Ziller M.J., Gu H., Müller F., Donaghey J., Tsai L.T.-Y., Kohlbacher O., De Jager P.L., Rosen E.D., Bennett D.A., Bernstein B.E., Gnirke A., Meissner A. 2013. Charting a dynamic DNA methylation landscape of the human genome. Nature. 500, 477–481.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schroeder D.I., Blair J.D., Lott P., Yu H.O.K., Hong D., Crary F., Ashwood P., Walker C., Korf I., Robinson W.P., LaSalle J.M. 2013. The human placenta methylome. Proc. Natl. Acad. Sci. U. S. A. 110, 6037–6042.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Loyfer N., Magenheim J., Peretz A., Cann G., Bredno J., Klochendler A., Fox-Fisher I., Shabi-Porat S., Hecht M., Pelet T., Moss J., Drawshy Z., Amini H., Moradi P., Nagaraju S., Bauman D., Shveiky D., Porat S., Dior U., Rivkin G., Or O., Hirshoren N., Carmon E., Pikarsky A., Khalaileh A., Zamir G., Grinbaum R., Abu Gazala M., Mizrahi I., Shussman N., Korach A., Wald O., Izhar U., Erez E., Yutkin V., Samet Y., Rotnemer Golinkin D., Spalding K.L., Druid H., Arner P., Shapiro A.M.J., Grompe M., Aravanis A., Venn O., Jamshidi A., Shemer R., Dor Y., Glaser B., Kaplan T. 2023. A DNA methylation atlas of normal human cell types. Nature. 613, 355–364.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hernando-Herraez I., Garcia-Perez R., Sharp A.J., Marques-Bonet T. 2015. DNA methylation: Insights into human evolution. PLoS Genet. 11, e1005661.

Article  PubMed  PubMed Central  Google Scholar 

Medvedeva Y.A., Fridman M.V., Oparina N.J., Malko D.B., Ermakova E.O., Kulakovskiy I.V., Heinzel A., Makeev V.J. 2010. Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC Genomics. 11, 1–16.

Article  Google Scholar 

Panchin A.Y., Makeev V.J., Medvedeva Y.A. 2016. Preservation of methylated CpG dinucleotides in human CpG islands. Biol. Direct. 11, 1–15.

Article  Google Scholar 

Pardo L.M., Rizzu P., Francescatto M., Vitezic M., Leday G.G.R., Sanchez J.S., Khamis A., Takahashi H., van de Berg W.D.J., Medvedeva Y.A., van de Wiel M.A., Daub C.O., Carninci P., Heutink P. 2013. Regional differences in gene expression and promoter usage in aged human brains. Neurobiol. Aging. 34, 1825–1836.

Article  CAS  PubMed  Google Scholar 

Lioznova A.V., Khamis A.M., Artemov A.V., Bese-dina E., Ramensky V., Bajic V.B., Kulakovskiy I.V., Medvedeva Y.A. 2019. CpG traffic lights are markers of regulatory regions in human genome. BMC Genomics. 20, 102.

Article  PubMed  PubMed Central  Google Scholar 

Pan X., Li X., Sun J., Xiong Z., Hu H., Ning S., Zhi H. 2022. Enhancer methylation dynamics drive core transcriptional regulatory circuitry in pan-cancer. Oncogene. 41, 3474–3484.

Article  CAS  PubMed  Google Scholar 

Benetatos L., Vartholomatos G. 2018. Enhancer DNA methylation in acute myeloid leukemia and myelodysplastic syndromes. Cell. Mol. Life Sci. 75, 1999–2009.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stein R., Razin A., Cedar H. 1982. In vitro methylation of the hamster adenine phosphoribosyltransferase gene inhibits its expression in mouse L cells. Proc. Natl. Acad. Sci. U. S. A. 79, 3418–3422.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Anastasiadi D., Esteve-Codina A., Piferrer F. 2018. Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. Epigenetics Chromatin. 11, 1–17.

Article  Google Scholar 

Kang J.G., Park J.S., Ko J.-H., Kim Y.-S. 2019. Regulation of gene expression by altered promoter methylation using a CRISPR/Cas9-mediated epigenetic editing system. Sci. Rep. 9, 1–12.

Article  Google Scholar 

Antequera F., Bird A. 1993. CpG islands. EXS. 64, 169–85.

CAS  PubMed  Google Scholar 

Deaton A.M., Bird A. 2011. CpG islands and the regulation of transcription. Genes Dev. 25, 1010–1022.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Meehan R., Lewis J., Cross S., Nan X., Jeppesen P., Bird A. 1992. Transcriptional repression by methylation of CpG. J. Cell Sci. Suppl. 16, 9–14.

Article  CAS  PubMed  Google Scholar 

Bird A.P. 1984. DNA methylation versus gene expression. J. Embryol. Exp. Morphol. 83 (Suppl.), 31–40.

CAS  PubMed  Google Scholar 

Eckhardt F., Lewin J., Cortese R., Rakyan V.K., Attwood J., Burger M., Burton J., Cox T.V., Davies R., Down T.A., Haefliger C., Horton R., Howe K., Jackson D.K., Kunde J., Koenig C., Liddle J., Niblett D., Otto T., Pettett R., Seemann S., Thompson C., West T., Rogers J., Olek A., Berlin K., Beck S. 2006. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378–1385.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Weber M., Hellmann I., Stadler M.B., Ramos L., Pääbo S., Rebhan M., Schübeler D. 2007. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466.

Article  CAS  PubMed  Google Scholar 

Jones P.A. 2012. Functions of DNA methylation: Islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484–492.

Article  CAS  PubMed  Google Scholar 

Sobiak B., Leśniak W. 2019. The effect of single CpG demethylation on the pattern of DNA-protein binding. Int. J. Mol. Sci. 20 (4), 914.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bordagaray M.J., Fernández A., Astorga J., Garrido M., Hernández P., Chaparro A., Lira M.J., Gebicke-Haerter P., Hernández M. 2022. CpG single-site methylation regulates TLR2 expression in proinflammatory PBMCs from apical periodontitis individuals. Front. Immunol. 13, 861665.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gohno T., Hanamura T., Kurosumi M., Takei H., Yamaguchi Y., Hayashi S.-I. 2022. One DNA methylation regulates gene expression of human breast cancer and predicts recurrence. Anticancer Res. 42, 759–766.

Article  CAS  PubMed  Google Scholar 

Lian B.S.X., Kawasaki T., Kano N., Ori D., Ikegawa M., Isotani A., Kawai T. 2022. Regulation of expression by single CpG methylation in downstream of transcription initiation site. iScience. 25, 104118.

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

Article  CAS  PubMed  Google Scholar 

Wu S.C., Zhang Y. 2010. Active DNA demethylation: Many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 11, 607–620.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Prasad R., Yen T.J., Bellacosa A. 2021. Active DNA demethylation—The epigenetic gatekeeper of development, immunity, and cancer. Adv. Genet. 2, e10033.

Article  PubMed  Google Scholar 

Moore L.D., Le T., Fan G. 2013. DNA methylation and its basic function. Neuropsychopharmacology. 38, 23–38.

Article  CAS  PubMed  Google Scholar 

Tahiliani M., Koh K.P., Shen Y., Pastor W.A., Bandukwala H., Brudno Y., Agarwal S., Iyer L.M., Liu D.R., Aravind L., Rao A. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 324, 930–935.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ito S., D’Alessio A.C., Taranova O.V., Hong K., Sowers L.C., Zhang Y. 2010. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 466, 1129–1133.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shi D.-Q., Ali I., Tang J., Yang W.-C. 2017. New insights into 5hmC DNA modification: Generation, distribution and function. Front. Genet. 8, 100.