Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590–607 (2019).

Article  CAS  Google Scholar 

Michalak, E. M., Burr, M. L., Bannister, A. J. & Dawson, M. A. The roles of DNA, RNA and histone methylation in ageing and cancer. Nat. Rev. Mol. Cell Biol. 20, 573–589 (2019).

Article  CAS  Google Scholar 

Jiang, X. et al. The role of m6A modification in the biological functions and diseases. Signal Transduct. Target. Ther. 6, 74 (2021).

Article  CAS  Google Scholar 

Sánchez-Romero, M. A. & Casadesús, J. The bacterial epigenome. Nat. Rev. Microbiol. 18, 7–20 (2020). This review summarizes epigenetic regulation by bacterial DNA methylation and its contribution to phenotypic heterogeneity in bacterial populations.

Article  Google Scholar 

Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: in the right place at the right time. Science 361, 1336–1340 (2018).

Article  CAS  Google Scholar 

Wu, X. & Zhang, Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517–534 (2017).

Article  CAS  Google Scholar 

Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371–384 (2018).

Article  CAS  Google Scholar 

Beaulaurier, J., Schadt, E. E. & Fang, G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat. Rev. Genet. 20, 157–172 (2019). This review discusses the potential of currently available methods, especially LRS technologies, for mapping and characterizing bacterial methylomes.

Article  CAS  Google Scholar 

Blow, M. J. et al. The epigenomic landscape of prokaryotes. PLoS Genet. 12, 1–28 (2016).

Article  Google Scholar 

Boulias, K. & Greer, E. L. Means, mechanisms and consequences of adenine methylation in DNA. Nat. Rev. Genet. https://doi.org/10.1038/s41576-022-00456-x (2022).

Article  Google Scholar 

Fang, G. et al. Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nat. Biotechnol. 30, 1232–1239 (2012). This paper applies SMRT sequencing to map 6mA in a bacterium at genome-wide scale and highlights the importance of FDR evaluation.

Article  CAS  Google Scholar 

Beaulaurier, J. et al. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat. Biotechnol. 36, 61–69 (2018).

Article  CAS  Google Scholar 

Kumar, S. & Mohapatra, T. Deciphering epitranscriptome: modification of mRNA bases provides a new perspective for post-transcriptional regulation of gene expression. Front. Cell Dev. Biol. 9, 1–22 (2021).

Article  Google Scholar 

Barbieri, I. & Kouzarides, T. Role of RNA modifications in cancer. Nat. Rev. Cancer 20, 303–322 (2020).

Article  CAS  Google Scholar 

Helm, M. & Motorin, Y. Detecting RNA modifications in the epitranscriptome: predict and validate. Nat. Rev. Genet. 18, 275–291 (2017). This review discusses the principles, advantages and drawbacks of new high-throughput methods for characterizing RNA modifications.

Article  CAS  Google Scholar 

Frye, M., Jaffrey, S. R., Pan, T., Rechavi, G. & Suzuki, T. RNA modifications: what have we learned and where are we headed? Nat. Rev. Genet. 17, 365–372 (2016).

Article  CAS  Google Scholar 

Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).

Article  CAS  Google Scholar 

Grozhik, A. V. & Jaffrey, S. R. Distinguishing RNA modifications from noise in epitranscriptome maps. Nat. Chem. Biol. 14, 215–225 (2018).

Article  CAS  Google Scholar 

Saletore, Y. et al. The birth of the epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 13, 175 (2012).

Article  CAS  Google Scholar 

Zaccara, S., Ries, R. J. & Jaffrey, S. R. Reading, writing and erasing mRNA methylation. Nat. Rev. Mol. Cell Biol. 20, 608–624 (2019).

Article  CAS  Google Scholar 

Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Methods 12, 767–772 (2015).

Article  CAS  Google Scholar 

He, C. Grand challenge commentary: RNA epigenetics? Nat. Chem. Biol. 6, 863–865 (2010).

Article  CAS  Google Scholar 

Xue, C. et al. Role of main RNA modifications in cancer: N6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct. Target. Ther. 7, 142 (2022).

Article  CAS  Google Scholar 

Tretyakova, N., Villalta, P. W. & Kotapati, S. Mass spectrometry of structurally modified DNA. Chem. Rev. 113, 2395–2436 (2013).

Article  CAS  Google Scholar 

Boulias, K. & Greer, E. L. in DNA Modifications: Methods and Protocols (eds Ruzov, A. & Gering, M.) 79–90 (Springer US, 2021).

Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009).

Article  CAS  Google Scholar 

Flusberg, B. A. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat. Methods 7, 461–465 (2010). This paper provides an early description of direct mapping of 5mC, 5hmC and 6mA using SMRT sequencing.

Article  CAS  Google Scholar 

Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).

Article  CAS  Google Scholar 

Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, K. F. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365 (2021).

Article  CAS  Google Scholar 

Laszlo, A. H. et al. Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc. Natl Acad. Sci. USA 110, 18904–18909 (2013).

Article  CAS  Google Scholar 

Amarasinghe, S. L. et al. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 21, 1–16 (2020).

Article  Google Scholar 

Krueger, F., Kreck, B., Franke, A. & Andrews, S. R. DNA methylome analysis using short bisulfite sequencing data. Nat. Methods 9, 145–151 (2012).

Article  CAS  Google Scholar 

Darst, R. P., Pardo, C. E., Ai, L., Brown, K. D. & Kladde, M. P. Bisulfite sequencing of DNA. Curr. Protoc. Mol. Biol. https://doi.org/10.1002/0471142727.mb0709s91 (2010).

Article  Google Scholar 

Shi, D. Q., Ali, I., Tang, J. & Yang, W. C. New insights into 5hmC DNA modification: generation, distribution and function. Front. Genet. 8, 1–11 (2017).

Article  Google Scholar 

Amente, S. et al. Genome-wide mapping of genomic DNA damage: methods and implications. Cell. Mol. Life Sci. 78, 6745–6762 (2021).

Article  CAS  Google Scholar 

Rybin, M. J. et al. Emerging technologies for genome-wide profiling of DNA breakage. Front. Genet. 11, 610386 (2021).

Article  Google Scholar 

Zhao, L. Y., Song, J., Liu, Y., Song, C. X. & Yi, C. Mapping the epigenetic modifications of DNA and RNA. Protein Cell 11, 792–808 (2020). This review summarizes high-throughput NGS-based methods for mapping five forms of DNA modifications and eight forms of RNA modifications, and also summarizes biological discoveries made using these methods.

Article  CAS  Google Scholar 

O’Brown, Z. K. et al. Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics 20, 1–15 (2019). This article reports sources of artefacts in measurements of 6mA and 4mC abundance in eukaryotic gDNA, including both quantification methods and mapping methods.

Article  Google Scholar 

Kong, Y. et al. Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution. Science 375, 515–522 (2022). This paper describes a machine learning method that can quantitatively deconvolve 6mA events into eukaryotic species of interest and other sources, and warns about bacterial contamination in the study of 6mA in eukaryotic samples.

Article  CAS  Google Scholar 

Patil, V. et al. Human mitochondrial DNA is extensively methylated in a non-CpG context. Nucleic Acids Res. 47, 10072–10085 (2019).

Article  CAS  Google Scholar 

Bellizzi, D. et al. The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern. DNA Res. 20, 537–547 (2013).

Article  CAS  Google Scholar 

Dou, X. et al. The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A. Genome Res. 29, 1622–1634 (2019).

Article  CAS  Google Scholar 

Sharma, N., Pasala, M. S. & Prakash, A. Mitochondrial DNA: epigenetics and environment. Environ. Mol. Mutagen. 60, 668–682 (2019).

Article  CAS  Google Scholar 

Owa, C., Poulin, M., Yan, L. & Shioda, T. Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: sources and avoidance of false-positive detection. PLoS ONE 13, 1–19 (2018).

Article  Google Scholar 

Bicci, I., Calabrese, C., Golder, Z. J., Gomez-Duran, A. & Chinnery, P. F. Single-molecule mitochondrial DNA sequencing shows no evidence of CpG methylation in human cells and tissues. Nucleic Acids Res. 49, 12757–12768 (2021). This paper describes the bias and technical concerns related to BS-seq in mapping 5mC in mtDNA and reports more reliable 5mC levels estimated by machine learning modelling of nanopore data.

Article  CAS  Google Scholar 

Mechta, M., Ingerslev, L. R., Fabre, O., Picard, M. & Barrès, R. Evidence suggesting absence of mitochondrial DNA methylation. Front. Genet. 8, 1–9 (2017).

Article  Google Scholar 

Matsuda, S. et al. Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA. Sci. Rep. 8, 1–13 (2018).

Article  Google Scholar 

Hong, E. E., Okitsu, C. Y., Smith, A. D. & Hsieh, C.-L. Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA. Mol. Cell. Biol. 33, 2683–2690 (2013).