Abbasi‐Moheb,, L., Mertel,, S., Gonsior,, M., Nouri‐Vahid,, L., Kahrizi,, K., Cirak,, S., … Kuss,, A. W. (2012). Mutations in NSUN2 cause autosomal‐recessive intellectual disability. American Journal of Human Genetics, 90(5), 847–855. https://doi.org/10.1016/j.ajhg.2012.03.021
Agris,, P. F. (2008). Bringing order to translation: The contributions of transfer RNA anticodon‐domain modifications. EMBO Reports, 9(7), 629–635. https://doi.org/10.1038/embor.2008.104
Aguilo,, F., Li,, S., Balasubramaniyan,, N., Sancho,, A., Benko,, S., Zhang,, F., … Walsh,, M. J. (2016). Deposition of 5‐methylcytosine on enhancer RNAs enables the coactivator function of PGC‐1α. Cell Reports, 14(3), 479–492. https://doi.org/10.1016/j.celrep.2015.12.043
Alexandrov,, A., Chernyakov,, I., Gu,, W., Hiley,, S. L., Hughes,, T. R., Grayhack,, E. J., & Phizicky,, E. M. (2006). Rapid tRNA decay can result from lack of nonessential modifications. Molecular Cell, 21(1), 87–96. https://doi.org/10.1016/j.molcel.2005.10.036
Amort,, T., Rieder,, D., Wille,, A., Khokhlova‐Cubberley,, D., Riml,, C., Trixl,, L., … Lusser,, A. (2017). Distinct 5‐methylcytosine profiles in poly(a) RNA from mouse embryonic stem cells and brain. Genome Biology, 18(1), 1. https://doi.org/10.1186/s13059-016-1139-1
Anreiter,, I., Mir,, Q., Simpson,, J. T., Janga,, S. C., & Soller,, M. (2021). New twists in detecting mRNA modification dynamics. Trends in Biotechnology, 39(1), 72–89. https://doi.org/10.1016/j.tibtech.2020.06.002
Auxilien,, S., Guérineau,, V., Szweykowska‐Kulińska,, Z., & Golinelli‐Pimpaneau,, B. (2012). The human tRNA m5C methyltransferase Misu is multisite‐specific. RNA Biology, 9(11), 1331–1338. https://doi.org/10.4161/rna.22180
Basanta‐Sanchez,, M., Wang,, R., Liu,, Z., Ye,, X., Li,, M., Shi,, X., … Sheng,, J. (2017). TET1‐mediated oxidation of 5‐formylcytosine (5fC) to 5‐carboxycytosine (5caC) in RNA. Chembiochem, 18(1), 72–76. https://doi.org/10.1002/cbic.201600328
Blanco,, S., Bandiera,, R., Popis,, M., Hussain,, S., Lombard,, P., Aleksic,, J., … Frye,, M. (2016). Stem cell function and stress response are controlled by protein synthesis. Nature, 534(7607), 335–340. https://doi.org/10.1038/nature18282
Blanco,, S., Dietmann,, S., Flores,, J. V., Hussain,, S., Kutter,, C., Humphreys,, P., … Frye,, M. (2014). Aberrant methylation of tRNAs links cellular stress to neuro‐developmental disorders. EMBO Journal, 33(18), 2020–2039. https://doi.org/10.15252/embj.201489282
Blanco,, S., & Frye,, M. (2014). Role of RNA methyltransferases in tissue renewal and pathology. Current Opinion in Cell Biology, 31, 1–7. https://doi.org/10.1016/j.ceb.2014.06.006
Blanco,, S., Kurowski,, A., Nichols,, J., Watt,, F. M., Benitah,, S. A., & Frye,, M. (2011). The RNA‐methyltransferase Misu (NSun2) poises epidermal stem cells to differentiate. PLoS Genetics, 7(12), e1002403. https://doi.org/10.1371/journal.pgen.1002403
Boccaletto,, P., Machnicka,, M. A., Purta,, E., Piątkowski,, P., Bagiński,, B., Wirecki,, T. K., … Bujnicki,, J. M. (2018). MODOMICS: A database of RNA modification pathways. 2017 update. Nucleic Acids Research, 46(D1), D303–D307. https://doi.org/10.1093/nar/gkx1030
Bohnsack,, K. E., Höbartner,, C., & Bohnsack,, M. T. (2019). Eukaryotic 5‐methylcytosine (m5C) RNA methyltransferases: Mechanisms, cellular functions, and links to disease. Genes (Basel), 10(2), 102. https://doi.org/10.3390/genes10020102
Bourgeois,, G., Ney,, M., Gaspar,, I., Aigueperse,, C., Schaefer,, M., Kellner,, S., … Motorin,, Y. (2015). Eukaryotic rRNA modification by yeast 5‐methylcytosine‐methyltransferases and human proliferation‐associated antigen p120. PLoS One, 10(7), e0133321. https://doi.org/10.1371/journal.pone.0133321
Brzezicha,, B., Schmidt,, M., Makalowska,, I., Jarmolowski,, A., Pieńkowska,, J., & Szweykowska‐Kulińska,, Z. (2006). Identification of human tRNA:m5C methyltransferase catalysing intron‐dependent m5C formation in the first position of the anticodon of the pre‐tRNALeu(CAA). Nucleic Acids Research, 34(20), 6034–6043. https://doi.org/10.1093/nar/gkl765
Burgess,, A. L., David,, R., & Searle,, I. R. (2015). Conservation of tRNA and rRNA 5‐methylcytosine in the kingdom Plantae. BMC Plant Biology, 15, 199. https://doi.org/10.1186/s12870-015-0580-8
Cámara,, Y., Asin‐Cayuela,, J., Park,, C. B., Metodiev,, M. D., Shi,, Y., Ruzzenente,, B., … Larsson,, N. G. (2011). MTERF4 regulates translation by targeting the methyltransferase NSUN4 to the mammalian mitochondrial ribosome. Cell Metabolism, 13(5), 527–539. https://doi.org/10.1016/j.cmet.2011.04.002
Chan,, C. T., Pang,, Y. L., Deng,, W., Babu,, I. R., Dyavaiah,, M., Begley,, T. J., & Dedon,, P. C. (2012). Reprogramming of tRNA modifications controls the oxidative stress response by codon‐biased translation of proteins. Nature Communications, 3, 937. https://doi.org/10.1038/ncomms1938
Chang,, C. T., Hautbergue,, G. M., Walsh,, M. J., Viphakone,, N., van Dijk,, T. B., Philipsen,, S., & Wilson,, S. A. (2013). Chtop is a component of the dynamic TREX mRNA export complex. EMBO Journal, 32(3), 473–486. https://doi.org/10.1038/emboj.2012.342
Chen,, P., Zhang,, T., Yuan,, Z., Shen,, B., & Chen,, L. (2019). Expression of the RNA methyltransferase Nsun5 is essential for developing cerebral cortex. Molecular Brain, 12(1), 74. https://doi.org/10.1186/s13041-019-0496-6
Chen,, X., Li,, A., Sun,, B. F., Yang,, Y., Han,, Y. N., Yuan,, X., … Yang,, Y. G. (2019). 5‐methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nature Cell Biology, 21(8), 978–990. https://doi.org/10.1038/s41556-019-0361-y
Cheng,, J. X., Chen,, L., Li,, Y., Cloe,, A., Yue,, M., Wei,, J., … Vardiman,, J. W. (2018). RNA cytosine methylation and methyltransferases mediate chromatin organization and 5‐azacytidine response and resistance in leukaemia. Nature Communications, 9(1), 1163. https://doi.org/10.1038/s41467-018-03513-4
Chernyakov,, I., Whipple,, J. M., Kotelawala,, L., Grayhack,, E. J., & Phizicky,, E. M. (2008). Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′‐3′ exonucleases Rat1 and Xrn1. Genes %26 Development, 22(10), 1369–1380. https://doi.org/10.1101/gad.1654308
Chi,, L., & Delgado‐Olguín,, P. (2013). Expression of NOL1/NOP2/sun domain (Nsun) RNA methyltransferase family genes in early mouse embryogenesis. Gene Expression Patterns, 13(8), 319–327. https://doi.org/10.1016/j.gep.2013.06.003
Courtney,, D. G., Chalem,, A., Bogerd,, H. P., Law,, B. A., Kennedy,, E. M., Holley,, C. L., & Cullen,, B. R. (2019). Extensive epitranscriptomic methylation of a and C residues on murine leukemia virus transcripts enhances viral gene expression. MBio, 10(3), e01209–e01219. https://doi.org/10.1128/MBio01209-19
Courtney,, D. G., Tsai,, K., Bogerd,, H. P., Kennedy,, E. M., Law,, B. A., Emery,, A., … Cullen,, B. R. (2019). Epitranscriptomic addition of m5C to HIV‐1 transcripts regulates viral gene expression. Cell Host %26 Microbe, 26(2), 217–227. https://doi.org/10.1016/j.chom.2019.07.005
Cui,, X., Liang,, Z., Shen,, L., Zhang,, Q., Bao,, S., Geng,, Y., … Yu,, H. (2017). 5‐methylcytosine RNA methylation in Arabidopsis thaliana. Molecular Plant, 10(11), 1387–1399. https://doi.org/10.1016/j.molp.2017.09.013
David,, R., Burgess,, A., Parker,, B., Li,, J., Pulsford,, K., Sibbritt,, T., … Searle,, I. R. (2017). Transcriptome‐wide mapping of RNA 5‐methylcytosine in Arabidopsis mRNAs and noncoding RNAs. Plant Cell, 29(3), 445–460. https://doi.org/10.1105/tpc.16.00751
Dubin,, D. T., & Taylor,, R. H. (1975). The methylation state of poly A‐containing messenger RNA from cultured hamster cells. Nucleic Acids Research, 2(10), 1653–1668. https://doi.org/10.1093/nar/2.10.1653
Dufu,, K., Livingstone,, M. J., Seebacher,, J., Gygi,, S. P., Wilson,, S. A., & Reed,, R. (2010). ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes %26 Development, 24(18), 2043–2053. https://doi.org/10.1101/gad.1898610
Durdevic,, Z., Hanna,, K., Gold,, B., Pollex,, T., Cherry,, S., Lyko,, F., & Schaefer,, M. (2013). Efficient RNA virus control in Drosophila requires the RNA methyltransferase Dnmt2. EMBO Reports, 14(3), 269–275. https://doi.org/10.1038/embor.2013.3
Flores,, J. V., Cordero‐Espinoza,, L., Oeztuerk‐Winder,, F., Andersson‐Rolf,, A., Selmi,, T., Blanco,, S., … Frye,, M. (2017). Cytosine‐5 RNA methylation regulates neural stem cell differentiation and motility. Stem Cell Reports, 8(1), 112–124. https://doi.org/10.1016/j.stemcr.2016.11.014
Fu,, L., Guerrero,, C. R., Zhong,, N., Amato,, N. J., Liu,, Y., Liu,, S., … Wang,, Y. (2014). Tet‐mediated formation of 5‐hydroxymethylcytosine in RNA. Journal of the American Chemical Society, 136(33), 11582–11585. https://doi.org/10.1021/ja505305z
Gao,, Y., Wang,, Z., Zhu,, Y., Zhu,, Q., Yang,, Y., Jin,, Y., … Hao,, Y. (2019). NOP2/Sun RNA methyltransferase 2 promotes tumor progression via its interacting partner RPL6 in gallbladder carcinoma. Cancer Science, 110(11), 3510–3519. https://doi.org/10.1111/cas.14190
Garalde,, D. R., Snell,, E. A., Jachimowicz,, D., Sipos,, B., Lloyd,, J. H, Bruce,, M., … Turner,, D. J. (2018). Highly parallel direct RNA sequencing on an array of nanopores. Nature Methods, 15(3), 201–206. http://dx.doi.org/10.1038/nmeth.4577.
García‐Vílchez,, R., Sevilla,, A., & Blanco,, S. (2019). Post‐transcriptional regulation by cytosine‐5 methylation of RNA. Biochimica et Biophysica Acta, Gene Regulatory Mechanisms, 1862(3), 240–252. https://doi.org/10.1016/j.bbagrm.2018.12.003
George,, H., Ule,, J., & Hussain,, S. (2017). Illustrating the epitranscriptome at nucleotide resolution using methylation‐iCLIP (miCLIP). Methods in Molecular Biology, 1562, 91–106. https://doi.org/10.1007/978-1-4939-6807-7_7
Gigova,, A., Duggimpudi,, S., Pollex,, T., Schaefer,, M., & Koš,, M. (2014). A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability. RNA, 20(10), 1632–1644. https://doi.org/10.1261/rna.043398.113
Goll,, M. G., Kirpekar,, F., Maggert,, K. A., Yoder,, J. A., Hsieh,, C. L., Zhang,, X., … Bestor,, T. H. (2006). Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science, 311(5759), 395–398. https://doi.org/10.1126/science.1120976
Goodarzi,, H., Liu,, X., Nguyen,, H. C., Zhang,, S., Fish,, L., & Tavazoie,, S. F. (2015). Endogenous tRNA‐derived fragments suppress breast cancer progression via YBX1 displacement. Cell, 161(4), 790–802. https://doi.org/10.1016/j.cell.2015.02.053
Guallar,, D., Bi,, X., Pardavila,, J. A., Huang,, X., Saenz,, C., Shi,, X., … Wang,, J. (2018). RNA‐dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells. Nature Genetics, 50(3), 443–451. https://doi.org/10.1038/s41588-018-0060-9
Haag,, S., Sloan,, K. E., Ranjan,, N., Warda,, A. S., Kretschmer,, J., Blessing,, C., … Bohnsack,, M. T. (2016). NSUN3 and ABH1 modify the wobble position of mt‐tRNAMet to expand codon recognition in mitochondrial translation. EMBO Journal, 35(19), 2104–2119. https://doi.org/10.15252/embj.201694885
Haag,, S., Warda,, A. S., Kretschmer,, J., Günnigmann,, M. A., Höbartner,, C., & Bohnsack,, M. T. (2015). NSUN6 is a human RNA methyltransferase that catalyzes formation of m5C72 in specific tRNAs. RNA, 21(9), 1532–1543. https://doi.org/10.1261/rna.051524.115
Han,, X., Liu,, H., Zhang,, Z., Yang,, W., Wu,, C., Liu,, X., … Ding,, W. (2020). Epitranscriptomic 5‐methylcytosine profile in PM2.5‐induced mouse pulmonary fibrosis. Genomics, Proteomics %26 Bioinformatics, S1672‐0229(20), 30020–30026. https://doi.org/10.1016/j.gpb.2019.11.005
Harris,, T., Marquez,, B., Suarez,, S., & Schimenti,, J. (2007). Sperm motility defects and infertility in male mice with a mutation in Nsun7, a member of the Sun domain‐containing family of putative RNA methyltransferases. Biology of Reproduction, 77(2), 376–382. https://doi.org/10.1095/biolreprod.106.058669
Heissenberger,, C., Liendl,, L., Nagelreiter,, F., Gonskikh,, Y., Yang,, G., Stelzer,, E. M., … Schosserer,, M. (2019). Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth. Nucleic Acids Research, 47(22), 11807–11825. https://doi.org/10.1093/nar/gkz1043
Hu,, J., Manduzio,, S., & Kang,, H. (2019). Epitranscriptomic RNA methylation in plant development and abiotic stress responses. Frontiers in Plant Science, 10, 500. https://doi.org/10.3389/fpls.2019.00500
Huang,, H., Weng,, H., Zhou,, K., Wu,, T., Zhao,, B. S., Sun,, M., … Chen,, J. (2019). Histone H3 trimethylation at lysine 36 guides m6A RNA modification co‐transcriptionally. Nature, 567(7748), 414–419. https://doi.org/10.1038/s41586-019-1016-7
Huang,, T., Chen,, W., Liu,, J., Gu,, N., & Zhang,, R. (2019). Genome‐wide identification of mRNA 5‐methylcytosine in mammals. Nature Structural %26 Molecular Biology, 26(5), 380–388. https://doi.org/10.1038/s41594-019-0218-x
Huber,, S. M., van Delft,, P., Mendil,, L., Bachman,, M., Smollett,, K., Werner,, F., … Balasubramanian,, S. (2015). Formation and abundance of 5‐hydroxymethylcytosine in RNA. Chembiochem, 16(5), 752–755. https://doi.org/10.1002/cbic.201500013
Hussain,, S., Benavente,, S. B., Nascimento,, E., Dragoni,, I., Kurowski,, A., Gillich,, A., … Frye,, M. (2009). The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability. Journal of Cell Biology, 186(1), 27–40. https://doi.org/10.1083/jcb.200810180
Hussain,, S., Sajini,, A. A., Blanco,, S., Dietmann,, S., Lombard,, P., Sugimoto,, Y., … Frye,, M. (2013). NSun2‐mediated cytosine‐5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Reports, 4(2), 255–261. https://doi.org/10.1016/j.celrep.2013.06.029
Hussain,, S., Tuorto,, F., Menon,, S., Blanco,, S., Cox,, C., Flores,, J. V., … Frye,, M. (2013). The mouse cytosine‐5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. Molecular and Cellular Biology, 33(8), 1561–1570. https://doi.org/10.1128/MCB.01523-12
Janin,, M., Ortiz‐Barahona,, V., de Moura,, M. C., Martinez‐Cardus,, A., Llinas‐Arias,, P., Soler,, M., … Esteller,, M. (2019). Epigenetic loss of RNA‐methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program. Acta Neuropathologica, 138(6), 1053–1074. https://doi.org/10.1007/s00401-019-02062-4
Jenjaroenpun,, P., Wongsurawat,, T., Wadley,, T. D., Wassenaar,, T. M., Liu,, J., Dai,, Q., … Nookaew,, I. (2020). Decoding the epitranscriptional landscape from native RNA sequences. Nucleic Acids Research, gkaa620. https://doi.org/10.1093/nar/gkaa620
Jia,, G., Fu,, Y., Zhao,, X., Dai,, Q., Zheng,, G., Yang,, Y., … He,, C. (2011). N6‐methyladenosine in nuclear RNA is a major substrate of the obesity‐associated FTO. Nature Chemical Biology, 7(12), 885–887. https://doi.org/10.1038/nchembio.687
Jüttermann,, R., Li,, E., & Jaenisch,, R. (1994). Toxicity of 5‐aza‐2′‐deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation. Proceedings of the National Academy of Sciences of the United States of America, 91(25), 11797–11801. https://doi.org/10.1073/pnas.91.25.11797
Kawarada,, L., Suzuki,, T., Ohira,, T., Hirata,, S., Miyauchi,, K., & Suzuki,, T. (2017). ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications. Nucleic Acids Research, 45(12), 7401–7415. https://doi.org/10.1093/nar/gkx354
Khoddami,, V., & Cairns,, B. R. (2013). Identification of direct targets and modified bases of RNA cytosine methyltransferases. Nature Biotechnology, 31(5), 458–464. https://doi.org/10.1038/nbt.2566
Khoddami,, V., & Cairns,, B. R. (2014). Transcriptome‐wide target profiling of RNA cytosine methyltransferases using the mechanism‐based enrichment procedure Aza‐IP. Nature Protocols, 9(2), 337–361. https://doi.org/10.1038/nprot.2014.014
Khoddami,, V., Yerra,, A., & Cairns,, B. R. (2015). Experimental approaches for target profiling of RNA cytosine methyltransferases. Methods in Enzymology, 560, 273–296. https://doi.org/10.1016/bs.mie.2015.03.008
Khosronezhad,, N., Colagar,, A. H., & Jorsarayi,, S. G. (2015). T26248G‐transversion mutation in exon7 of the putative methyltransferase Nsun7 gene causes a change in protein folding associated with reduced sperm motility in asthenospermic men. Reproduction, Fertility and Development, 27(3), 471–480. https://doi.org/10.1071/RD13371
Kiani,, J., Grandjean,, V., Liebers,, R., Tuorto,, F., Ghanbarian,, H., Lyko,, F., … Rassoulzadegan,, M. (2013). RNA‐mediated epigenetic heredity requires the cytosine methyltransferase Dnmt2. PLoS Genetics, 9(5), e1003498. https://doi.org/10.1371/journal.pgen.1003498
King,, M. Y., & Redman,, K. L. (2002). RNA methyltransferases utilize two cysteine residues in the formation of 5‐methylcytosine. Biochemistry, 41(37), 11218–11225. https://doi.org/10.1021/bi026055q
Kong,, W., Biswas,, A., Zhou,, D., Fiches,, G., Fujinaga,, K., Santoso,, N., & Zhu,, J. (2020). Nucleolar protein NOP2/NSUN1 suppresses HIV‐1 transcription and promotes viral latency by competing with tat for TAR binding and methylation. PLoS Pathogens, 16(3), e1008430. https://doi.org/10.1371/journal.ppat.1008430
Li,, C., Wang,, S., Xing,, Z., Lin,, A., Liang,, K., Song,, J., … Yang,, L. (2017). A ROR1‐HER3‐lncRNA signalling axis modulates the hippo‐YAP pathway to regulate bone metastasis. Nature Cell Biology, 19(2), 106–119. https://doi.org/10.1038/ncb3464
Li,, J., Li,, H., Long,, T., Dong,, H., Wang,, E. D., & Liu,, R. J. (2019). Archaeal NSUN6 catalyzes m5C72 modification on a wide‐range of specific tRNAs. Nucleic Acids Research, 47(4), 2041–2055. https://doi.org/10.1093/nar/gky1236
Liang,, W., Lin,, Z., Du,, C., Qiu,, D., & Zhang,, Q. (2020). mRNA modification orchestrates cancer stem cell fate decisions. Molecular Cancer, 19(1), 38. https://doi.org/10.1186/s12943-020-01166-w
Liu,, F., Clark,, W., Luo,, G., Wang,, X., Fu,, Y., Wei,, J., … He,, C. (2016). ALKBH1‐mediated tRNA demethylation regulates translation. Cell, 167(3), 816–828. https://doi.org/10.1016/j.cell.2016.09.038
Liu,, H., Begik,, O., Lucas,, M. C., Ramirez,, J. M., Mason,, C. E., Wiener,, D., … Novoa,, E. M. (2019). Accurate detection of m6A RNA modifications in native RNA sequences. Nature Communications, 10(1), 4079. https://doi.org/10.1038/s41467-019-11713-9
Liu,, J., Yue,, Y., Han,, D., Wang,, X., Fu,, Y., Zhang,, L., … He,, C. (2014). A METTL3‐METTL14 complex mediates mammalian nuclear RNA N6‐adenosine methylation. Nature Chemical Biology, 10(2), 93–95. https://doi.org/10.1038/nchembio.1432
Liu,, R. J., Long,, T., Li,, J., Li,, H., & Wang,, E. D. (2017). Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. Nucleic Acids Research, 45(11), 6684–6697. https://doi.org/10.1093/nar/gkx473
Liu,, Y., & Santi,, D. V. (2000). m5C RNA and m5C DNA methyl transferases usedifferent cysteine residues as catalysts. Proceedings of the National Academy of Sciences of the United States of America, 97(15), 8263–8265. https://doi.org/10.1073/pnas.97.15.8263
Long,, T., Li,, J., Li,, H., Zhou,, M., Zhou,, X. L., Liu,, R. J., & Wang,, E. D. (2016). Sequence‐specific and shape‐selective RNA recognition by the human RNA 5‐Methylcytosine methyltransferase NSun6. Journal of Biological Chemistry, 291(46), 24293–24303. https://doi.org/10.1074/jbc.M116.742569
Lorenz,, D. A., Sathe,, S., Einstein,, J. M., & Yeo,, G. W. (2020). Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base‐specific resolution. RNA, 26(1), 19–28. https://doi.org/10.1261/rna.072785.119
Martinez,, F. J., Lee,, J. H., Lee,, J. E., Blanco,, S., Nickerson,, E., Gabriel,, S., … Gleeson,, J. G. (2012). Whole exome sequencing identifies a splicing mutation in NSUN2 as a cause of a Dubowitz‐like syndrome. Journal of Medical Genetics, 49(6), 380–385. https://doi.org/10.1136/jmedgenet-2011-100686
Metodiev,, M. D., Spåhr,, H., Loguercio Polosa,, P., Meharg,, C., Becker,, C., Altmueller,, J., … Ruzzenente,, B. (2014). NSUN4 is a dual function mitochondrial protein required for both methylation of 12S rRNA and coordination of mitoribosomal assembly. PLoS Genetics, 10(2), e1004110. https://doi.org/10.1371/journal.pgen.1004110
Motorin,, Y., & Helm,, M. (2011). RNA nucleotide methylation. WIREs RNA, 2(5), 611–631. https://doi.org/10.1002/wrna.79
Nakano,, S., Suzuki,, T., Kawarada,, L., Iwata,, H., Asano,, K., & Suzuki,, T. (2016). NSUN3 methylase initiates 5‐formylcytidine biogenesis in human mitochondrial tRNAMet. Nature Chemical Biology, 12(7), 546–551. https://doi.org/10.1038/nchembio.2099
Ougland,, R., Jonson,, I., Moen,, M. N., Nesse,, G., Asker,, G., Klungland,, A., & Larsen,, E. (2016). Role of ALKBH1 in the core transcriptional network of embryonic stem cells. Cellular Physiology and Biochemistry, 38(1), 173–184. https://doi.org/10.1159/000438619
Ougland,, R., Lando,, D., Jonson,, I., Dahl,, J. A., Moen,, M. N., Nordstrand,, L. M., … Larsen,, E. (2012). ALKBH1 is a histone H2A dioxygenase involved in neural differentiation. Stem Cells, 30(12), 2672–2682. https://doi.org/10.1002/stem.1228
Parker,, M. T., Knop,, K., Sherwood,, A. V., Schurch,, N. J., Mackinnon,, K., Gould,, P. D., … Simpson,, G. G. (2020). Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife, 9, e49658. https://doi.org/10.7554/eLife.49658
Peng,, Z., Wang,, J., Shan,, B., Li,, B., Peng,, W., Dong,, Y., … Duan,, C. (2018). The long noncoding RNA LINC00312 induces lung adenocarcinoma migration and vasculogenic mimicry through directly binding YBX1. Molecular Cancer, 17(1), 167. https://doi.org/10.1186/s12943-018-0920-z
Rang,, F. J., Kloosterman,, W. P., & de Ridder,, J. (2018). From squiggle to basepair: Computational approaches for improving nanopore sequencing read accuracy. Genome Biology, 19(1), 90. https://doi.org/10.1186/s13059-018-1462-9
Redman,, K. L. (2006). Assembly of protein‐RNA complexes using natural RNA and mutant forms of an RNA cytosine methyltransferase. Biomacromolecules, 7(12), 3321–3326. https://doi.org/10.1021/bm051012l
Reid,, R., Greene,, P. J., & Santi,, D. V. (1999). Exposition of a family of RNA m5C methyltransferases from searching genomic and proteomic sequences. Nucleic Acids Research, 27(15), 3138–3145. https://doi.org/10.1093/nar/27.15.3138
Ren,, H. Y., Zhong,, R., Ding,, X. P., Chen,, Z. Y., & Jing,, Y. L. (2015). Investigation of polymorphisms in exon7 of the NSUN7 gene among Chinese Han men with asthenospermia. Genetics and Molecular Research, 14(3), 9261–9268. https://doi.org/10.4238/2015.August.10.6
Sajini,, A. A., Choudhury,, N. R., Wagner,, R. E., Bornelov,, S., Selmi,, T., Spanos,, C., … Frye,, M. (2019). Loss of 5‐methylcytosine alters the biogenesis of vault‐derived small RNAs to coordinate epidermal differentiation. Nature Communications, 10(1), 2550. https://doi.org/10.1038/s41467-019-10020-7
Sarkozy,, P., Jobbágy,, Á., & Antal,, P. (2018). Calling homopolymer stretches from raw Nanopore reads by analyzing k‐mer dwell times. IFMBE Proceedings, 65, 241–244. https://doi.org/10.1007/978-981-10-5122-7_61
Schaefer,, M. (2015). RNA 5‐methylcytosine analysis by bisulfite sequencing. Methods in Enzymology, 560, 297–329. https://doi.org/10.1016/bs.mie.2015.03.007
Schaefer,, M., & Lyko,, F. (2010). Solving the Dnmt2 enigma. Chromosoma, 119(1), 35–40. https://doi.org/10.1007/s00412-009-0240-6
Schaefer,, M., Pollex,, T., Hanna,, K., & Lyko,, F. (2009). RNA cytosine methylation analysis by bisulfite sequencing. Nucleic Acids Research, 37(2), e12. https://doi.org/10.1093/nar/gkn954
Schaefer,, M., Pollex,, T., Hanna,, K., Tuorto,, F., Meusburger,, M., Helm,, M., & Lyko,, F. (2010). RNA methylation by Dnmt2 protects transfer RNAs against stress‐induced cleavage. Genes %26 Development, 24(15), 1590–1595. https://doi.org/10.1101/gad.586710
Schosserer,, M., Minois,, N., Angerer,, T. B., Amring,, M., Dellago,, H., Harreither,, E., … Grillari,, J. (2015). Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nature Communications, 6, 6158. https://doi.org/10.1038/ncomms7158
Shanmugam,, R., Fierer,, J., Kaiser,, S., Helm,, M., Jurkowski,, T. P., & Jeltsch,, A. (2015). Cytosine methylation of tRNA‐asp by DNMT2 has a role in translation of proteins containing poly‐Asp sequences. Cell Discovery, 1, 15010. https://doi.org/10.1038/celldisc.2015.10
Shen,, Q., Zhang,, Q., Shi,, Y., Shi,, Q., Jiang,, Y., Gu,, Y., … Cao,, X. (2018). Tet2 promotes pathogen infection‐induced myelopoiesis through mRNA oxidation. Nature, 554(7690), 123–127. https://doi.org/10.1038/nature25434
Song,, J., & Yi,, C. (2019). Reading chemical modifications in the transcriptome. Journal of Molecular Biology, 432(6), 1824–1839. https://doi.org/10.1016/j.jmb.2019.10.006
Squires,, J. E., Patel,, H. R., Nousch,, M., Sibbritt,, T., Humphreys,, D. T., Parker,, B. J., … Preiss,, T. (2012). Widespread occurrence of 5‐methylcytosine in human coding and non‐coding RNA. Nucleic Acids Research, 40(11), 5023–5033. https://doi.org/10.1093/nar/gks144
Sun,, J., Yan,, L., Shen,, W., & Meng,, A. (2018). Maternal Ybx1 safeguards zebrafish oocyte maturation and maternal‐to‐zygotic transition by repressing global translation. Development, 145(19), dev166587. https://doi.org/10.1242/dev.166587
Suresh,, P. S., Tsutsumi,, R., & Venkatesh,, T. (2018). YBX1 at the crossroads of non‐coding transcriptome, exosomal, and cytoplasmic granular signaling. European Journal of Cell Biology, 97(3), 163–167. https://doi.org/10.1016/j.ejcb.2018.02.003
Taiaroa,, G., Rawlinson,, D., Featherstone,, L., Pitt,, M., Caly,, L., Druce,, J., … Duchene,, S. (2020). Direct RNA sequencing and early evolution of SARS‐CoV‐2. bioRxiv, 2020, 976167. https://doi.org/10.1101/2020.03.05.976167
Takemoto,, C., Spremulli,, L. L., Benkowski,, L. A., Ueda,, T., Yokogawa,, T., & Watanabe,, K. (2009). Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Research, 37(5), 1616–1627. https://doi.org/10.1093/nar/gkp001
Tang,, Y., Gao,, C., Gao,, Y., Ying,, Y., Shi,, B., Yu,, J., … Chong,, K. (2020). OsNSUN2‐mediated 5‐methylcytidine mRNA modification enhances rice adaptation to high‐temperature. Developmental Cell, 53(3), 272–286. https://doi.org/10.1016/j.devcel.2020.03.009
Trerè,, D., Migaldi,, M., Montanaro,, L., Pession,, A., & Derenzini,, M. (2000). p120 expression provides a reliable indication of the rapidity of cell duplication in cancer cells independently of tumour origin. Journal of Pathology, 192(2), 216–220. https://doi.org/10.1002/1096-9896(2000)9999:9999%3C::AID-PATH695%3E3.0.CO;2-L
Trixl,, L., Amort,, T., Wille,, A., Zinni,, M., Ebner,, S., Hechenberger,, C., … Lusser,, A. (2018). RNA cytosine methyltransferase Nsun3 regulates embryonic stem cell differentiation by promoting mitochondrial activity. Cellular and Molecular Life Sciences, 75(8), 1483–1497. https://doi.org/10.1007/s00018-017-2700-0
Trixl,, L., & Lusser,, A. (2019). The dynamic RNA modification 5‐methylcytosine and its emerging role as an epitranscriptomic mark. WIREs RNA, 10(1), e1510. https://doi.org/10.1002/wrna.1510
Tuorto,, F., Herbst,, F., Alerasool,, N., Bender,, S., Popp,, O., Federico,, G., … Lyko,, F. (2015). The tRNA methyltransferase Dnmt2 is required for accurate polypeptide synthesis during haematopoiesis. EMBO Journal, 34(18), 2350–2362. https://doi.org/10.15252/embj.201591382
Tuorto,, F., Liebers,, R., Musch,, T., Schaefer,, M., Hofmann,, S., Kellner,, S., … Lyko,, F. (2012). RNA cytosine methylation by Dnmt2 and NSun2 promotes tRNA stability and protein synthesis. Nature Structural %26 Molecular Biology, 19(9), 900–905. https://doi.org/10.1038/nsmb.2357
Uchiyama,, B., Saijo,, Y., Kumano,, N., Abe,, T., Fujimura,, S., Ohkuda,, K., … Nukiwa,, T. (1997). Expression of nucleolar protein p120 in human lung cancer difference in histological types as a marker for proliferation. Clinical Cancer Research, 3(10), 1873–1877.
Van Haute,, L., Dietmann,, S., Kremer,, L., Hussain,, S., Pearce,, S. F., Powell,, C. A., … Minczuk,, M. (2016). Deficient methylation and formylation of mt‐tRNAMet wobble cytosine in a patient carrying mutations in NSUN3. Nature Communications, 7, 12039. https://doi.org/10.1038/ncomms12039
Väre,, V. Y., Eruysal,, E. R., Narendran,, A., Sarachan,, K. L., & Agris,, P. F. (2017). Chemical and conformational diversity of modified nucleosides affects tRNA structure and function. Biomolecules, 7(1), 29. https://doi.org/10.3390/biom7010029
Westbye,, M. P., Feyzi,, E., Aas,, P. A., Vågbø,, C. B., Talstad,, V. A., Kavli,, B., … Krokan,, H. E. (2008). Human AlkB homolog 1 is a mitochondrial protein that demethylates 3‐methylcytosine in DNA and RNA. Journal of Biological Chemistry, 283(36), 25046–25056. https://doi.org/10.1074/jbc.M803776200
Wu,, T. P., Wang,, T., Seetin,, M. G., Lai,, Y., Zhu,, S., Lin,, K., … Xiao,, A. Z. (2016). DNA methylation on N6‐adenine in mammalian embryonic stem cells. Nature, 532(7599), 329–333. https://doi.org/10.1038/nature17640
Xue,, S., Xu,, H., Sun,, Z., Shen,, H., Chen,, S., Ouyang,, J., … Cui,, H. (2019). Depletion of TRDMT1 affects 5‐methylcytosine modification of mRNA and inhibits HEK293 cell proliferation and migration. Biochemical and Biophysical Research Communications, 520(1), 60–66. https://doi.org/10.1016/j.bbrc.2019.09.098
Yakubovskaya,, E., Guja,, K. E., Mejia,, E., Castano,, S., Hambardjieva,, E., Choi,, W. S., & Garcia‐Diaz,, M. (2012). Structure of the essential MTERF4:NSUN4 protein complex reveals how an MTERF protein collaborates to facilitate rRNA modification. Structure, 20(11), 1940–1947. https://doi.org/10.1016/j.str.2012.08.027
Yang,, L., Perrera,, V., Saplaoura,, E., Apelt,, F., Bahin,, M., Kramdi,, A., … Kragler,, F. (2019). m5C methylation guides systemic transport of messenger RNA over graft junctions in plants. Current Biology, 29(15), 2465–2476. https://doi.org/10.1016/j.cub.2019.06.042
Yang,, X., Yang,, Y., Sun,, B. F., Chen,, Y. S., Xu,, J. W., Lai,, W. Y., … Yang,, Y. G. (2017). 5‐methylcytosine promotes mRNA export ‐ NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Research, 27(5), 606–625. https://doi.org/10.1038/cr.2017.55
Yang,, Y., Wang,, L., Han,, X., Yang,, W. L., Zhang,, M., Ma,, H. L., … Yang,, Y. G. (2019). RNA 5‐methylcytosine facilitates the maternal‐to‐zygotic transition by preventing maternal mRNA decay. Molecular Cell, 75(6), 1188–1202.e1111. https://doi.org/10.1016/j.molcel.2019.06.033
Yuan,, F., Bi,, Y., Siejka‐Zielinska,, P., Zhou,, Y. L., Zhang,, X. X., & Song,, C. X. (2019). Bisulfite‐free and base‐resolution analysis of 5‐methylcytidine and 5‐hydroxymethylcytidine in RNA with peroxotungstate. Chemical Communications (Cambridge, England), 55(16), 2328–2331. https://doi.org/10.1039/c9cc00274j
Yuan,, Z., Chen,, P., Zhang,, T., Shen,, B., & Chen,, L. (2019). Agenesis and Hypomyelination of corpus callosum in mice lacking Nsun5, an RNA Methyltransferase. Cell, 8(6), 552. https://doi.org/10.3390/cells8060552
Zhang,, S., Li,, R., Zhang,, L., Chen,, S., Xie,, M., Yang,, L., … Lam,, H. M. (2020). New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs. Nucleic Acids Research, 48(14), 7700–7711. https://doi.org/10.1093/nar/gkaa588
Zhang,, T., Chen,, P., Li,, W., Sha,, S., Wang,, Y., Yuan,, Z., … Chen,, L. (2019). Cognitive deficits in mice lacking Nsun5, a cytosine‐5 RNA methyltransferase, with impairment of oligodendrocyte precursor cells. Glia, 67(4), 688–702. https://doi.org/10.1002/glia.23565
Zheng,, G., Dahl,, J. A., Niu,, Y., Fedorcsak,, P., Huang,, C. M., Li,, C. J., … He,, C. (2013). ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Molecular Cell, 49(1), 18–29. https://doi.org/10.1016/j.molcel.2012.10.015
Zou,, F., Tu,, R., Duan,, B., Yang,, Z., Ping,, Z., Song,, X., … Xie,, T. (2020). Drosophila YBX1 homolog YPS promotes ovarian germ line stem cell development by preferentially recognizing 5‐methylcytosine RNAs. Proceedings of the National Academy of Sciences of the United States of America, 117(7), 3603–3609. https://doi.org/10.1073/pnas.1910862117