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).
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).
Jiang, X. et al. The role of m6A modification in the biological functions and diseases. Signal Transduct. Target. Ther. 6, 74 (2021).
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.
Luo, C., Hajkova, P. & Ecker, J. R. Dynamic DNA methylation: in the right place at the right time. Science 361, 1336–1340 (2018).
Wu, X. & Zhang, Y. TET-mediated active DNA demethylation: mechanism, function and beyond. Nat. Rev. Genet. 18, 517–534 (2017).
Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371–384 (2018).
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.
Blow, M. J. et al. The epigenomic landscape of prokaryotes. PLoS Genet. 12, 1–28 (2016).
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).
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.
Beaulaurier, J. et al. Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation. Nat. Biotechnol. 36, 61–69 (2018).
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).
Barbieri, I. & Kouzarides, T. Role of RNA modifications in cancer. Nat. Rev. Cancer 20, 303–322 (2020).
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.
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).
Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).
Grozhik, A. V. & Jaffrey, S. R. Distinguishing RNA modifications from noise in epitranscriptome maps. Nat. Chem. Biol. 14, 215–225 (2018).
Saletore, Y. et al. The birth of the epitranscriptome: deciphering the function of RNA modifications. Genome Biol. 13, 175 (2012).
Zaccara, S., Ries, R. J. & Jaffrey, S. R. Reading, writing and erasing mRNA methylation. Nat. Rev. Mol. Cell Biol. 20, 608–624 (2019).
Linder, B. et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat. Methods 12, 767–772 (2015).
He, C. Grand challenge commentary: RNA epigenetics? Nat. Chem. Biol. 6, 863–865 (2010).
Xue, C. et al. Role of main RNA modifications in cancer: N6-methyladenosine, 5-methylcytosine, and pseudouridine. Signal Transduct. Target. Ther. 7, 142 (2022).
Tretyakova, N., Villalta, P. W. & Kotapati, S. Mass spectrometry of structurally modified DNA. Chem. Rev. 113, 2395–2436 (2013).
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).
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.
Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nat. Biotechnol. 34, 518–524 (2016).
Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, K. F. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365 (2021).
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).
Amarasinghe, S. L. et al. Opportunities and challenges in long-read sequencing data analysis. Genome Biol. 21, 1–16 (2020).
Krueger, F., Kreck, B., Franke, A. & Andrews, S. R. DNA methylome analysis using short bisulfite sequencing data. Nat. Methods 9, 145–151 (2012).
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).
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).
Amente, S. et al. Genome-wide mapping of genomic DNA damage: methods and implications. Cell. Mol. Life Sci. 78, 6745–6762 (2021).
Rybin, M. J. et al. Emerging technologies for genome-wide profiling of DNA breakage. Front. Genet. 11, 610386 (2021).
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.
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.
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.
Patil, V. et al. Human mitochondrial DNA is extensively methylated in a non-CpG context. Nucleic Acids Res. 47, 10072–10085 (2019).
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).
Dou, X. et al. The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A. Genome Res. 29, 1622–1634 (2019).
Sharma, N., Pasala, M. S. & Prakash, A. Mitochondrial DNA: epigenetics and environment. Environ. Mol. Mutagen. 60, 668–682 (2019).
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).
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.
Mechta, M., Ingerslev, L. R., Fabre, O., Picard, M. & Barrès, R. Evidence suggesting absence of mitochondrial DNA methylation. Front. Genet. 8, 1–9 (2017).
Matsuda, S. et al. Accurate estimation of 5-methylcytosine in mammalian mitochondrial DNA. Sci. Rep. 8, 1–13 (2018).
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).
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