Abstract
2’-O-methylation (2’-O-me or Nm) is a common RNA modification, which was initially discovered in various non-coding RNAs. Recent researches also revealed its prevalence and regulatory importance in mRNA. In this work, we first demonstrate that the Nm sites can be accurately predicted by the RNA sequence features. By utilizing simple one-hot encoding scheme of positional nucleotide sequence and the random forest machine learning algorithm, we developed a computational prediction tool named NmSEER to predict Nm sites in HeLa cells, HEK293 cells or both of them. Based on our observation of the subgrouping of the Nm sites, we proposed a specialized subgroup-wise prediction strategy to further enhance the prediction performance for the Nm sites with the consensus AGAT motif. Our predictor has achieved a promising performance in both the cross-validation test and the independent test (AUROC = 0.909 and 0.928 for predicting AGAT-sites and non-AGAT sites in independent test, respectively). NmSEER is implemented as a user-friendly web server, which is freely available at http://www.rnanut.net/nmseer/.
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References
Li, S., Mason, C.E.: The pivotal regulatory landscape of RNA modifications. Ann. Rev. Genomics Hum. Genet. 15, 127–150 (2014)
Boccaletto, P., Machnicka, M.A., Purta, E., Piatkowski, P., Baginski, B., Wirecki, T.K., de Crecy-Lagard, V., Ross, R., Limbach, P.A., Kotter, A., Helm, M., Bujnicki, J.M.: MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 46, D303–D307 (2018)
Hengesbach, M., Schwalbe, H.: Structural basis for regulation of ribosomal RNA 2’-o-methylation. Angew. Chem. Int. Ed. Engl. 53, 1742–1744 (2014)
Jockel, S., Nees, G., Sommer, R., Zhao, Y., Cherkasov, D., Hori, H., Ehm, G., Schnare, M., Nain, M., Kaufmann, A., Bauer, S.: The 2’-O-methylation status of a single guanosine controls transfer RNA-mediated toll-like receptor 7 activation or inhibition. J. Exp. Med. 209, 235–241 (2012)
Guy, M.P., Shaw, M., Weiner, C.L., Hobson, L., Stark, Z., Rose, K., Kalscheuer, V.M., Gecz, J., Phizicky, E.M.: Defects in tRNA anticodon loop 2’-O-Methylation are implicated in nonsyndromic X-linked intellectual disability due to mutations in FTSJ1. Hum. Mutat. 36, 1176–1187 (2015)
Abe, M., Naqvi, A., Hendriks, G.J., Feltzin, V., Zhu, Y., Grigoriev, A., Bonini, N.M.: Impact of age-associated increase in 2’-O-methylation of miRNAs on aging and neurodegeneration in Drosophila. Genes Dev. 28, 44–57 (2014)
Somme, J., Van Laer, B., Roovers, M., Steyaert, J., Versees, W., Droogmans, L.: Characterization of two homologous 2’-O-methyltransferases showing different specificities for their tRNA substrates. RNA 20, 1257–1271 (2014)
Shubina, M.Y., Musinova, Y.R., Sheval, E.V.: Nucleolar methyltransferase fibrillarin: evolution of structure and functions. Biochemistry (Mosc) 81, 941–950 (2016)
Choi, J., Indrisiunaite, G., DeMirci, H., Ieong, K.W., Wang, J., Petrov, A., Prabhakar, A., Rechavi, G., Dominissini, D., He, C., Ehrenberg, M., Puglisi, J.D.: 2’-O-methylation in mRNA disrupts tRNA decoding during translation elongation. Nat. Struct. Mol. Biol. 25, 208–216 (2018)
Dai, Q., Moshitch-Moshkovitz, S., Han, D., Kol, N., Amariglio, N., Rechavi, G., Dominissini, D., He, C.: Nm-seq maps 2’-O-methylation sites in human mRNA with base precision. Nat. Methods 14, 695–698 (2017)
Kersey, P.J., Allen, J.E., Allot, A., Barba, M., Boddu, S., Bolt, B.J., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., McDowall, M.D., Maheswari, U., Naamati, G., Newman, V., Ong, C.K., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R.D., Urban, M., Hammond-Kosack, K.E., Bolser, D.M., De Silva, N., Howe, K.L., Langridge, N., Maslen, G., Staines, D.M., Yates, A.: Ensembl genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Res. 46, D802–D808 (2018)
Zhou, Y., Zeng, P., Li, Y.H., Zhang, Z., Cui, Q.: SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. Nucleic Acids Res. 44, e91 (2016)
Chen, W., Tran, H., Liang, Z., Lin, H., Zhang, L.: Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome. Sci. Rep. 5, 13859 (2015)
Wang, X., Yan, R.: RFAthM6A: a new tool for predicting m(6)A sites in Arabidopsis thaliana. Plant Mol. Biol. 96, 327–337 (2018)
Acknowledgement
This study was supported by the National Natural Science Foundation of China (Grant Nos. 81670462 to Qinghua Cui) and Fundamental Research Funds for Central Universities (Grant Nos. BMU2017YJ004 to Yuan Zhou).
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Zhou, Y., Cui, Q., Zhou, Y. (2018). NmSEER: A Prediction Tool for 2’-O-Methylation (Nm) Sites Based on Random Forest. In: Huang, DS., Bevilacqua, V., Premaratne, P., Gupta, P. (eds) Intelligent Computing Theories and Application. ICIC 2018. Lecture Notes in Computer Science(), vol 10954. Springer, Cham. https://doi.org/10.1007/978-3-319-95930-6_90
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DOI: https://doi.org/10.1007/978-3-319-95930-6_90
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