Schubeler, D. Function and information content of DNA methylation. Nature 517, 321–326 (2015).
Jurkowska, R. Z., Jurkowski, T. P. & Jeltsch, A. Structure and function of mammalian DNA methyltransferases. ChemBioChem 12, 206–222 (2011).
Bogdanovic, O. & Veenstra, G. J. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 118, 549–565 (2009).
Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).
Ross, S. E. & Bogdanovic, O. TET enzymes, DNA demethylation and pluripotency. Biochem. Soc. Trans. 47, 875–885 (2019).
Pastor, W. A., Aravind, L. & Rao, A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14, 341–356 (2013).
Kohli, R. M. & Zhang, Y. TET enzymes, TDG and the dynamics of DNA demethylation. Nature 502, 472–479 (2013).
Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).
Xu, G. L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).
Hendrich, B., Guy, J., Ramsahoye, B., Wilson, V. A. & Bird, A. Closely related proteins MBD2 and MBD3 play distinctive but interacting roles in mouse development. Genes Dev. 15, 710–723 (2001).
Guy, J., Hendrich, B., Holmes, M., Martin, J. E. & Bird, A. A mouse Mecp2-null mutation causes neurological symptoms that mimic Rett syndrome. Nat. Genet. 27, 322–326 (2001).
Dai, H. Q. et al. TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling. Nature 538, 528–532 (2016).
Bogdanovic, O. et al. Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat. Genet. 48, 417–26 (2016).
Li, C. et al. Overlapping requirements for Tet2 and Tet3 in normal development and hematopoietic stem cell emergence. Cell Rep. 12, 1133–1143 (2015).
Robertson, K. D. DNA methylation, methyltransferases, and cancer. Oncogene 20, 3139–3155 (2001).
Nishiyama, A. & Nakanishi, M. Navigating the DNA methylation landscape of cancer. Trends Genet. 37, 1012–1027 (2021).
Reichard, J. & Zimmer-Bensch, G. The epigenome in neurodevelopmental disorders. Front. Neurosci. 15, 776809 (2021).
Ciptasari, U. & van Bokhoven, H. The phenomenal epigenome in neurodevelopmental disorders. Hum. Mol. Genet. 29, R42–R50 (2020).
Ballestar, E., Sawalha, A. H. & Lu, Q. Clinical value of DNA methylation markers in autoimmune rheumatic diseases. Nat. Rev. Rheumatol. 16, 514–524 (2020).
Mazzone, R. et al. The emerging role of epigenetics in human autoimmune disorders. Clin. Epigenetics 11, 34 (2019).
Horvath, S. & Raj, K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat. Rev. Genet. 19, 371–384 (2018).
Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
de Mendoza, A., Lister, R. & Bogdanovic, O. Evolution of DNA methylome diversity in eukaryotes. J. Mol. Biol. 432, 1687–1705 (2019).
Zhang, H., Lang, Z. & Zhu, J. K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 (2018).
Kumar, S. & Mohapatra, T. Dynamics of DNA methylation and its functions in plant growth and development. Front. Plant Sci. 12, 596236 (2021).
Salomon, R. & Kaye, A. M. Methylation of mouse DNA in vivo: di- and tripyrimidine sequences containing 5-methylcytosine. Biochim. Biophys. Acta 204, 340–351 (1970).
Grafstrom, R. H., Yuan, R. & Hamilton, D. L. The characteristics of DNA methylation in an in vitro DNA synthesizing system from mouse fibroblasts. Nucleic Acids Res. 13, 2827–2842 (1985).
Patil, V., Ward, R. L. & Hesson, L. B. The evidence for functional non-CpG methylation in mammalian cells. Epigenetics 9, 823–828 (2014).
Ziller, M. J. et al. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 7, e1002389 (2011).
Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523–536 (2008).
Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).
Shirane, K. et al. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet. 9, e1003439 (2013).
Kubo, N. et al. DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis. BMC Genomics 16, 624 (2015).
Lister, R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 1237905 (2013).
De Mendoza, A. et al. The emergence of the brain non-CpG methylation system in vertebrates. Nat. Ecol. Evol. 5, 369–378 (2021).
Ross, S. E., Angeloni, A., Geng, F. S., de Mendoza, A. & Bogdanovic, O. Developmental remodelling of non-CG methylation at satellite DNA repeats. Nucleic Acids Res. 48, 12675–12688 (2020).
Ross, S. E. et al. Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species. Nucleic Acids Res. 51, 9658–9671 (2023).
Bonasio, R. et al. Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr. Biol. 22, 1755–1764 (2012).
Klughammer, J. et al. Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species. Nat. Commun. 14, 232 (2023).
Ross, S. E., Hesselson, D. & Bogdanovic, O. Developmental accumulation of gene body and transposon non-CpG methylation in the zebrafish brain. Front. Cell Dev. Biol. 9, 643603 (2021).
Fu, Y., Timp, W. & Sedlazeck, F. J. Computational analysis of DNA methylation from long-read sequencing. Nat. Rev. Genet. 26, 620–634 (2025).
Liu, T. & Conesa, A. Profiling the epigenome using long-read sequencing. Nat. Genet. 57, 27–41 (2025).
Schultz, M. D. et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523, 212–216 (2015).
He, Y. & Ecker, J. R. Non-CG methylation in the human genome. Annu Rev. Genomics Hum. Genet. 16, 55–77 (2015).
Tan, H. K. et al. DNMT3B shapes the mCA landscape and regulates mCG for promoter bivalency in human embryonic stem cells. Nucleic Acids Res. 47, 7460–7475 (2019).
Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68–73 (2011).
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Kim, K. et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat. Biotechnol. 29, 1117–1119 (2011).
Ohi, Y. et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat. Cell Biol. 13, 541–549 (2011).
Yamanaka, S. & Blau, H. M. Nuclear reprogramming to a pluripotent state by three approaches. Nature 465, 704–712 (2010).
Liu, X. et al. Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nat. Methods 14, 1055–1062 (2017).
Giulitti, S. et al. Direct generation of human naive induced pluripotent stem cells from somatic cells in microfluidics. Nat. Cell Biol. 21, 275–286 (2019).
Pastor, W. A. et al. Naive human pluripotent cells feature a methylation landscape devoid of blastocyst or germline memory. Cell Stem Cell 18, 323–329 (2016).
Wang, Y. et al. Unique molecular events during reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) at naive state. eLife 7, e29518 (2018).
Buckberry, S. et al. Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 620, 863–872 (2023).
Guo, H. et al. The DNA methylation landscape of human early embryos. Nature 511, 606–610 (2014).
Wang, L. et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157, 979–991 (2014).
Arand, J. et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 8, e1002750 (2012).
Butcher, L. M. et al. Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells. Nat. Commun. 7, 10458 (2016).
Joe, S. & Nam, H. Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers. BMC Bioinformatics 21, 175 (2020).
Ichiyanagi, T., Ichiyanagi, K., Miyake, M. & Sasaki, H. Accumulation and loss of asymmetric non-CpG methylation during male germ-cell development. Nucleic Acids Res. 41, 738–745 (2013).
Kobayashi, H. et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res. 23, 616–627 (2013).
Tomizawa, S. et al. Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development 138, 811–820 (2011).
Demond, H., Khan, S., Castillo-Fernandez, J., Hanna, C. W. & Kelsey, G. Transcriptome and DNA methylation profiling during the NSN to SN transition in mouse oocytes. BMC Mol. Cell Biol. 26, 2 (2025).
Kubo, N. et al. Combined and differential roles of ADD domains of DNMT3A and DNMT3L on DNA methylation landscapes in mouse germ cells. Nat. Commun. 15, 3266 (2024).
Yu, B. et al. Single-cell analysis of transcriptome and DNA methylome in human oocyte maturation. PLoS ONE 15, e0241698 (2020).
Castillo-Fernandez, J. et al. Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis. Aging Cell 19, e13278 (2020).
Lee, J. H., Park, S. J. & Nakai, K. Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s. Sci. Rep. 7, 11295 (2017).
Jeltsch, A., Adam, S., Dukatz, M., Emperle, M. & Bashtrykov, P. Deep enzymology studies on DNA methyltransferases reveal novel connections between flanking sequences and enzyme activity. J. Mol. Biol. 433, 167186 (2021).
Baubec, T. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520, 243–247 (2015).
Neri, F. et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature 543, 72–77 (2017).
Otani, J. et al. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain. EMBO Rep. 10, 1235–1241 (2009).
Mo, A. et al. Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron 86, 1369–1384 (2015).
Boxer, L. D. et al. MeCP2 represses the rate of transcriptional initiation of highly methylated long genes. Mol. Cell 77, 294–309 (2020).
Hamagami, N. et al. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. Mol. Cell 83, 1412–1428 (2023).
Angeloni, A. et al. Extensive DNA methylome rearrangement during early lamprey embryogenesis. Nat. Commun. 15, 1977 (2024).
Lagger, S. et al. MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain. PLoS Genet. 13, e1006793 (2017).
Tillotson, R. & Bird, A. The molecular basis of MeCP2 function in the brain. J. Mol. Biol. 432, 1602–1623 (2019).
Skene, P. J. et al. Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol. Cell 37, 457–468 (2010).
Rube, H. T. et al. Sequence features accurately predict genome-wide MeCP2 binding in vivo. Nat. Commun. 7, 11025 (2016).
Amir, R. E. et al. Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat. Genet. 23, 185–188 (1999).
Lyst, M. J. et al. Rett syndrome mutations abolish the interaction of MeCP2 with the NCoR/SMRT co-repressor. Nat. Neurosci. 16, 898–902 (2013).
Tillotson, R. et al. Neuronal non-CG methylation is an essential target for MeCP2 function. Mol. Cell 81, 1260–1275 (2021).
Lavery, L. A. et al. Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome. eLife 9, e52981 (2020).
Li, J. et al. Dnmt3a knockout in excitatory neurons impairs postnatal synapse maturation and increases the repressive histone modification H3K27me3. eLife 11, e66909 (2022).
Fuks, F., Burgers, W. A., Godin, N., Kasai, M. & Kouzarides, T. Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription. EMBO J. 20, 2536–2544 (2001).
Liu, Y. et al. Exploring the complexity of MECP2 function in Rett syndrome. Nat. Rev. Neurosci. 26, 379–398 (2025).
Renthal, W. et al. Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing. Nat. Neurosci. 21, 1670–1679 (2018).
Santistevan, N. J., Ford, C. T., Gilsdorf, C. S. & Grinblat, Y. Behavioral and transcriptomic analyses of mecp2 function in zebrafish. Am. J. Med. Genet. B Neuropsychiatr. Genet. 195, e32981 (2024).
Moore, J. R. et al. MeCP2 and non-CG DNA methylation stabilize the expression of long genes that distinguish closely related neuron types. Nat. Neurosci. 28, 1185–1198 (2025).
Tian, W. et al. Single-cell DNA methylation and 3D genome architecture in the human brain. Science 382, eadf5357 (2023).
Liu, H. et al. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. Nature 624, 366–377 (2023).
Zhou, J. et al. Human body single-cell atlas of 3D genome organization and DNA methylation. Preprint at bioRxiv https://doi.org/10.1101/2025.03.23.644697 (2025).
Goll, M. G. & Halpern, M. E. DNA methylation in zebrafish. Prog. Mol. Biol. Transl. Sci. 101, 193–218 (2011).
Yin, L. M., Schnoor, M. & Jun, C. D. Structural characteristics, binding partners and related diseases of the calponin homology (CH) domain. Front. Cell Dev. Biol. 8, 342 (2020).
Wu, S. F., Zhang, H. & Cairns, B. R. Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm. Genome Res. 21, 578–589 (2011).
Hong, Y. et al. Establishment of a normal medakafish spermatogonial cell line capable of sperm production in vitro. Proc. Natl Acad. Sci. USA 101, 8011–8016 (2004).
Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D. & Zemach, A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics Chromatin 12, 62 (2019).
Cingolani, P. et al. Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. BMC Genomics 14, 666 (2013).
Royle, J. W., Hurwood, D., Sadowski, P. & Dudley, K. J. Non-CG DNA methylation marks the transition from pupa to adult in Helicoverpa armigera. Insect Mol. Biol. 33, 493–502 (2024).
Gu, Z. et al. Whole-genome bisulfite sequencing reveals the function of DNA methylation in the allotransplantation immunity of pearl oysters. Front. Immunol. 14, 1247544 (2023).
Yang, Y., Zheng, Y., Sun, L. & Chen, M. Genome-wide DNA methylation signatures of sea cucumber Apostichopus japonicus during environmental induced aestivation. Genes (Basel) 11, 1020 (2020).
Song, X. et al. Genome-wide DNA methylomes from discrete developmental stages reveal the predominance of non-CpG methylation in Tribolium castaneum. DNA Res. 24, 445–457 (2017).
Schulz, N. K. E. et al. Dnmt1 has an essential function despite the absence of CpG DNA methylation in the red flour beetle Tribolium castaneum. Sci. Rep. 8, 16462 (2018).
De Koning, A. P., Gu, W., Castoe, T. A., Batzer, M. A. & Pollock, D. D. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 7, e1002384 (2011).
Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).
Schartl, M. et al. The genomes of all lungfish inform on genome expansion and tetrapod evolution. Nature 634, 96–103 (2024).
Du, J., Johnson, L. M., Jacobsen, S. E. & Patel, D. J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 16, 519–532 (2015).
Gouil, Q. & Baulcombe, D. C. DNA methylation signatures of the plant chromomethyltransferases. PLoS Genet. 12, e1006526 (2016).
Stroud, H. et al. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat. Struct. Mol. Biol. 21, 64–72 (2014).
Kazazian, H. H. Jr Mobile elements: drivers of genome evolution. Science 303, 1626–1632 (2004).
Tooley, K. B. et al. Differential usage of DNA modifications in neurons, astrocytes, and microglia. Epigenetics Chromatin 16, 45 (2023).
Derks, M. F. et al. Gene and transposable element methylation in great tit (Parus major) brain and blood. BMC Genomics 17, 332 (2016).
Muotri, A. R. et al. L1 retrotransposition in neurons is modulated by MeCP2. Nature 468, 443–446 (2010).
Novo, C. L. et al. Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells. Nat. Commun. 13, 3525 (2022).
Guo, W., Zhang, M. Q. & Wu, H. Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Sci. Rep. 6, 32207 (2016).
Olova, N. et al. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. Genome Biol. 19, 33 (2018).
Vaisvila, R. et al. Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA. Genome Res. 31, 1280–1289 (2021).
Liu, Y. et al. Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution. Nat. Biotechnol. 37, 424–429 (2019).
Wang, M. et al. Engineered APOBEC3C sequencing enables bisulfite-free and direct detection of DNA methylation at a single-base resolution. Anal. Chem. 95, 1556–1565 (2023).
Wang, T. et al. Bisulfite-free sequencing of 5-hydroxymethylcytosine with APOBEC-coupled epigenetic sequencing (ACE-seq). Methods Mol. Biol. 2198, 349–367 (2021).
Han, Y. et al. Comparison of EM-seq and PBAT methylome library methods for low-input DNA. Epigenetics 17, 1195–1204 (2022).
Liu, Y. et al. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. Genome Biol. 22, 295 (2021).
Angeloni, A., Ferguson, J. & Bogdanovic, O. Nanopore sequencing and data analysis for base-resolution genome-wide 5-methylcytosine profiling. Methods Mol. Biol. 2458, 75–94 (2022).
Goldsmith, C. et al. Low biological fluctuation of mitochondrial CpG and non-CpG methylation at the single-molecule level. Sci. Rep. 11, 8032 (2021).
Liau, Y. et al. Low-pass nanopore sequencing for measurement of global methylation levels in plants. BMC Genomics 25, 1235 (2024).
Kong, Y. et al. Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications. Preprint at bioRxiv https://doi.org/10.1101/2024.11.19.624260 (2024).
Ni, P. et al. Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning. Nat. Commun. 12, 5976 (2021).
Chen, H. X. et al. Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant. Nat. Commun. 16, 3227 (2025).
Holmes, E. E. et al. Performance evaluation of kits for bisulfite-conversion of DNA from tissues, cell lines, FFPE tissues, aspirates, lavages, effusions, plasma, serum, and urine. PLoS ONE 9, e93933 (2014).
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).
Kint, S., De Spiegelaere, W., De Kesel, J., Vandekerckhove, L. & Van Criekinge, W. Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR. PLoS ONE 13, e0199091 (2018).
Dou, X. et al. The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A. Genome Res. 29, 1622–1634 (2019).
Guitton, R., Nido, G. S. & Tzoulis, C. No evidence of extensive non-CpG methylation in mtDNA. Nucleic Acids Res. 50, 9190–9194 (2022).
Urich, M. A., Nery, J. R., Lister, R., Schmitz, R. J. & Ecker, J. R. MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat. Protoc. 10, 475–483 (2015).
Gong, W. et al. Benchmarking DNA methylation analysis of 14 alignment algorithms for whole genome bisulfite sequencing in mammals. Comput Struct. Biotechnol. J. 20, 4704–4716 (2022).
Treangen, T. J. & Salzberg, S. L. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet. 13, 36–46 (2011).
Teissandier, A., Servant, N., Barillot, E. & Bourc’his, D. Tools and best practices for retrotransposon analysis using high-throughput sequencing data. Mob. DNA 10, 52 (2019).
Mizuguchi, T. et al. Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases. J. Hum. Genet. 64, 191–197 (2019).
Stevanovski, I. et al. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. Sci. Adv. 8, eabm5386 (2022).
Karst, S. M. et al. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat. Methods 18, 165–169 (2021).
Delahaye, C. & Nicolas, J. Sequencing DNA with nanopores: troubles and biases. PLoS ONE 16, e0257521 (2021).
Catoni, M., Tsang, J. M., Greco, A. P. & Zabet, N. R. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acids Res. 46, e114 (2018).
Ma, H. et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177–183 (2014).
Tatton-Brown, K. et al. Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability. Nat. Genet. 46, 385–388 (2014).
Cree, S. L. et al. DNA G-quadruplexes show strong interaction with DNA methyltransferases in vitro. FEBS Lett. 590, 2870–2883 (2016).
Jin, J. et al. The effects of cytosine methylation on general transcription factors. Sci. Rep. 6, 29119 (2016).
Abhishek, S., Nakarakanti, N. K., Deeksha, W. & Rajakumara, E. Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Int. J. Biol. Macromol. 170, 514–522 (2021).
Spruijt, C. G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146–1159 (2013).
Roth, G. V., Gengaro, I. R. & Qi, L. S. Precision epigenetic editing: technological advances, enduring challenges, and therapeutic applications. Cell Chem. Biol. https://doi.org/10.1016/j.chembiol.2024.07.007 (2024).
Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).
Domb, K. et al. DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation. Proc. Natl Acad. Sci. USA 117, 33700–33710 (2020).
Yaari, R. et al. RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs. Nat. Commun. 10, 1613 (2019).
Ikeda, Y. et al. Loss of CG methylation in Marchantia polymorpha causes disorganization of cell division and reveals unique DNA methylation regulatory mechanisms of non-CG methylation. Plant Cell Physiol. 59, 2421–2431 (2018).
Zemach, A. et al. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153, 193–205 (2013).
Law, J. A. & Jacobsen, S. E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).
Bewick, A. J. et al. Diversity of cytosine methylation across the fungal tree of life. Nat. Ecol. Evol. 3, 479–490 (2019).
Shi, J. et al. DNA methylation plays important roles in lifestyle transition of Arthrobotrys oligospora. IET Syst. Biol. 18, 92–102 (2024).
Nai, Y. S., Huang, Y. C., Yen, M. R. & Chen, P. Y. Diversity of fungal DNA methyltransferases and their association with DNA methylation patterns. Front. Microbiol. 11, 616922 (2020).
Chen, Y. Y. et al. DNA methylation-dependent epigenetic regulation of Verticillium dahliae virulence in plants. aBIOTECH 4, 185–201 (2023).
So, K. K. et al. Global DNA methylation in the chestnut blight fungus Cryphonectria parasitica and genome-wide changes in DNA methylation accompanied with sectorization. Front. Plant Sci. 9, 103 (2018).
Malagnac, F. et al. A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure. Cell 91, 281–290 (1997).
Sarre, L. A., Gastellou Peralta, G. A., Romero Charria, P., Ovchinnikov, V. & de Mendoza, A. Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes. Mol. Biol. Evol. 42, msaf176 (2025).
De Mendoza, A. et al. Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons. Nat. Commun. 9, 1341 (2018).
Sarre, L. A. et al. DNA methylation enables recurrent endogenization of giant viruses in an animal relative. Sci. Adv. 10, eado6406 (2024).
Huff, J. T. & Zilberman, D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 156, 1286–1297 (2014).
Clark, S. J., Harrison, J., Paul, C. L. & Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 22, 2990–2997 (1994).
Tse, O. Y. O. et al. Genome-wide detection of cytosine methylation by single molecule real-time sequencing. Proc. Natl Acad. Sci. USA 118, e2019768118 (2021).
Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, K. F. Nanopore sequencing technology, bioinformatics and applications. Nat. Biotechnol. 39, 1348–1365 (2021).
Kulkarni, O. et al. Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation. Preprint at bioRxiv https://doi.org/10.1101/2024.11.09.622763 (2024).