1*Zainab Basim Mohammed,2Elaf ismael Mahdi
1,2Ibn Sina University of Medical and Pharmaceutical Sciences, Baghdad, Iraq.
ABSTRACT
Although the use of antiviral drugs has improved, human viral infections are still a serious health problem in the world, as they have the capacity to evade host immunity, to persist and to not be completely eliminated. The methylation of RNA at the N6 position of adenine (N6-methyladenosine or m6A) is the most common internal modification of eukaryotic messenger RNAs, and recent findings have shown that m6A plays an important role in regulating the expression of both host and viral genes. The involvement of m6A writers, erasers and readers in regulating RNA stability, translation, splicing and degradation has been shown to regulate multiple stages of the viral life cycle. Previous studies have shown that persistent viruses, such as human immunodeficiency virus (HIV), hepatitis B virus (HBV), hepatitis C virus (HCV), human papillomavirus (HPV), Epstein–Barr virus (EBV), cytomegalovirus (CMV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), hijack host m6A machinery to amplify viral replication, control latency and inhibit antiviral immune responses. Moreover, m6A remodeling of epitranscriptomes plays a role in immune escape, including by dampening innate immune sensing, blocking interferon signaling, decreasing antigen presentation, and driving immune tolerance, which all enable chronic infection. The results have revealed m6A regulatory processes as potential targets for novel antiviral therapies. There are, however, significant challenges to clinical translation due to the context-dependent functions of m6A, the virus-specific regulatory mechanisms, and the possibility of off-target effects. This review highlights the present understanding on the molecular machinery of m6A modification, how m6A modification is involved in viral replication and immune evasion, how it is involved in the regulation of persistent human viruses, and emerging therapeutic strategies targeting m6A modification. Lastly, the paper explores the potential for personalized antiviral therapies based on epitranscriptomic profiling, multi-omics technologies, and AI to improve long-term clinical outcomes and overcome the limitations of existing treatment strategies in persistent viral infections.
REFERENCES
1) Afonso, C. L., Amarasinghe, G. K., Banyai, K., Bao, Y., Basler, C. F., Bavari, S., et al. (2016). Taxonomy of the order mononegavirales: update 2016. Arch. Virol. 161 (8), 2351–2360. doi: 10.1007/s00705-016-2880-1
2) Aherkar, V. V., Mohammed, A. A., Al-Shimary, A. A., Kshirsagar, V., Shendage, R., Ubale, P. A., … & Ovhal, R. M. (2025). Photocatalytic dye degradation efficacy and antimicrobial potency of zinc oxide nanoparticles synthesized via sol-gel method. Next Materials, 9, 100972.
3) Aitken, C. E., and Lorsch, J. R. (2012). A mechanistic overview of translation initiation in eukaryotes. Nat. Struct. Mol. Biol. 19 (6), 568–576. doi: 10.1038/nsmb.2303
4) Alarcon, C. R., Goodarzi, H., Lee, H., Liu, X., Tavazoie, S., and Tavazoie, S. F. (2015a). HNRNPA2B1 is a mediator of m(6)A-dependent nuclear RNA processing events. Cell 162 (6), 1299–1308. doi: 10.1016/j.cell.2015.08.011
5) Alarcon, C. R., Lee, H., Goodarzi, H., Halberg, N., and Tavazoie, S. F. (2015b). N6- methyladenosine marks primary microRNAs for processing. Nature 519 (7544), 482– 485. doi: 10.1038/nature14281
6) Arguello, A. E., DeLiberto, A. N., and Kleiner, R. E. (2017). RNA Chemical proteomics reveals the N(6)-methyladenosine (m(6)A)-regulated protein-RNA interactome. J. Am. Chem. Soc. 139 (48), 17249–17252. doi: 10.1021/jacs.7b09213
7) Boccaletto, P., Machnicka, M. A., Purta, E., Piatkowski, P., Baginski, B., Wirecki, T. K., et al. (2018). MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 46 (D1), D303–D307. doi: 10.1093/nar/gkx1030
8) Boeckh, M., and Geballe, A. P. (2011). Cytomegalovirus: pathogen, paradigm, and puzzle. J. Clin. Invest. 121 (5), 1673–1680. doi: 10.1172/JCI45449
9) Burgess, H. M., Depledge, D. P., Thompson, L., Srinivas, K. P., Grande, R. C., Vink, E. I., et al. (2021). Targeting the m(6)A RNA modification pathway blocks SARS-CoV- 2 and HCoV-OC43 replication. Genes Dev. 35 (13-14), 1005–1019. doi: 10.1101/ gad.348320.121
10) Canaani, D., Kahana, C., Lavi, S., and Groner, Y. (1979). Identification and mapping of N6-methyladenosine containing sequences in simian virus 40 RNA. Nucleic Acids Res. 6 (8), 2879–2899. doi: 10.1093/nar/6.8.2879
11) Chelmicki, T., Roger, E., Teissandier, A., Dura, M., Bonneville, L., Rucli, S., et al (2021). m(6)A RNA methylation regulates the fate of endogenous retroviruses. Nature 591 (7849), 312–316. doi: 10.1038/s41586-020-03135-1
12) Chen, J., Jin, L., Wang, Z., Wang, L., Chen, Q., Cui, Y., et al. (2020). N6- methyladenosine regulates PEDV replication and host gene expression. Virology 548, 59–72. doi: 10.1016/j.virol.2020.06.008
13) Chen, S., Kumar, S., Espada, C. E., Tirumuru, N., Cahill, M. P., Hu, L., et al. (2021). N6-methyladenosine modification of HIV-1 RNA suppresses type-I interferon induction in differentiated monocytic cells and primary macrophages. PloS Pathog. 17 (3), e1009421. doi: 10.1371/journal.ppat.1009421
14) Chen, Y. G., Chen, R., Ahmad, S., Verma, R., Kasturi, S. P., Amaya, L., et al. (2019). N6-methyladenosine modification controls circular RNA immunity. Mol. Cell 76 (1), 96–109 e109. doi: 10.1016/j.molcel.2019.07.016
15) Cheng, Y., Fu, Y., Wang, Y., and Wang, J. (2020). The m6A methyltransferase METTL3 is functionally implicated in DLBCL development by regulating m6A modification in PEDF. Front. Genet. 11. doi: 10.3389/fgene.2020.00955
16) Chen-Kiang, S., Nevins, J. R., and Darnell, J. E.Jr. (1979). N-6-methyl-adenosine in adenovirus type 2 nuclear RNA is conserved in the formation of messenger RNA. J. Mol. Biol. 135 (3), 733–752. doi: 10.1016/0022-2836(79)90174-8
17) Chow, K. T., Gale, M.Jr., and Loo, Y. M. (2018). RIG-I and other RNA sensors in antiviral immunity. Annu. Rev. Immunol. 36, 667–694. doi: 10.1146/annurevimmunol- 042617-053309
18) Collins, P. L., and Graham, B. S. (2008). Viral and host factors in human respiratory syncytial virus pathogenesis. J. Virol. 82 (5), 2040–2055. doi: 10.1128/JVI.01625-07
19) Coots, R. A., Liu, X. M., Mao, Y., Dong, L., Zhou, J., Wan, J., et al. (2017). m(6)A facilitates eIF4F-independent mRNA translation. Mol. Cell 68(3), 504-514 e507. doi: 10.1016/j.molcel.2017.10.002
20) Courtney, D. G., Kennedy, E. M., Dumm, R. E., Bogerd, H. P., Tsai, K., Heaton, N. S., et al. (2017). Epitranscriptomic enhancement of influenza a virus gene expression and replication. Cell Host Microbe 22 (3), 377–386 e375. doi: 10.1016/j.chom.2017.08.004
21) Crawford, S. E., Ramani, S., Tate, J. E., Parashar, U. D., Svensson, L., Hagbom, M., et al. (2017). Rotavirus infection. Nat. Rev. Dis. Primers 3, 17083. doi: 10.1038/ nrdp.2017.83
22) Csepany, T., Lin, A., Baldick, C. J.Jr., and Beemon, K. (1990). Sequence specificity of mRNA N6-adenosine methyltransferase. J. Biol. Chem. 265 (33), 20117–20122. doi: 10.1016/S0021-9258(17)30477-5
23) Dina, C., Meyre, D., Gallina, S., Durand, E., Korner, A., Jacobson, P., et al. (2007). Variation in FTO contributes to childhoo
24) Khamees, H. H., Mohammed, A. A., Hussein, S. A. M., Ahmed, M. A., & Raoof, A. S. M. (2024). In-Silico Study OF Destabilizing Alzheimer’s Aβ42 Protofibrils with Curcumin. International Journal of Medical Science and Dental Health, 10(05), 76-84.
25) Lichinchi, G., Zhao, B. S., Wu, Y., Lu, Z., Qin, Y., He, C., et al. (2016b). Dynamics of human and viral RNA methylation during zika virus infection. Cell Host Microbe 20 (5), 666–673. doi: 10.1016/j.chom.2016.10.002
26) Lin, S., Choe, J., Du, P., Triboulet, R., and Gregory, R. I. (2016). The m(6)A methyltransferase METTL3 promotes translation in human cancer cells. Mol. Cell 62 (3), 335–345. doi: 10.1016/j.molcel.2016.03.021
27) Liu, J., Dou, X., Chen, C., Chen, C., Liu, C., Xu, M. M., et al. (2020). N (6)- methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science 367 (6477), 580–586. doi: 10.1126/science.aay6018
28) Liu, J., Xu, Y. P., Li, K., Ye, Q., Zhou, H. Y., Sun, H., et al. (2021a). The m(6)A methylome of SARS-CoV-2 in host cells. Cell Res. 31 (4), 404–414. doi: 10.1038/s41422- 020-00465-7
29) Liu, J., Yue, Y., Han, D., Wang, X., Fu, Y., Zhang, L., et al. (2014). A METTL3- METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat. Chem. Biol. 10 (2), 93–95. doi: 10.1038/nchembio.1432
30) Liu, N., Dai, Q., Zheng, G., He, C., Parisien, M., and Pan, T. (2015). N(6)- methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature 518 (7540), 560–564. doi: 10.1038/nature14234
31) Liu, N., Zhou, K. I., Parisien, M., Dai, Q., Diatchenko, L., and Pan, T. (2017). N6- methyladenosine alters RNA structure to regulate binding of a low-complexity protein. Nucleic Acids Res. 45 (10), 6051–6063. doi: 10.1093/nar/gkx141
32) Liu, R., Kasowitz, S. D., Homolka, D., Leu, N. A., Shaked, J. T., Ruthel, G., et al. (2021b). YTHDC2 is essential for pachytene progression and prevents aberrant microtubule-driven telomere clustering in male meiosis. Cell Rep. 37 (11), 110110. doi: 10.1016/j.celrep.2021.110110
33) Lou, X., Wang, J. J., Wei, Y. Q., and Sun, J. J. (2021). Emerging role of RNA modification N6-methyladenosine in immune evasion. Cell Death Dis. 12 (4), 300. doi: 10.1038/s41419-021-03585-z
34) Lu, M., Xue, M., Wang, H. T., Kairis, E. L., Ahmad, S., Wei, J., et al. (2021). Nonsegmented negative-sense RNA viruses utilize n (6)-methyladenosine (m(6)A) as a common strategy to evade host innate immunity. J. Virol. 95 (9), e01939–20. doi: 10.1128/JVI.01939-20
35) Lu, M., Zhang, Z., Xue, M., Zhao, B. S., Harder, O., Li, A., et al. (2020). N(6)- methyladenosine modification enables viral RNA to escape recognition by RNA sensor RIG-I. Nat. Microbiol. 5 (4), 584–598. doi: 10.1038/s41564-019-0653-9
36) Lu, W., Tirumuru, N., St Gelais, C., Koneru, P. C., Liu, C., Kvaratskhelia, M., et al. (2018). N(6)-methyladenosine-binding proteins suppress HIV-1 infectivity and viral production. J. Biol. Chem. 293 (34), 12992–13005. doi: 10.1074/jbc.RA118.004215
37) Luo, S., and Tong, L. (2014). Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain. Proc. Natl. Acad. Sci. U.S.A. 111 (38), 13834–13839. doi: 10.1073/pnas.1412742111
38) Mauer, J., Luo, X., Blanjoie, A., Jiao, X., Grozhik, A. V., Patil, D. P., et al. (2017). Reversible methylation of m(6)Am in the 5′ cap controls mRNA stability. Nature 541 (7637), 371–375. doi: 10.1038/nature21022
39) McFadden, M. J., McIntyre, A. B. R., Mourelatos, H., Abell, N. S., Gokhale, N. S., Ipas, H., et al. (2021). Post-transcriptional regulation of antiviral gene expression by N6-methyladenosine. Cell Rep. 34 (9), 108798. doi: 10.1016/j.celrep. 2021.108798
40) McIntyre, W., Netzband, R., Bonenfant, G., Biegel, J. M., Miller, C., Fuchs, G., et al. (2018). Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res. 46 (11), 5776–5791. doi: 10.1093/nar/gky029
41) Meyer, K. D., Patil, D. P., Zhou, J., Zinoviev, A., Skabkin, M. A., Elemento, O., et al. (2015). 5′ UTR m(6)A promotes cap-independent translation. Cell 163 (4), 999–1010.doi: 10.1016/j.cell.2015.10.012
42) Meyer, K. D., Patil, D. P., Zhou, J., Zinoviev, A., Skabkin, M. A., Elemento, O., et al. (2015). 5′ UTR m(6)A promotes cap-independent translation. Cell 163 (4), 999–1010. doi: 10.1016/j.cell.2015.10.012
43) Mohammed, A. A., Mahmoud, H. Q., Daham, R. I., Yaseen, O. Q., Sardal, M. H., Jasim, B. H., & Mohammed, K. R. (2025). Biochemical and Neuroendocrine Markers of Academic Stress in Iraqi Postgraduate Students: A Narrative Review. International Journal of Body, Mind & Culture (2345-5802), 12(8).
44) Moss, B., Gershowitz, A., Stringer, J. R., Holland, L. E., and Wagner, E. K. (1977). 5′- terminal and internal methylated nucleosides in herpes simplex virus type 1 mRNA. J. Virol. 23 (2), 234–239. doi: 10.1128/JVI.23.2.234-239.1977
45) Moss, B., Gershowitz, A., Stringer, J. R., Holland, L. E., and Wagner, E. K. (1977). 5′- terminal and internal methylated nucleosides in herpes simplex virus type 1 mRNA. J. Virol. 23 (2), 234–239. doi: 10.1128/JVI.23.2.234-239.1977
46) Nadaf, N. H., Mohammed, A. A., & Nadaf, S. H. (2025). Inspiration from Natural Biomass Utilization System for a Sustainable Lignocellulosic Refinery. In Recent Trends in Lignocellulosic Biofuels and Bioenergy: Advancements and Sustainability Assessment (pp. 123-141). Singapore: Springer Nature Singapore.
47) Narayan, P., Ayers, D. F., Rottman, F. M., Maroney, P. A., and Nilsen, T. W. (1987). Unequal distribution of N6-methyladenosine in influenza virus mRNAs. Mol. Cell Biol. 7 (4), 1572–1575. doi: 10.1128/mcb.7.4.1572-1575.1987
48) Narayan, P., Ayers, D. F., Rottman, F. M., Maroney, P. A., and Nilsen, T. W. (1987). Unequal distribution of N6-methyladenosine in influenza virus mRNAs. Mol. Cell Biol. 7 (4), 1572–1575. doi: 10.1128/mcb.7.4.1572-1575.1987
49) N’Da Konan, S., Segeral, E., Bejjani, F., Bendoumou, M., Ait Said, M., GalloisMontbrun, S., et al. (2022). YTHDC1 regulates distinct post-integration steps of HIV-1 replication and is important for viral infectivity. Retrovirology 19 (1), 4. doi: 10.1186/ s12977-022-00589-1
50) N’Da Konan, S., Segeral, E., Bejjani, F., Bendoumou, M., Ait Said, M., GalloisMontbrun, S., et al. (2022). YTHDC1 regulates distinct post-integration steps of HIV-1 replication and is important for viral infectivity. Retrovirology 19 (1), 4. doi: 10.1186/ s12977-022-00589-1
51) Ping, X. L., Sun, B. F., Wang, L., Xiao, W., Yang, X., Wang, W. J., et al. (2014). Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 24 (2), 177–189. doi: 10.1038/cr.2014.3
52) Price, A. M., Hayer, K. E., McIntyre, A. B. R., Gokhale, N. S., Abebe, J. S., Della Fera, A. N., et al. (2020). Direct RNA sequencing reveals m(6)A modifications on adenovirus RNA are necessary for efficient splicing. Nat. Commun. 11 (1), 6016. doi: 10.1038/ s41467-020-19787-6
53) Qiu, W., Zhang, Q., Zhang, R., Lu, Y., Wang, X., Tian, H., et al. (2021). N(6)- methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA. Nat. Commun. 12 (1), 1582. doi: 10.1038/s41467- 021-21904-y
54) Ren, W., Lu, J., Huang, M., Gao, L., Li, D., Wang, G. G., et al. (2019). Structure and regulation of ZCCHC4 in m(6)A-methylation of 28S rRNA. Nat. Commun. 10 (1), 5042. doi: 10.1038/s41467-019-12923-x
55) Ries, R. J., Zaccara, S., Klein, P., Olarerin-George, A., Namkoong, S., Pickering, B. F., et al. (2019). m(6)A enhances the phase separation potential of mRNA. Nature 571 (7765), 424–428. doi: 10.1038/s41586-019-1374-1
56) Ringeard, M., Marchand, V., Decroly, E., Motorin, Y., and Bennasser, Y. (2019). FTSJ3 is an RNA 2′-o-methyltransferase recruited by HIV to avoid innate immune sensing. Nature 565 (7740), 500–504. doi: 10.1038/s41586-018-0841-4
57) Riquelme-Barrios, S., Pereira-Montecinos, C., Valiente-Echeverria, F., and Soto-Rifo, R. (2018). Emerging roles of N(6)-methyladenosine on HIV-1 RNA metabolism and viral replication. Front. Microbiol. 9. doi: 10.3389/fmicb.2018.00576
58) Roundtree, I. A., Luo, G. Z., Zhang, Z., Wang, X., Zhou, T., Cui, Y., et al. (2017). YTHDC1 mediates nuclear export of N(6)-methyladenosine methylated mRNAs. Elife 6, e31311. doi: 10.7554/eLife.31311
59) Rubio, R. M., Depledge, D. P., Bianco, C., Thompson, L., and Mohr, I. (2018). RNA m(6) a modification enzymes shape innate responses to DNA by regulating interferon beta. Genes Dev. 32 (23-24), 1472–1484. doi: 10.1101/gad.319475.118
60) Runge, S., Sparrer, K. M., Lassig, C., Hembach, K., Baum, A., Garcia-Sastre, A., et al. (2014). In vivo ligands of MDA5 and RIG-I in measles virus-infected cells. PloS Pathog. 10 (4), e1004081. doi: 10.1371/journal.ppat.1004081
61) Shi, H., Wang, X., Lu, Z., Zhao, B. S., Ma, H., Hsu, P. J., et al. (2017). YTHDF3 facilitates translation and decay of N(6)-methyladenosine-modified RNA. Cell Res. 27 (3), 315–328. doi: 10.1038/cr.2017.15
62) Shulman, Z., and Stern-Ginossar, N. (2020). The RNA modification N(6)- methyladenosine as a novel regulator of the immune system. Nat. Immunol. 21 (5), 501–512. doi: 10.1038/s41590-020-0650-4
63) Shuman, S. (2002). What messenger RNA capping tells us about eukaryotic evolution. Nat. Rev. Mol. Cell Biol. 3 (8), 619–625. doi: 10.1038/nrm880
Cite this article
Mohammed, Z. B., & Mahdi, E. I. (2026). Viral Immune Escape: The Role of RNA M6a Modifications in Persistent Human Viral Infections and Precision Antiviral Therapy Limitations. INTERNATIONAL JOURNAL OF HEALTH & MEDICAL RESEARCH, 5(7), 616-623. https://doi.org/10.58806/ijhmr.2026.v5i7n06
