10.3389/fimmu.2019.01586. PubMed DOI PMC

Hyde JL, Diamond MS. 2015. Innate immune restriction and antagonism of viral RNA lacking 2’-O methylation. Virology 479–480:66–74. doi:10.1016/j.virol.2015.01.019. PubMed DOI PMC

Diamond MS. 2014. IFIT1: a dual sensor and effector molecule that detects non-2’-O methylated viral RNA and inhibits its translation. Cytokine Growth Factor Rev 25:543–550. doi:10.1016/j.cytogfr.2014.05.002. PubMed DOI PMC

Abbas YM, Laudenbach BT, Martínez-Montero S, Cencic R, Habjan M, Pichlmair A, Damha MJ, Pelletier J, Nagar B. 2017. Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2′-O methylations. Proc Natl Acad Sci U S A 114:E2106–E2115. doi:10.1073/pnas.1612444114. PubMed DOI PMC

Kumar P, Sweeney TR, Skabkin MA, Skabkina OV, Hellen CUT, Pestova TV. 2014. Inhibition of translation by IFIT family members is determined by their ability to interact selectively with the 5’-terminal regions of cap0-, cap1- and 5’ppp- mRNAs. Nucleic Acids Res 42:3228–3245. doi:10.1093/nar/gkt1321. PubMed DOI PMC

Diamond MS, Farzan M. 2013. The broad-spectrum antiviral functions of IFIT and IFITM proteins. Nat Rev Immunol 13:46–57. doi:10.1038/nri3344. PubMed DOI PMC

Ringeard M, Marchand V, Decroly E, Motorin Y, Bennasser Y. 2019. FTSJ3 is an RNA 2′-O-methyltransferase recruited by HIV to avoid innate immune sensing. Nature 565:500–504. doi:10.1038/s41586-018-0841-4. PubMed DOI

Zhang Y, Wei Y, Zhang X, Cai H, Niewiesk S, Li J. 2014. Rational design of human metapneumovirus live attenuated vaccine candidates by inhibiting viral mRNA cap methyltransferase. J Virol 88:11411–11429. doi:10.1128/JVI.00876-14. PubMed DOI PMC

Li S-H, Dong H, Li X-F, Xie X, Zhao H, Deng Y-Q, Wang X-Y, Ye Q, Zhu S-Y, Wang H-J, Zhang B, Leng Q-B, Zuest R, Qin E-D, Qin C-F, Shi P-Y. 2013. Rational design of a flavivirus vaccine by abolishing viral RNA 2’-O methylation. J Virol 87:5812–5819. doi:10.1128/JVI.02806-12. PubMed DOI PMC

Menachery VD, Yount BL, Josset L, Gralinski LE, Scobey T, Agnihothram S, Katze MG, Baric RS. 2014. Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2’-O-methyltransferase activity. J Virol 88:4251–4264. doi:10.1128/JVI.03571-13. PubMed DOI PMC

Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, Regev A. 2014. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159:148–162. doi:10.1016/j.cell.2014.08.028. PubMed DOI PMC

Marceau CD, Puschnik AS, Majzoub K, Ooi YS, Brewer SM, Fuchs G, Swaminathan K, Mata MA, Elias JE, Sarnow P, Carette JE. 2016. Genetic dissection of Flaviviridae host factors through genome-scale CRISPR screens. Nature 535:159–163. doi:10.1038/nature18631. PubMed DOI PMC

Saito T, Owen DM, Jiang F, Marcotrigiano J, Gale M. 2008. Innate immunity induced by composition-dependent RIG-I recognition of hepatitis C virus RNA. Nature 454:523–527. doi:10.1038/nature07106. PubMed DOI PMC

McIntyre W, Netzband R, Bonenfant G, Biegel JM, Miller C, Fuchs G, Henderson E, Arra M, Canki M, Fabris D, Pager CT. 2018. Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res 46:5776–5791. doi:10.1093/nar/gky029. PubMed DOI PMC

Safra M, Sas-Chen A, Nir R, Winkler R, Nachshon A, Bar-Yaacov D, Erlacher M, Rossmanith W, Stern-Ginossar N, Schwartz S. 2017. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature 551:251–255. doi:10.1038/nature24456. PubMed DOI

Eckwahl MJ, Arnion H, Kharytonchyk S, Zang T, Bieniasz PD, Telesnitsky A, Wolin SL. 2016. Analysis of the human immunodeficiency virus-1 RNA packageome. RNA 22:1228–1238. doi:10.1261/rna.057299.116. PubMed DOI PMC

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. doi:10.1038/nmeth.1226. PubMed DOI

Limbach PA, Paulines MJ. 2017. Going global: the new era of mapping modifications in RNA. Wiley Interdiscip Rev RNA 8. doi:10.1002/wrna.1367. PubMed DOI PMC

Lodish H. 2013. Molecular cell biology. W.H. Freeman and Co., New York, NY, USA.

Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR. 2015. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods 12:767–772. doi:10.1038/nmeth.3453. PubMed DOI PMC

Edelheit S, Schwartz S, Mumbach MR, Wurtzel O, Sorek R. 2013. Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet 9:e1003602. doi:10.1371/journal.pgen.1003602. PubMed DOI PMC

Slama K, Galliot A, Weichmann F, Hertler J, Feederle R, Meister G, Helm M. 2019. Determination of enrichment factors for modified RNA in MeRIP experiments. Methods 156:102–109. doi:10.1016/j.ymeth.2018.10.020. PubMed DOI

Aschenbrenner J, Werner S, Marchand V, Adam M, Motorin Y, Helm M, Marx A. 2018. Engineering of a DNA polymerase for direct m 6 A sequencing. Angew Chem Int Ed Engl 57:417–421. doi:10.1002/anie.201710209. PubMed DOI PMC

Garcia-Campos MA, Edelheit S, Toth U, Safra M, Shachar R, Viukov S, Winkler R, Nir R, Lasman L, Brandis A, Hanna JH, Rossmanith W, Schwartz S. 2019. Deciphering the “m6A code” via antibody-independent quantitative profiling. Cell 178:731–747.e16. doi:10.1016/j.cell.2019.06.013. PubMed DOI

Liu N, Parisien M, Dai Q, Zheng G, He C, Pan T. 2013. Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA. RNA 19:1848–1856. doi:10.1261/rna.041178.113. PubMed DOI PMC

Meyer KD. 2019. DART-seq: an antibody-free method for global m6A detection. Nat Methods 16:1275–1280. doi:10.1038/s41592-019-0570-0. PubMed DOI PMC

Li Y, Tollefsbol TO. 2011. DNA methylation detection: bisulfite genomic sequencing analysis. Methods Mol Biol 791:11–21. doi:10.1007/978-1-61779-316-5_2. PubMed DOI PMC

Gu W, Hurto RL, Hopper AK, Grayhack EJ, Phizicky EM. 2005. Depletion of Saccharomyces cerevisiae tRNA(His) guanylyltransferase Thg1p leads to uncharged tRNAHis with additional m(5)C. Mol Cell Biol 25:8191–8201. doi:10.1128/MCB.25.18.8191-8201.2005. PubMed DOI PMC

Sabban EL, Bhanot OS. 1982. The effects of bisulfite-induced C to U transitions on aminoacylation of Escherichia coli glycine tRNA. J Biol Chem 257:4796–4805. PubMed

Schaefer M, Pollex T, Hanna K, Lyko F. 2009. RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Res 37:e12. doi:10.1093/nar/gkn954. PubMed DOI PMC

Amort T, Rieder D, Wille A, Khokhlova-Cubberley D, Riml C, Trixl L, Jia XY, Micura R, Lusser A. 2017. Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain. Genome Biol 18:1. doi:10.1186/s13059-016-1139-1. PubMed DOI PMC

Khoddami V, Yerra A, Mosbruger TL, Fleming AM, Burrows CJ, Cairns BR. 2019. Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution. Proc Natl Acad Sci U S A 116:6784–6789. doi:10.1073/pnas.1817334116. PubMed DOI PMC

Chen K, Lu Z, Wang X, Fu Y, Luo GZ, Liu N, Han D, Dominissini D, Dai Q, Pan T, He C. 2015. High-resolution N6-methyladenosine (m6A) map using photo-crosslinking-assisted m6A sequencing. Angew Chem Int Ed Engl 54:1587–1590. doi:10.1002/anie.201410647. PubMed DOI PMC

Hartstock K, Nilges BS, Ovcharenko A, Cornelissen NV, Püllen N, Lawrence-Dörner AM, Leidel SA, Rentmeister A. 2018. Enzymatic or in vivo installation of propargyl groups in combination with click chemistry for the enrichment and detection of methyltransferase target sites in RNA. Angew Chem Int Ed Engl 57:6342–6346. doi:10.1002/anie.201800188. PubMed DOI

Khoddami V, Cairns BR. 2013. Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nat Biotechnol 31:458–464. doi:10.1038/nbt.2566. PubMed DOI PMC

Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. 2013. NSUN2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep 4:255–261. doi:10.1016/j.celrep.2013.06.029. PubMed DOI PMC

Levanon EY, Eisenberg E, Yelin R, Nemzer S, Hallegger M, Shemesh R, Fligelman ZY, Shoshan A, Pollock SR, Sztybel D, Olshansky M, Rechavi G, Jantsch MF. 2004. Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22:1001–1005. doi:10.1038/nbt996. PubMed DOI

Kleinman CL, Majewski J. 2012. Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science 335:1302. doi:10.1126/science.1209658. PubMed DOI

Pickrell JK, Gilad Y, Pritchard JK. 2012. Comment on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science 335:1302. doi:10.1126/science.1210484. PubMed DOI PMC

Sakurai M, Yano T, Kawabata H, Ueda H, Suzuki T. 2010. Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol 6:733–740. doi:10.1038/nchembio.434. PubMed DOI

Sakurai M, Ueda H, Yano T, Okada S, Terajima H, Mitsuyama T, Toyoda A, Fujiyama A, Kawabata H, Suzuki T. 2014. A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res 24:522–534. doi:10.1101/gr.162537.113. PubMed DOI PMC

Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC. 2019. Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA. Nucleic Acids Res 47:e130. doi:10.1093/nar/gkz751. PubMed DOI PMC

Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. 2015. Profiling of ribose methylations in RNA by high-throughput sequencing. Angew Chem Int Ed Engl 54:451–455. doi:10.1002/anie.201408362. PubMed DOI

Marchand V, Blanloeil-Oillo F, Helm M, Motorin Y. 2016. Illumina-based RiboMethSeq approach for mapping of 2′-O-Me residues in RNA. Nucleic Acids Res 44:e135–e135. doi:10.1093/nar/gkw547. PubMed DOI PMC

Zhu Y, Pirnie SP, Carmichael GG. 2017. High-throughput and site-specific identification of 2′-O-methylation sites using ribose oxidation sequencing (RibOxi-seq). RNA 23:1303–1314. doi:10.1261/rna.061549.117. PubMed DOI PMC

Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, Dominissini D, He C. 2017. Nm-seq maps 2′-O-methylation sites in human mRNA with base precision. Nat Methods 14:695–698. doi:10.1038/nmeth.4294. PubMed DOI PMC

Dai Q, Moshitch-Moshkovitz S, Han D, Kol N, Amariglio N, Rechavi G, Dominissini D, He C. 2018. Correction: corrigendum: Nm-seq maps 2′-O-methylation sites in human mRNA with base precision. Nat Methods 15:226–227. doi:10.1038/nmeth0318-226c. PubMed DOI PMC

Keller MW, Rambo-Martin BL, Wilson MM, Ridenour CA, Shepard SS, Stark TJ, Neuhaus EB, Dugan VG, Wentworth DE, Barnes JR. 2018. Author correction: direct RNA sequencing of the coding complete influenza A virus genome. Sci Rep 8:15746. doi:10.1038/s41598-018-34067-6. PubMed DOI PMC

Garalde DR, Snell EA, Jachimowicz D, Sipos B, Lloyd JH, Bruce M, Pantic N, Admassu T, James P, Warland A, Jordan M, Ciccone J, Serra S, Keenan J, Martin S, McNeill L, Wallace EJ, Jayasinghe L, Wright C, Blasco J, Young S, Brocklebank D, Juul S, Clarke J, Heron AJ, Turner DJ. 2018. Highly parallel direct RN A sequencing on an array of nanopores. Nat Methods 15:201–206. doi:10.1038/nmeth.4577. PubMed DOI

Liu H, Begik O, Lucas MC, Ramirez JM, Mason CE, Wiener D, Schwartz S, Mattick JS, Smith MA, Novoa EM. 2019. Accurate detection of m6A RNA modifications in native RNA sequences. Nat Commun 10:4079. doi:10.1038/s41467-019-11713-9. PubMed DOI PMC

Leger A, Amaral PP, Pandolfini L, Capitanchik C, Capraro F, Barbieri I, Migliori V, Luscombe NM, Enright AJ, Tzelepis K, Ule J, Fitzgerald T, Birney E, Leonardi T, Kouzarides T. 2019. RNA modifications detection by comparative Nanopore direct RNA sequencing. bioRxiv 843136. doi:10.1101/843136. PubMed DOI PMC

Hudeček O, Benoni R, Reyes-Gutierrez PE, Culka M, Šanderová H, Hubálek M, Rulíšek L, Cvačka J, Krásný L, Cahová H. 2020. Dinucleoside polyphosphates act as 5′-RNA caps in bacteria. Nat Commun 11:1052. doi:10.1038/s41467-020-14896-8. PubMed DOI PMC

Parrish S, Hurchalla M, Liu SW, Moss B. 2009. The African swine fever virus g5R protein possesses mRNA decapping activity. Virology 393:177–182. doi:10.1016/j.virol.2009.07.026. PubMed DOI PMC

Parrish S, Resch W, Moss B. 2007. Vaccinia virus D10 protein has mRNA decapping activity, providing a mechanism for control of host and viral gene expression. Proc Natl Acad Sci U S A 104:2139–2144. doi:10.1073/pnas.0611685104. PubMed DOI PMC

Courtney DG, Kennedy EM, Dumm RE, Bogerd HP, Tsai K, Heaton NS, Cullen BR. 2017. Epitranscriptomic enhancement of influenza A virus gene expression and replication. Cell Host Microbe 22:377–386. doi:10.1016/j.chom.2017.08.004. PubMed DOI PMC

Tsai K, Courtney DG, Cullen BR. 2018. Addition of m6A to SV40 late mRNAs enhances viral structural gene expression and replication. PLoS Pathog 14:e1006919. doi:10.1371/journal.ppat.1006919. PubMed DOI PMC

Hao H, Hao S, Chen H, Chen Z, Zhang Y, Wang J, Wang H, Zhang B, Qiu J, Deng F, Guan W. 2019. N 6 -methyladenosine modification and METTL3 modulate enterovirus 71 replication. Nucleic Acids Res 47:362–374. doi:10.1093/nar/gky1007. PubMed DOI PMC

Beemon K, Hunter T. 1977. In vitro translation yields a possible Rous sarcoma virus src gene product. Proc Natl Acad Sci U S A 74:3302–3306. doi:10.1073/pnas.74.8.3302. PubMed DOI PMC

Kane SE, Beemon K. 1985. Precise localization of m6A in Rous sarcoma virus RNA reveals clustering of methylation sites: implications for RNA processing. Mol Cell Biol 5:2298–2306. doi:10.1128/mcb.5.9.2298. PubMed DOI PMC

Stoltzfus CM, Dane RW. 1982. Accumulation of spliced avian retrovirus mRNA is inhibited in S-adenosylmethionine-depleted chicken embryo fibroblasts. J Virol 42:918–931. doi:10.1128/JVI.42.3.918-931.1982. PubMed DOI PMC

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129–141. doi:10.1016/j.cell.2010.03.009. PubMed DOI PMC

Krug RM, Morgan MA, Shatkin AJ. 1976. Influenza viral mRNA contains internal N6-methyladenosine and 5’-terminal 7-methylguanosine in cap structures. J Virol 20:45–53. doi:10.1128/JVI.20.1.45-53.1976. PubMed DOI PMC

Narayan P, Ayers DF, Rottman FM, Maroney PA, Nilsen TW. 1987. Unequal distribution of N6-methyladenosine in influenza virus mRNAs. Mol Cell Biol 7:1572–1575. doi:10.1128/mcb.7.4.1572. PubMed DOI PMC

Phuphuakrat A, Kraiwong R, Boonarkart C, Lauhakirti D, Lee T-H, Auewarakul P. 2008. Double-stranded RNA adenosine deaminases enhance expression of human immunodeficiency virus type 1 proteins. J Virol 82:10864–10872. doi:10.1128/JVI.00238-08. PubMed DOI PMC

Khrustalev VV, Khrustaleva TA, Sharma N, Giri R. 2017. Mutational pressure in Zika virus: local ADAR-editing areas associated with pauses in translation and replication. Front Cell Infect Microbiol 7:44. doi:10.3389/fcimb.2017.00044. PubMed DOI PMC

Piontkivska H, Frederick M, Miyamoto MM, Wayne ML. 2017. RNA editing by the host ADAR system affects the molecular evolution of the Zika virus. Ecol Evol 7:4475–4485. doi:10.1002/ece3.3033. PubMed DOI PMC

Casey JL. 2006. RNA editing in hepatitis delta virus. Curr Top Microbiol Immunol 307:67–89. doi:10.1007/3-540-29802-9_4. PubMed DOI

Cattaneo R, Schmid A, Eschle D, Baczko K, ter Meulen V, Billeter MA. 1988. Biased hypermutation and other genetic changes in defective measles viruses in human brain infections. Cell 55:255–265. doi:10.1016/0092-8674(88)90048-7. PubMed DOI PMC

Pfaller CK, Mastorakos GM, Matchett WE, Ma X, Samuel CE, Cattaneo R. 2015. Measles virus defective interfering RNAs are generated frequently and early in the absence of C protein and can be destabilized by adenosine deaminase acting on RNA-1-like hypermutations. J Virol 89:7735–7747. doi:10.1128/JVI.01017-15. PubMed DOI PMC

Dong H, Chang DC, Hua MHC, Lim SP, Chionh YH, Hia F, Lee YH, Kukkaro P, Lok S-M, Dedon PC, Shi P-Y. 2012. 2′-O methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS Pathog 8:e1002642. doi:10.1371/journal.ppat.1002642. PubMed DOI PMC

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