563
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Global and single-nucleotide resolution detection of 7-methylguanosine in RNA

, , , , , , , , , & ORCID Icon show all
Pages 1-18 | Accepted 27 Mar 2024, Published online: 02 Apr 2024

References

  • Shi H, Chai P, Jia R, et al. Novel insight into the regulatory roles of diverse RNA modifications: re-defining the bridge between transcription and translation. Mol Cancer. 2020;19(1):78. doi: 10.1186/s12943-020-01194-6
  • Nombela P, Miguel-Lopez B, Blanco S. The role of m6A, m5C and Ψ RNA modifications in cancer: novel therapeutic opportunities. Mol Cancer. 2021;20(1):18. doi: 10.1186/s12943-020-01263-w
  • Delaunay S, Frye M. RNA modifications regulating cell fate in cancer. Nat Cell Biol. 2019;21(5):552–559. doi: 10.1038/s41556-019-0319-0
  • Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends Mol Med. 2014;20(6):306–314. doi: 10.1016/j.molmed.2014.01.008
  • Garcia-Vilchez R, Anazco-Guenkova AM, Lopez J, et al. N7-methylguanosine methylation of tRnas regulates survival to stress in cancer. Oncogene. 2023;42(43):3169–3181. doi: 10.1038/s41388-023-02825-0
  • Wu Y, Zhan S, Xu Y, et al. RNA modifications in cardiovascular diseases, the potential therapeutic targets. Life Sci. 2021;278:119565. doi: 10.1016/j.lfs.2021.119565
  • Jonkhout N, Tran J, Smith MA, et al. The RNA modification landscape in human disease. RNA. 2017;23(12):1754–1769. doi: 10.1261/rna.063503.117
  • Barbieri I, Kouzarides T. Role of RNA modifications in cancer. Nat Rev Cancer. 2020;20(6):303–322. doi: 10.1038/s41568-020-0253-2
  • Chatterjee B, Shen CJ, Majumder P. RNA modifications and RNA metabolism in neurological disease pathogenesis. Int J Mol Sci. 2021;22(21):22. doi: 10.3390/ijms222111870
  • Helm M, Motorin Y. Detecting RNA modifications in the epitranscriptome: predict and validate. Nat Rev Genet. 2017;18(5):275–291. doi: 10.1038/nrg.2016.169
  • Meyer KD, Saletore Y, Zumbo P, et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell. 2012;149(7):1635–1646. doi: 10.1016/j.cell.2012.05.003
  • Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485(7397):201–206. doi: 10.1038/nature11112
  • Zhao LY, Song J, Liu Y, et al. Mapping the epigenetic modifications of DNA and RNA. Protein Cell. 2020;11(11):792–808. doi: 10.1007/s13238-020-00733-7
  • Boccaletto P, Stefaniak F, Ray A, et al. MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic Acids Res. 2022;50(D1):D231–D5. doi: 10.1093/nar/gkab1083
  • Rosace D, Lopez J, Blanco S. Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol. 2020;17(8):1196–1213. doi: 10.1080/15476286.2020.1737442
  • Suzuki T. The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol. 2021;22(6):375–392. doi: 10.1038/s41580-021-00342-0
  • Alexandrov A, Martzen MR, Phizicky EM. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA. 2002;8(10):1253–1266. doi: 10.1017/S1355838202024019
  • Lin S, Liu Q, Lelyveld VS, et al. Mettl1/Wdr4-mediated m(7)G tRNA methylome is required for normal mRNA translation and embryonic stem cell self-renewal and differentiation. Mol Cell. 2018;71(2):244–55 e5. doi: 10.1016/j.molcel.2018.06.001
  • Orellana EA, Liu Q, Yankova E, et al. METTL1-mediated m(7)G modification of arg-TCT tRNA drives oncogenic transformation. Mol Cell. 2021;81(16):3323–38 e14. doi: 10.1016/j.molcel.2021.06.031
  • Chen J, Li K, Chen J, et al. Aberrant translation regulated by METTL1/WDR4-mediated tRNA N7-methylguanosine modification drives head and neck squamous cell carcinoma progression. Cancer Commun (Lond). 2022;42(3):223–244. doi: 10.1002/cac2.12273
  • Chen Z, Zhu W, Zhu S, et al. METTL1 promotes hepatocarcinogenesis via m 7 G tRNA modification-dependent translation control. Clin Transl Med. 2021;11(12):e661. doi: 10.1002/ctm2.661
  • Ma J, Han H, Huang Y, et al. METTL1/WDR4-mediated m(7)G tRNA modifications and m(7)G codon usage promote mRNA translation and lung cancer progression. Mol Ther. 2021;29(12):3422–3435. doi: 10.1016/j.ymthe.2021.08.005
  • Garcia-Vilchez R, Anazco-Guenkova AM, Dietmann S, et al. METTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer. Mol Cancer. 2023;22(1):119. doi: 10.1186/s12943-023-01809-8
  • Deng Y, Zhou Z, Ji W, et al. METTL1-mediated m(7)G methylation maintains pluripotency in human stem cells and limits mesoderm differentiation and vascular development. Stem Cell Res Ther. 2020;11(1):306. doi: 10.1186/s13287-020-01814-4
  • Dai Z, Liu H, Liao J, et al. N(7)-methylguanosine tRNA modification enhances oncogenic mRNA translation and promotes intrahepatic cholangiocarcinoma progression. Mol Cell. 2021;81(16):3339–55 e8. doi: 10.1016/j.molcel.2021.07.003
  • Pandolfini L, Barbieri I, Bannister AJ, et al. METTL1 promotes let-7 MicroRNA processing via m7G methylation. Mol Cell. 2019;74(6):1278–90 e9. doi: 10.1016/j.molcel.2019.03.040
  • Tian QH, Zhang MF, Zeng JS, et al. METTL1 overexpression is correlated with poor prognosis and promotes hepatocellular carcinoma via PTEN. J Mol Med (Berl). 2019;97(11):1535–1545. doi: 10.1007/s00109-019-01830-9
  • Zhou W, Li J, Lu X, et al. Derivation and validation of a prognostic Model for cancer dependency genes based on CRISPR-Cas9 in gastric adenocarcinoma. Front Oncol. 2021;11:617289. doi: 10.3389/fonc.2021.617289
  • Li L, Yang Y, Wang Z, et al. Prognostic role of METTL1 in glioma. Cancer Cell Int. 2021;21(1):633. doi: 10.1186/s12935-021-02346-4
  • Ying X, Liu B, Yuan Z, et al. METTL1-m 7 G-EGFR/EFEMP1 axis promotes the bladder cancer development. Clin Transl Med. 2021;11(12):e675. doi: 10.1002/ctm2.675
  • Lin S, Liu Q, Jiang YZ, et al. Nucleotide resolution profiling of m(7)G tRNA modification by TRAC-Seq. Nat Protoc. 2019;14(11):3220–3242. doi: 10.1038/s41596-019-0226-7
  • Marchand V, Ayadi L, Ernst FGM, et al. AlkAniline-Seq: profiling of m 7 G and m 3 C RNA modifications at single nucleotide resolution. Angew Chem Int Ed Engl. 2018;57(51):16785–16790. doi: 10.1002/anie.201810946
  • Zhang LS, Liu C, Ma H, et al. Transcriptome-wide mapping of internal N(7)-methylguanosine methylome in mammalian mRNA. Mol Cell. 2019;74(6):1304–16 e8. doi: 10.1016/j.molcel.2019.03.036
  • Zhang LS, Liu C, He C. Transcriptome-wide detection of internal N(7)-Methylguanosine. Methods Mol Biol. 2021;2298:97–104.
  • Enroth C, Poulsen LD, Iversen S, et al. Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing. Nucleic Acids Res. 2019;47(20):e126. doi: 10.1093/nar/gkz736
  • Zhang LS, Ju CW, Liu C, et al. M 7 G-quant-seq: quantitative detection of RNA internal N 7 -methylguanosine. ACS Chem Biol. 2022;17(12):3306–3312. doi: 10.1021/acschembio.2c00792
  • Chetsanga CJ, Bearie B, Makaroff C. Alkaline opening of imidazole ring of 7-methylguanosine. 1. Analysis of the resulting pyrimidine derivatives. Chem Biol Interact. 1982;41(2):217–233. doi: 10.1016/0009-2797(82)90091-6
  • Wintermeyer W, Zachau HG. Tertiary structure interactions of 7-methylguanosine in yeast tRNA phe as studied by borohydride reduction. FEBS Lett. 1975;58(1–2):306–309. doi: 10.1016/0014-5793(75)80285-7
  • Wintermeyer W, Zachau HG. A specific chemical chain scission of tRNA at 7-methylguanosine. FEBS Lett. 1970;11(3):160–164. doi: 10.1016/0014-5793(70)80518-X
  • Zueva VS, Mankin AS, Bogdanov AA, et al. Specific fragmentation of tRNA and rRNA at a 7-methylguanine residue in the presence of methylated carrier RNA. Eur J Biochem. 1985;146(3):679–687. doi: 10.1111/j.1432-1033.1985.tb08704.x
  • Peattie DA. Direct chemical method for sequencing RNA. Proc Natl Acad Sci USA. 1979;76(4):1760–1764. doi: 10.1073/pnas.76.4.1760
  • Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977;74(2):560–564. doi: 10.1073/pnas.74.2.560
  • Bujnicki JM, Rychlewski L. Sequence analysis and structure prediction of aminoglycoside-resistance 16S rRNA: m7G methyltransferases. Acta Microbiol Pol. 2001;50:7–17.
  • AbouHaidar MG, Ivanov IG. Non-enzymatic RNA hydrolysis promoted by the combined catalytic activity of buffers and magnesium ions. Zeitschrift für Naturforschung C. 1999;54(7–8):542–548. doi: 10.1515/znc-1999-7-813
  • Blanco S, Dietmann S, Flores JV, et al. Aberrant methylation of tRnas links cellular stress to neuro-developmental disorders. EMBO J. 2014;33(18):2020–2039. doi: 10.15252/embj.201489282
  • Hoffmann A, Fallmann J, Vilardo E, et al. Accurate mapping of tRNA reads. Bioinformatics. 2018;34(7):1116–1124. doi: 10.1093/bioinformatics/btx756
  • Kupfer PA, Leumann CJ. The chemical stability of abasic RNA compared to abasic DNA. Nucleic Acids Res. 2007;35(1):58–68. doi: 10.1093/nar/gkl948
  • Das U, Shuman S. Mechanism of RNA 2′,3′-cyclic phosphate end healing by T4 polynucleotide kinase–phosphatase. Nucleic Acids Res. 2013;41(1):355–365. doi: 10.1093/nar/gks977
  • Kellner S, Burhenne J, Helm M. Detection of RNA modifications. RNA Biol. 2010;7(2):237–247. doi: 10.4161/rna.7.2.11468
  • Hanski C, Stehlik G. Increased concentration of 7-methylguanine and 1-methylhypoxanthine in urine of rats bearing Yoshida tumour. Cancer Lett. 1980;9(4):339–343. doi: 10.1016/0304-3835(80)90027-0
  • Loft S, Svoboda P, Kasai H, et al. Prospective study of urinary excretion of 7-methylguanine and the risk of lung cancer: effect modification by mu class glutathione-S-transferases. Int J Cancer. 2007;121(7):1579–1584. doi: 10.1002/ijc.22863
  • Stillwell WG, Glogowski J, Xu HX, et al. Urinary excretion of nitrate, N-nitrosoproline, 3-methyladenine, and 7-methylguanine in a Colombian population at high risk for stomach cancer. Cancer Res. 1991;51:190–194.
  • Fernandez-Peralbo MA, Gomez-Gomez E, Calderon-Santiago M, et al. Prostate cancer patients–negative biopsy controls discrimination by untargeted metabolomics analysis of urine by LC-QTOF: upstream information on other omics. Sci Rep. 2016;6(1):38243. doi: 10.1038/srep38243
  • Lakings DB, Waalkes TP, Borek E, et al. Composition, associated tissue methyltransferase activity, and catabolic end products of transfer RNA from carcinogen-induced hepatoma and normal monkey livers. Cancer Res. 1977;37:285–292.
  • Aganezov S, Yan SM, Soto DC, et al. A complete reference genome improves analysis of human genetic variation. Science. 2022;376(6588):eabl3533. doi: 10.1126/science.abl3533
  • Chan PP, Lowe TM. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucleic Acids Res. 2016;44(D1):D184–9. doi: 10.1093/nar/gkv1309
  • Lowe TM, Chan PP. tRnascan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44(W1):W54–7. doi: 10.1093/nar/gkw413
  • Quinlan AR. Bedtools: the swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47(1):11 2 1–34. doi: 10.1002/0471250953.bi1112s47
  • Rognes T, Flouri T, Nichols B, et al. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. doi: 10.7717/peerj.2584
  • Chen S, Zhou Y, Chen Y, et al. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–i90. doi: 10.1093/bioinformatics/bty560
  • Kielbasa SM, Wan R, Sato K, et al. Adaptive seeds tame genomic sequence comparison. Genome Res. 2011;21(3):487–493. doi: 10.1101/gr.113985.110
  • Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):10. doi: 10.1093/gigascience/giab008
  • Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–192. doi: 10.1093/bib/bbs017
  • Nawrocki EP, Eddy SR. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013;29(22):2933–2935. doi: 10.1093/bioinformatics/btt509
  • Will S, Joshi T, Hofacker IL, et al. LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA. 2012;18:900–914. doi: 10.1261/rna.029041.111
  • Di Tommaso P, Chatzou M, Floden EW, et al. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319. doi: 10.1038/nbt.3820