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Abstract

Modification of DNA bases plays important roles in the epigenetic regulation of eukaryotic gene expression. Among the different types of DNA methylation, 5-methylcytosine (5mC) is common in higher eukaryotes. Although bisulfite sequencing is the established detection method for this modification, newer methods, such as Oxford nanopore sequencing, have been developed as quick and reliable alternatives. An earlier study using sensitive liquid chromatography tandem mass spectrometry (LC-MS/MS) indicated the presence of 5mC at very low concentration in . More recently, a comprehensive study of the yeast genome found 40 5mC sites using the computational tool Nanopolish on nanopore sequencing output raw data. In the present study, we are trying to validate the prediction of the 5mC modifications in yeast with Nanopolish and two other nanopore software tools, Tombo and DeepSignal. Using publicly available genome sequencing data, we compared the open-access computational tools, including Tombo, Nanopolish and DeepSignal, for predicting 5mC. Our results suggest that these tools are indeed capable of predicting DNA 5mC modifications at a specific location from Oxford nanopore sequencing data. We also predicted that 5mC present in the genome might be located predominantly at the locus of chromosome 12.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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/content/journal/acmi/10.1099/acmi.0.000363
2022-06-10
2022-06-25
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References

  1. Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet 2013; 14:204–220 [View Article] [PubMed]
    [Google Scholar]
  2. Robertson KD. DNA methylation and human disease. Nat Rev Genet 2005; 6:597–610 [View Article] [PubMed]
    [Google Scholar]
  3. Li Y, Tollefsbol TO. DNA methylation detection: bisulfite genomic sequencing analysis. Methods Mol Biol 2011; 791:11–21 [View Article]
    [Google Scholar]
  4. Schreiber J, Wescoe ZL, Abu-Shumays R, Vivian JT, Baatar B et al. Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands. Proc Natl Acad Sci U S A 2013; 110:18910–18915 [View Article] [PubMed]
    [Google Scholar]
  5. Schatz MC. Nanopore sequencing meets epigenetics. Nat Methods 2017; 14:347–348 [View Article] [PubMed]
    [Google Scholar]
  6. Gouil Q, Keniry A. Latest techniques to study DNA methylation. Essays Biochem 2019; 63:639–648 [View Article] [PubMed]
    [Google Scholar]
  7. Xu L, Seki M. Recent advances in the detection of base modifications using the Nanopore sequencer. J Hum Genet 2020; 65:25–33 [View Article] [PubMed]
    [Google Scholar]
  8. Simpson JT, Workman RE, Zuzarte PC, David M, Dursi LJ et al. Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods 2017; 14:407–410 [View Article] [PubMed]
    [Google Scholar]
  9. Ni P, Huang N, Zhang Z, Wang D-P, Liang F et al. DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning. Bioinformatics 2019; 35:4586–4595 [View Article] [PubMed]
    [Google Scholar]
  10. Stoiber M, Quick J, Egan R, Eun Lee J, Celniker S et al. De novo identification of DNA modifications enabled by genome-guided nanopore signal processing. Bioinformatics 2016; 094672: [View Article]
    [Google Scholar]
  11. Liu Q, Fang L, Yu G, Wang D, Xiao CL et al. Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data. Nat Commun 2019; 10:2449 [View Article] [PubMed]
    [Google Scholar]
  12. Tang Y, Gao X-D, Wang Y, Yuan B-F, Feng Y-Q. Widespread existence of cytosine methylation in yeast DNA measured by gas chromatography/mass spectrometry. Anal Chem 2012; 84:7249–7255 [View Article] [PubMed]
    [Google Scholar]
  13. Jenjaroenpun P, Wongsurawat T, Pereira R, Patumcharoenpol P, Ussery DW et al. Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D. Nucleic Acids Res 2018; 46:e38 [View Article] [PubMed]
    [Google Scholar]
  14. Egidi A, Di Felice F, Camilloni G. Saccharomyces cerevisiae rDNA as super-hub: the region where replication, transcription and recombination meet. Cell Mol Life Sci 2020; 77:4787–4798 [View Article] [PubMed]
    [Google Scholar]
  15. Briggs SD, Bryk M, Strahl BD, Cheung WL, Davie JK et al. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev 2001; 15:3286–3295 [View Article] [PubMed]
    [Google Scholar]
  16. Smith JS, Caputo E, Boeke JD. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol Cell Biol 1999; 19:3184–3197 [View Article] [PubMed]
    [Google Scholar]
  17. Merz K, Hondele M, Goetze H, Gmelch K, Stoeckl U et al. Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev 2008; 22:1190–1204 [View Article] [PubMed]
    [Google Scholar]
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