The diverse roles of DNA methylation in mammalian development and disease

Abstract

DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: DNA methylation machinery and mechanisms.
Fig. 2: Targeting DNA methylation to CGI promoters.
Fig. 3: DNA methylation-based regulation of transposons.
Fig. 4: DNA methylation reprogramming in development.

References

  1. 1.

    Zemach, A., McDaniel, I. E., Silva, P. & Zilberman, D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328, 916–919 (2010).

  2. 2.

    Feng, S. et al. Conservation and divergence of methylation patterning in plants and animals. Proc. Natl Acad. Sci. USA 107, 8689–8694 (2010).

  3. 3.

    Doskočil, J. & Šorm, F. Distribution of 5-methylcytosine in pyrimidine sequences of deoxyribonucleic acids. Biochim. Biophys. Acta 55, 953–959 (1962).

  4. 4.

    Riggs, A. D. X inactivation, differentiation, and DNA methylation. Cytogenet. Cell Genet. 14, 9–25 (1975).

  5. 5.

    Bird, A. P. Use of restriction enzymes to study eukaryotic DNA methylation. II. The symmetry of methylated sites supports semi-conservative copying of the methylation pattern. J. Mol. Biol. 118, 49–60 (1978).

  6. 6.

    Ben-Hattar, J. & Jiricny, J. Methylation of single CpG dinucleotides within a promoter element of the Herpes simplex virus tk gene reduces its transcription in vivo. Gene 65, 219–227 (1988).

  7. 7.

    Watt, F. & Molloy, P. L. Cytosine methylation prevents binding to DNA of a HeLa cell transcription factor required for optimal expression of the adenovirus major late promoter. Genes Dev. 2, 1136–1143 (1988).

  8. 8.

    Iguchi-Ariga, S. M. & Schaffner, W. CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. Genes Dev. 3, 612–619 (1989).

  9. 9.

    Ferguson-Smith, A. C., Sasaki, H., Cattanach, B. M. & Surani, M. A. Parental-origin-specific epigenetic modification of the mouse H19 gene. Nature 362, 751–755 (1993).

  10. 10.

    Li, E., Beard, C. & Jaenisch, R. Role for DNA methylation in genomic imprinting. Nature 366, 362–365 (1993).

  11. 11.

    Bartolomei, M. S., Webber, A. L., Brunkow, M. E. & Tilghman, S. M. Epigenetic mechanisms underlying the imprinting of the mouse H19 gene. Genes Dev. 7, 1663–1673 (1993).

  12. 12.

    Stöger, R. et al. Maternal-specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal. Cell 73, 61–71 (1993).

  13. 13.

    Mohandas, T., Sparkes, R. S. & Shapiro, L. J. Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation. Science 211, 393–396 (1981).

  14. 14.

    Lock, L. F., Takagi, N. & Martin, G. R. Methylation of the Hprt gene on the inactive X occurs after chromosome inactivation. Cell 48, 39–46 (1987).

  15. 15.

    Zemach, A. & Zilberman, D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Curr. Biol. 20, R780–R785 (2010).

  16. 16.

    Raddatz, G. et al. Dnmt2-dependent methylomes lack defined DNA methylation patterns. Proc. Natl Acad. Sci. USA 110, 8627–8631 (2013).

  17. 17.

    Holliday, R. & Grigg, G. W. DNA methylation and mutation. Mutat. Res. 285, 61–67 (1993).

  18. 18.

    Bird, A. P. & Taggart, M. H. Variable patterns of total DNA and rDNA methylation in animals. Nucleic Acids Res. 8, 1485–1497 (1980).

  19. 19.

    Cooper, D. N. & Krawczak, M. Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum. Genet. 83, 181–188 (1989).

  20. 20.

    Rošić, S. et al. Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity. Nat. Genet. 50, 452–459 (2018).

  21. 21.

    Li, E. & Zhang, Y. DNA methylation in mammals. Cold Spring Harb. Perspect. Biol. 6, a019133 (2014).

  22. 22.

    Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).

  23. 23.

    Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

  24. 24.

    Baylin, S. B. & Jones, P. A. Epigenetic determinants of cancer. Cold Spring Harb. Perspect. Biol. 8, a019505 (2016).

  25. 25.

    Arand, J. et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLOS Genet. 8, e1002750 (2012).

  26. 26.

    Walsh, C. P., Chaillet, J. R. & Bestor, T. H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116–117 (1998).

  27. 27.

    Borgel, J. et al. Targets and dynamics of promoter DNA methylation during early mouse development. Nat. Genet. 42, 1093–1100 (2010).

  28. 28.

    Lewis, J. D. et al. Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69, 905–914 (1992).

  29. 29.

    Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462, 315–322 (2009).

  30. 30.

    Monk, M., Boubelik, M. & Lehnert, S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382 (1987).

  31. 31.

    Sanford, J. P., Clark, H. J., Chapman, V. M. & Rossant, J. Differences in DNA methylation during oogenesis and spermatogenesis and their persistence during early embryogenesis in the mouse. Genes Dev. 1, 1039–1046 (1987).

  32. 32.

    Okano, M., Xie, S. & Li, E. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nat. Genet. 19, 219–220 (1998).

  33. 33.

    Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

  34. 34.

    Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).

  35. 35.

    Bourc’his, D., Xu, G. L., Lin, C. S., Bollman, B. & Bestor, T. H. Dnmt3L and the establishment of maternal genomic imprints. Science 294, 2536–2539 (2001).

  36. 36.

    Piunti, A. & Shilatifard, A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science 352, aad9780 (2016).

  37. 37.

    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).

  38. 38.

    Zhang, Y. et al. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res. 38, 4246–4253 (2010).

  39. 39.

    Guo, X. et al. Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 517, 640–644 (2015).

  40. 40.

    Krogan, N. J. et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 23, 4207–4218 (2003).

  41. 41.

    Sun, X. J. et al. Identification and characterization of a novel human histone H3 lysine 36-specific methyltransferase. J. Biol. Chem. 280, 35261–35271 (2005).

  42. 42.

    Dhayalan, A. et al. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation. J. Biol. Chem. 285, 26114–26120 (2010).

  43. 43.

    Baubec, T. et al. Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation. Nature 520, 243–247 (2015).

  44. 44.

    Xu, Q. et al. SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development. Nat. Genet. 51, 844–856 (2019).

  45. 45.

    Bostick, M. et al. UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764 (2007).

  46. 46.

    Sharif, J. et al. The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Nature 450, 908–912 (2007).

  47. 47.

    Nady, N. et al. Recognition of multivalent histone states associated with heterochromatin by UHRF1 protein. J. Biol. Chem. 286, 24300–24311 (2011).

  48. 48.

    Arita, K. et al. Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1. Proc. Natl Acad. Sci. USA 109, 12950–12955 (2012).

  49. 49.

    Rothbart, S. B. et al. Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nat. Struct. Mol. Biol. 19, 1155–1160 (2012).

  50. 50.

    Rothbart, S. B. et al. Multivalent histone engagement by the linked tandem tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes Dev. 27, 1288–1298 (2013).

  51. 51.

    Song, J., Rechkoblit, O., Bestor, T. H. & Patel, D. J. Structure of DNMT1–DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331, 1036–1040 (2011).

  52. 52.

    Takeshita, K. et al. Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1). Proc. Natl Acad. Sci. USA 108, 9055–9059 (2011).

  53. 53.

    Ishiyama, S. et al. Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on Histone H3 reveals the basis for DNA methylation maintenance. Mol. Cell 68, 350–360 (2017).

  54. 54.

    Nishiyama, A. et al. Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication. Nature 502, 249–253 (2013).

  55. 55.

    Qin, W. et al. DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination. Cell Res. 25, 911–929 (2015).

  56. 56.

    Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in purkinje neurons and the brain. Science 324, 929–930 (2009).

  57. 57.

    Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009).

  58. 58.

    Ito, S. et al. Role of tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010).

  59. 59.

    Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300–1303 (2011).

  60. 60.

    He, Y. F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307 (2011).

  61. 61.

    Hashimoto, H. et al. Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation. Nucleic Acids Res. 40, 4841–4849 (2012).

  62. 62.

    Otani, J. et al. Cell cycle-dependent turnover of 5-hydroxymethyl cytosine in mouse embryonic stem cells. PLOS ONE 8, e82961 (2013).

  63. 63.

    Maiti, A. & Drohat, A. C. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: Potential implications for active demethylation of CpG sites. J. Biol. Chem. 286, 35334–35338 (2011).

  64. 64.

    Weber, A. R. et al. Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism. Nat. Commun. 7, 10806 (2016).

  65. 65.

    Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).

  66. 66.

    Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011).

  67. 67.

    Yin, Y. et al. Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science 356, eaaj2239 (2017).

  68. 68.

    Dennis, K., Fan, T., Geiman, T., Yan, Q. & Muegge, K. Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev. 15, 2940–2944 (2001).

  69. 69.

    Myant, K. et al. LSH and G9a/GLP complex are required for developmentally programmed DNA methylation. Genome Res. 21, 83–94 (2011).

  70. 70.

    Tao, Y. et al. Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences. Proc. Natl Acad. Sci. USA 108, 5626–5631 (2011).

  71. 71.

    Esteve, P. O. et al. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev. 20, 3089–3103 (2006).

  72. 72.

    Epsztejn-Litman, S. et al. De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat. Struct. Mol. Biol. 15, 1176–1183 (2008).

  73. 73.

    Fuks, F., Burgers, W. A., Brehm, A., Hughes-Davies, L. & Kouzarides, T. DNA methyltransferase Dnmt1 associates with histone deacetylase activity. Nat. Genet. 24, 88–91 (2000).

  74. 74.

    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).

  75. 75.

    Deplus, R. et al. Dnmt3L is a transcriptional repressor that recruits histone deacetylase. Nucleic Acids Res. 30, 3831–3838 (2002).

  76. 76.

    Meehan, R. R., Lewis, J. D., McKay, S., Kleiner, E. L. & Bird, A. P. Identification of a mammalian protein that binds specifically to DNA containing methylated CpGs. Cell 58, 499–507 (1989).

  77. 77.

    Hendrich, B. & Bird, A. Identification and characterization of a family of mammalian methyl-CpG binding proteins. Mol Cell Biol 18, 6538–6547 (1998).

  78. 78.

    Baubec, T., Ivánek, R., Lienert, F. & Schübeler, D. methylation-dependent and -independent genomic targeting principles of the MBD protein family. Cell 153, 480–492 (2013).

  79. 79.

    Saito, M. & Ishikawa, F. The mCpG-binding domain of human MBD3 does not bind to mCpG but interacts with NuRD/Mi2 components HDAC1 and MTA2. J. Biol. Chem. 277, 35434–35439 (2002).

  80. 80.

    Nan, X. et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386–389 (1998).

  81. 81.

    Ng, H. H. et al. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat. Genet. 23, 58–61 (1999).

  82. 82.

    Ren, R., Horton, J. R., Zhang, X., Blumenthal, R. M. & Cheng, X. Detecting and interpreting DNA methylation marks. Curr. Opin. Struct. Biol. 53, 88–99 (2018).

  83. 83.

    Gardiner-Garden, M. & Frommer, M. CpG Islands in vertebrate genomes. J. Mol. Biol. 196, 261–282 (1987).

  84. 84.

    Larsen, F., Gundersen, G., Lopez, R. & Prydz, H. CpG islands as gene markers in the human genome. Genomics 13, 1095–1107 (1992).

  85. 85.

    Ku, M. et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLOS Genet. 4, e1000242 (2008).

  86. 86.

    Bird, A., Taggart, M., Frommer, M., Miller, O. J. & Macleod, D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40, 91–99 (1985).

  87. 87.

    Marasca, F., Bodega, B. & Orlando, V. How polycomb-mediated cell memory deals with a changing environment. BioEssays 40, e1700137 (2018).

  88. 88.

    Singer-Sam, J. et al. Use of a HpaII-polymerase chain reaction assay to study DNA methylation in the Pgk-1 CpG island of mouse embryos at the time of X-chromosome inactivation. Mol. Cell. Biol. 10, 4987–4989 (1990).

  89. 89.

    Grant, M., Zuccotti, M. & Monk, M. Methylation of CpG sites of two X-linked genes coincides with X-inactivation in the female mouse embryo but not in the germ line. Nat. Genet. 2, 161–166 (1992).

  90. 90.

    Keohane, A. M., O’Neill, L. P., Belyaev, N. D., Lavender, J. S. & Turner, B. M. X-inactivation and histone H4 acetylation in embryonic stem cells. Dev. Biol. 180, 618–630 (1996).

  91. 91.

    Gendrel, A.-V. et al. Smchd1-dependent and -independent pathways determine developmental dynamics of CpG Island methylation on the inactive X chromosome. Dev. Cell 23, 265–279 (2012).

  92. 92.

    Blewitt, M. E. et al. SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation. Nat. Genet. 40, 663–669 (2008).

  93. 93.

    Gdula, M. R. et al. The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome. Nat. Commun. 10, 30 (2019).

  94. 94.

    Nozawa, R. S. et al. Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway. Nat. Struct. Mol. Biol. 20, 566–573 (2013).

  95. 95.

    Wutz, A. et al. Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745–749 (1997).

  96. 96.

    Thorvaldsen, J. L., Duran, K. L. & Bartolomei, M. S. Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes Dev. 12, 3693–3702 (1998).

  97. 97.

    Yang, T. et al. A mouse model for Prader–Willi syndrome imprinting-centre mutations. Nat. Genet. 19, 25–31 (1998).

  98. 98.

    Fitzpatrick, G. V., Soloway, P. D. & Higgins, M. J. Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat. Genet. 32, 426–431 (2002).

  99. 99.

    Lin, S. P. et al. Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat. Genet. 35, 97–102 (2003).

  100. 100.

    Williamson, C. M. et al. Identification of an imprinting control region affecting the expression of all transcripts in the Gnas cluster. Nat. Genet. 38, 350–355 (2006).

  101. 101.

    Proudhon, C. et al. Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes. Mol. Cell 47, 909–920 (2012).

  102. 102.

    Kaneda, M. et al. Genetic evidence for Dnmt3a-dependent imprinting during oocyte growth obtained by conditional knockout with Zp3-Cre and complete exclusion of Dnmt3b by chimera formation. Genes Cells 15, 169–179 (2010).

  103. 103.

    Chotalia, M. et al. Transcription is required for establishment of germline methylation marks at imprinted genes. Genes Dev. 23, 105–117 (2009).

  104. 104.

    Smith, E. Y., Futtner, C. R., Chamberlain, S. J., Johnstone, K. A. & Resnick, J. L. Transcription is required to establish maternal imprinting at the Prader–Willi syndrome and Angelman syndrome locus. PLOS Genet. 7, e1002422 (2011).

  105. 105.

    Smallwood, S. A. et al. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat. Genet. 43, 811–814 (2011).

  106. 106.

    Veselovska, L. et al. Deep sequencing and de novo assembly of the mouse oocyte transcriptome define the contribution of transcription to the DNA methylation landscape. Genome Biol. 16, 209 (2015).

  107. 107.

    Peaston, A. E. et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597–606 (2004).

  108. 108.

    Franke, V. et al. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. 27, 1384–1394 (2017).

  109. 109.

    Brind’Amour, J. et al. LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat. Commun. 9, 3331 (2018).

  110. 110.

    Li, X. et al. A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Dev. Cell 15, 547–557 (2008).

  111. 111.

    Quenneville, S. et al. In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions. Mol. Cell 44, 361–372 (2011).

  112. 112.

    Strogantsev, R. et al. Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression. Genome Biol. 16, 112 (2015).

  113. 113.

    Messerschmidt, D. M. et al. Trim28 is required for epigenetic stability during mouse oocyte to embryo transition. Science 335, 1499–1502 (2012).

  114. 114.

    Galonska, C., Ziller, M. J., Karnik, R. & Meissner, A. Ground State Conditions Induce Rapid Reorganization of Core Pluripotency Factor Binding before Global Epigenetic Reprogramming. Cell Stem Cell 17, 462–470 (2015).

  115. 115.

    Takahashi, N. et al. ZNF445 is a primary regulator of genomic imprinting. Genes Dev. 33, 49–54 (2019).

  116. 116.

    Auclair, G., Guibert, S., Bender, A. & Weber, M. Ontogeny of CpG island methylation and specificity of DNMT3 methyltransferases during embryonic development in the mouse. Genome Biol. 15, 545 (2014).

  117. 117.

    Karimi, M. M. et al. DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 8, 676–687 (2011).

  118. 118.

    O’Neill, K. M. et al. Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression. Epigenetics Chromatin 11, 12 (2018).

  119. 119.

    Auclair, G. et al. EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos. Genome Res. 26, 192–202 (2016).

  120. 120.

    Velasco, G. & Francastel, C. Genetics meets DNA methylation in rare diseases. Clin. Genet. 95, 210–220 (2019).

  121. 121.

    Endoh, M. et al. PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. eLife 6, e21064 (2017).

  122. 122.

    Stielow, B., Finkernagel, F., Stiewe, T., Nist, A. & Suske, G. MGA, L3MBTL2 and E2F6 determine genomic binding of the non-canonical Polycomb repressive complex PRC1.6. PLOS Genet. 14, e1007193 (2018).

  123. 123.

    Gao, Z. et al. PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol. Cell 45, 344–356 (2012).

  124. 124.

    Maeda, I. et al. Max is a repressor of germ cell-related gene expression in mouse embryonic stem cells. Nat. Commun. 4, 1754 (2013).

  125. 125.

    Velasco, G. et al. Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues. Proc. Natl Acad. Sci. USA 107, 9281–9286 (2010).

  126. 126.

    Qin, J. et al. The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. Cell Stem Cell 11, 319–332 (2012).

  127. 127.

    Trojer, P. et al. L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol. Cell 42, 438–450 (2011).

  128. 128.

    Yoder, J. A., Walsh, C. P. & Bestor, T. H. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 13, 335–340 (1997).

  129. 129.

    Barau, J. et al. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 354, 909–912 (2016).

  130. 130.

    Sanchez-Delgado, M. et al. Human oocyte-derived methylation differences persist in the placenta revealing widespread transient imprinting. PLOS Genet. 12, e1006427 (2016).

  131. 131.

    Walsh, C. P., Chaillet, J. R. & Bestor, T. H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat. Genet. 20, 116–117 (1998).

  132. 132.

    Jain, D. et al. rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline. PLOS Genet. 13, e1006964 (2017).

  133. 133.

    Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908–917 (2008).

  134. 134.

    Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol Cell 31, 785–799 (2008).

  135. 135.

    Aravin, A. A., Hannon, G. J. & Brennecke, J. The Piwi–piRNA pathway provides an adaptive defense in the transposon arms race. Science 318, 761–764 (2007).

  136. 136.

    Carmell, M. A. et al. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12, 503–514 (2007).

  137. 137.

    Molaro, A. et al. Two waves of de novo methylation during mouse germ cell development. Genes Dev. 28, 1544–1549 (2014).

  138. 138.

    Manakov, S. A. et al. MIWI2 and MILI have differential effects on piRNA biogenesis and DNA methylation. Cell Rep. 12, 1234–1243 (2015).

  139. 139.

    Barau, J. et al. The novel DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science 354, 909–912 (2016).

  140. 140.

    Jordà, M. et al. The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells. Genome Res. 27, 118–132 (2017).

  141. 141.

    Zamudio, N. et al. DNA methylation restrains transposons from adopting a chromatin signature permissive for meiotic recombination. Genes Dev. 29, 1256–1270 (2015).

  142. 142.

    Nishibuchi, G. & Déjardin, J. The molecular basis of the organization of repetitive DNA-containing constitutive heterochromatin in mammals. Chromosom. Res. 25, 77–87 (2017).

  143. 143.

    Hutnick, L. K., Huang, X., Loo, T.-C., Ma, Z. & Fan, G. Repression of retrotransposal elements in mouse embryonic stem cells is primarily mediated by a DNA methylation-independent mechanism. J. Biol. Chem. 285, 21082–21091 (2010).

  144. 144.

    Matsui, T. et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 464, 927 (2010).

  145. 145.

    Walter, M. et al. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. eLife 5, e11418 (2016).

  146. 146.

    Sharif, J. et al. Activation of endogenous retroviruses in Dnmt1−/− ESCs involves disruption of SETDB1-mediated repression by NP95 binding to hemimethylated DNA. Cell Stem Cell 19, 81–94 (2016).

  147. 147.

    Berrens, R. V. et al. An endosiRNA-based repression mechanism counteracts transposon activation during global DNA demethylation in embryonic stem cells. Cell Stem Cell 21, 694–703 (2017).

  148. 148.

    Bender, C. M. et al. Roles of cell division and gene transcription in the methylation of CpG islands. Mol. Cell. Biol. 19, 6690–6698 (1999).

  149. 149.

    Varley, K. E. et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 23, 555–567 (2013).

  150. 150.

    Laurent, L. et al. Dynamic changes in the human methylome during differentiation. Genome Res. 20, 320–331 (2010).

  151. 151.

    Gelfman, S., Cohen, N., Yearim, A. & Ast, G. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res. 23, 789–799 (2013).

  152. 152.

    Shayevitch, R., Askayo, D., Keydar, I. & Ast, G. The importance of DNA methylation of exons on alternative splicing. RNA 24, 1351–1362 (2018).

  153. 153.

    Yang, X. et al. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 26, 577–590 (2014).

  154. 154.

    Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74–79 (2011).

  155. 155.

    Maunakea, A. K., Chepelev, I., Cui, K. & Zhao, K. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res. 23, 1256–1269 (2013).

  156. 156.

    Yearim, A. et al. HP1 is involved in regulating the global impact of DNA methylation on alternative splicing. Cell Rep. 10, 1122–1134 (2015).

  157. 157.

    Carrozza, M. J. et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581–592 (2005).

  158. 158.

    Maunakea, A. K. et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466, 253–257 (2010).

  159. 159.

    Neri, F. et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature 543, 72–77 (2017).

  160. 160.

    Teissandier, A. & Bourc’his, D. Gene body DNA methylation conspires with H3K36me3 to preclude aberrant transcription. EMBO J. 36, 1471–1473 (2017).

  161. 161.

    Guibert, S., Forné, T. & Weber, M. Global profiling of DNA methylation erasure in mouse primordial germ cells. Genome Res. 22, 633–641 (2012).

  162. 162.

    Vincent, J. J. et al. Stage-specific roles for Tet1 and Tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell 12, 470–478 (2013).

  163. 163.

    Yamaguchi, S. et al. Dynamics of 5-methylcytosine and 5-hydroxymethylcytosine during germ cell reprogramming. Cell Res. 23, 329–339 (2013).

  164. 164.

    Yamaguchi, S. et al. Tet1 controls meiosis by regulating meiotic gene expression. Nature 492, 443–447 (2012).

  165. 165.

    Yamaguchi, S., Shen, L., Liu, Y., Sendler, D. & Zhang, Y. Role of Tet1 in erasure of genomic imprinting. Nature 504, 460–464 (2013).

  166. 166.

    Hackett, J. A. et al. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339, 448–452 (2013).

  167. 167.

    Gu, T.-P. et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606–610 (2011).

  168. 168.

    Wossidlo, M. et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. 2, 241 (2011).

  169. 169.

    Iqbal, K., Jin, S.-G., Pfeifer, G. P. & Szabo, P. E. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl Acad. Sci. USA 108, 3642–3647 (2011).

  170. 170.

    Howell, C. Y. et al. Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene. Cell 104, 829–838 (2001).

  171. 171.

    Wang, L. et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157, 979–991 (2014).

  172. 172.

    Guo, F. et al. Active and passive demethylation of male and female pronuclear DNA in the mammalian zygote. Cell Stem Cell 15, 447–459 (2014).

  173. 173.

    Shen, L. et al. Tet3 and DNA replication mediate demethylation of both the maternal and paternal genomes in mouse zygotes. Cell Stem Cell 15, 459–470 (2014).

  174. 174.

    Amouroux, R. et al. De novo DNA methylation drives 5hmC accumulation in mouse zygotes. Nat. Cell Biol. 18, 225–233 (2016).

  175. 175.

    Santos, F. et al. Active demethylation in mouse zygotes involves cytosine deamination and base excision repair. Epigenetics Chromatin 6, 39 (2013).

  176. 176.

    Smith, Z. D. et al. DNA methylation dynamics of the human preimplantation embryo. Nature 511, 611–615 (2014).

  177. 177.

    Okae, H. et al. Genome-wide analysis of DNA methylation dynamics during early human development. PLOS Genet. 10, e1004868 (2014).

  178. 178.

    Guo, H. et al. The DNA methylation landscape of human early embryos. Nature 511, 606 (2014).

  179. 179.

    Zhu, P. et al. Single-cell DNA methylome sequencing of human preimplantation embryos. Nat. Genet. 50, 12–19 (2018).

  180. 180.

    Hill, S. et al. Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte. Nature 555, 392–396 (2018).

  181. 181.

    Skvortsova, K., Iovino, N. & Bogdanović, O. Functions and mechanisms of epigenetic inheritance in animals. Nat. Rev. Mol. Cell Biol. 19, 774–790 (2018).

  182. 182.

    Duffié, R. et al. The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals. Genes Dev. 28, 463–478 (2014).

  183. 183.

    Greenberg, M. V. C. et al. Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth. Nat. Genet. 49, 110–118 (2017).

  184. 184.

    Lane, N. et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35, 88–93 (2003).

  185. 185.

    Smith, Z. D. et al. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature 484, 339–344 (2012).

  186. 186.

    Rowe, H. M. et al. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 463, 237–240 (2010).

  187. 187.

    Ecco, G., Imbeault, M. & Trono, D. KRAB zinc finger proteins. Development 144, 2719–2729 (2017).

  188. 188.

    Kazachenka, A. et al. Identification, characterization, and heritability of murine metastable epialleles: implications for non-genetic inheritance. Cell 175, 1259–1271 (2018).

  189. 189.

    Gkountela, S. et al. DNA demethylation dynamics in the human prenatal germline. Cell 161, 1425–1436 (2015).

  190. 190.

    Tang, W. W. C. et al. A unique gene regulatory network resets the human germline epigenome for development. Cell 161, 1453–1467 (2015).

  191. 191.

    Hajkova, P. et al. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 117, 15–23 (2002).

  192. 192.

    Kobayashi, H. et al. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLOS Genet. 8, e1002440 (2012).

  193. 193.

    Li, Y. et al. Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1. Nature 564, 136–140 (2018).

  194. 194.

    Smith, Z. D. et al. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549, 543–547 (2017).

  195. 195.

    Zhang, Y. et al. Dynamic epigenomic landscapes during early lineage specification in mouse embryos. Nat. Genet. 50, 96–105 (2018).

  196. 196.

    Gama-Sosa, M. A. et al. Tissue-specific differences in DNA methylation in various mammals. Biochim. Biophys. Acta 740, 212–219 (1983).

  197. 197.

    Hon, G. C. et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat. Genet. 45, 1198–1206 (2013).

  198. 198.

    Seisenberger, S. et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012).

  199. 199.

    Schultz, M. D. et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523, 212–216 (2015).

  200. 200.

    Ziller, M. J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477–481 (2013).

  201. 201.

    Sardina, J. L. et al. Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate. Cell Stem Cell 23, 727–741 (2018).

  202. 202.

    Rasmussen, K. D. et al. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Res. 29, 564–575 (2019).

  203. 203.

    Lister, R. et al. Global epigenomic reconfiguration during mammalian brain development. Science 341, 6146 (2013).

  204. 204.

    Guo, J. U. et al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat. Neurosci. 17, 215–222 (2014).

  205. 205.

    Gabel, H. W. et al. Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature 522, 89–93 (2015).

  206. 206.

    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).

  207. 207.

    Stroud, H. et al. Early-life gene expression in neurons modulates lasting epigenetic states. Cell 171, 1151–1164 (2017).

  208. 208.

    Ziller, M. J. et al. Dissecting the functional consequences of de novo DNA methylation dynamics in human motor neuron differentiation and physiology. Cell Stem Cell 22, 559–574 (2018).

  209. 209.

    Klein, C. J. et al. Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat. Genet. 43, 595 (2011).

  210. 210.

    Winkelmann, J. et al. Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy. Hum. Mol. Genet. 21, 2205–2210 (2012).

  211. 211.

    Baets, J. et al. Defects of mutant DNMT1 are linked to a spectrum of neurological disorders. Brain 138, 845–861 (2015).

  212. 212.

    Sun, Z. et al. Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E AU. Epigenetics 9, 1184–1193 (2014).

  213. 213.

    Kernohan, K. D. et al. Identification of a methylation profile for DNMT1-associated autosomal dominant cerebellar ataxia, deafness, and narcolepsy. Clin. Epigenetics 8, 91 (2016).

  214. 214.

    Jeanpierre, M. et al. An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome. Hum. Mol. Genet. 2, 731–735 (1993).

  215. 215.

    Xu, G. L. et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402, 187–191 (1999).

  216. 216.

    Thijssen, P. E. et al. Mutations in CDCA7 and HELLS cause immunodeficiency–centromeric instability–facial anomalies syndrome. Nat. Commun. 6, 7870 (2015).

  217. 217.

    de Greef, J. C. et al. Mutations in ZBTB24 are associated with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2. Am. J. Hum. Genet. 88, 796–804 (2011).

  218. 218.

    Velasco, G. et al. Comparative methylome analysis of ICF patients identifies heterochromatin loci that require ZBTB24, CDCA7 and HELLS for their methylated state. Hum. Mol. Genet. 27, 2409–2424 (2018).

  219. 219.

    Ueda, Y. et al. Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 133, 1183–1192 (2006).

  220. 220.

    Wu, H. et al. Converging disease genes in ICF syndrome: ZBTB24 controls expression of CDCA7 in mammals. Hum. Mol. Genet. 25, 4041–4051 (2016).

  221. 221.

    Rajshekar, S. et al. Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLife 7, e39658 (2018).

  222. 222.

    Heyn, P. et al. Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions. Nat. Genet. 51, 96–105 (2019).

  223. 223.

    Li, Y. et al. Genome-wide analyses reveal a role of Polycomb in promoting hypomethylation of DNA methylation valleys. Genome Biol. 19, 18 (2018).

  224. 224.

    Jeong, M. et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat. Genet. 46, 17–23 (2014).

  225. 225.

    Sendžikaitė, G., Hanna, C. W., Stewart-Morgan, K. R., Ivanova, E. & Kelsey, G. A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice. Nat. Commun. 10, 1884 (2019).

  226. 226.

    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).

  227. 227.

    Challen, G. A. et al. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat. Genet. 44, 23–31 (2012).

  228. 228.

    Wu, H. et al. Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329, 444–448 (2010).

  229. 229.

    Tatton-Brown, K. et al. Mutations in epigenetic regulation genes are a major cause of overgrowth with intellectual disability. Am. J. Hum. Genet. 100, 725–736 (2017).

  230. 230.

    Russler-Germain, D. A. et al. The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers. Cancer Cell 25, 442–454 (2014).

  231. 231.

    Spencer, D. H. et al. CpG island hypermethylation mediated by DNMT3A is a consequence of AML progression. Cell 168, 801–816 (2017).

  232. 232.

    Kosaki, R., Terashima, H., Kubota, M. & Kosaki, K. Acute myeloid leukemia-associated DNMT3A p.Arg882His mutation in a patient with Tatton-Brown–Rahman overgrowth syndrome as a constitutional mutation. Am. J. Med. Genet. Part A 173, 250–253 (2017).

  233. 233.

    Langemeijer, S. M. C. et al. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat. Genet. 41, 838–842 (2009).

  234. 234.

    Cimmino, L. et al. Restoration of TET2 function blocks aberrant self-renewal and leukemia progression. Cell 170, 1079–1095 (2017).

  235. 235.

    Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839–843 (2010).

  236. 236.

    Rasmussen, K. D. et al. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis. Genes Dev. 29, 910–922 (2015).

  237. 237.

    Madzo, J. et al. Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis. Cell Rep. 6, 231–244 (2014).

  238. 238.

    Spruijt, C. G. et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152, 1146–1159 (2013).

  239. 239.

    Zhang, X. et al. DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells. Nat. Genet. 48, 1014–1023 (2016).

  240. 240.

    Turcan, S. et al. IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 483, 479–483 (2012).

  241. 241.

    Xiao, M. et al. Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors. Genes Dev. 26, 1326–1338 (2012).

  242. 242.

    Letouzé, E. et al. SDH mutations establish a hypermethylator phenotype in paraganglioma. Cancer Cell 23, 739–752 (2013).

  243. 243.

    Killian, J. K. et al. Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. Cancer Discov. 3, 648–657 (2013).

  244. 244.

    Zhang, H., Lang, Z. & Zhu, J.-K. Dynamics and function of DNA methylation in plants. Nat. Rev. Mol. Cell Biol. 19, 489–506 (2018).

  245. 245.

    Bewick, A. J. et al. Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics Chromatin 12, 6 (2019).

  246. 246.

    Hu, S. et al. DNA methylation presents distinct binding sites for human transcription factors. eLife 2, e00726 (2013).

  247. 247.

    Liu, Y. et al. Structural basis for Klf4 recognition of methylated DNA. Nucleic Acids Res. 42, 4859–4867 (2014).

  248. 248.

    Hashimoto, H. et al. Distinctive Klf4 mutants determine preference for DNA methylation status. Nucleic Acids Res. 44, 10177–10185 (2016).

  249. 249.

    Rishi, V. et al. CpG methylation of half-CRE sequences creates C/EBPα binding sites that activate some tissue-specific genes. Proc. Natl Acad. Sci. USA 107, 20311–20316 (2010).

  250. 250.

    Tanay, A., O’Donnell, A. H., Damelin, M. & Bestor, T. H. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc. Natl Acad. Sci. USA 104, 5521–5526 (2007).

  251. 251.

    Brinkman, A. B. et al. Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128–1138 (2012).

  252. 252.

    Statham, A. L. et al. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 22, 1120–1127 (2012).

  253. 253.

    Jermann, P., Hoerner, L., Burger, L. & Schubeler, D. Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation. Proc. Natl Acad. Sci. USA 111, E3415–E3421 (2014).

  254. 254.

    Hon, G. C. et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 22, 246–258 (2012).

  255. 255.

    Bahar Halpern, K., Vana, T. & Walker, M. D. Paradoxical role of DNA methylation in activation of FoxA2 gene expression during endoderm development. J. Biol. Chem. 289, 23882–23892 (2014).

  256. 256.

    Takahashi, Y. et al. Integration of CpG-free DNA induces de novo methylation of CpG islands in pluripotent stem cells. Science 356, 503–508 (2017).

  257. 257.

    Li, F. et al. Chimeric DNA methyltransferases target DNA methylation to specific DNA sequences and repress expression of target genes. Nucleic Acids Res. 35, 100–112 (2007).

  258. 258.

    Bernstein, D. L., Le Lay, J. E., Ruano, E. G. & Kaestner, K. H. TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts. J. Clin. Invest. 125, 1998–2006 (2015).

  259. 259.

    Maeder, M. L. et al. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol. 31, 1137–1142 (2013).

  260. 260.

    Valton, J. et al. Overcoming transcription activator-like effector (TALE) DNA binding domain sensitivity to cytosine methylation. J. Biol. Chem. 287, 38427–38432 (2012).

  261. 261.

    Vojta, A. et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res 44, 5615–28 (2016).

  262. 262.

    Liu, X. S. et al. Editing DNA methylation in the mammalian genome. Cell 167, 233–247 (2016).

  263. 263.

    Lei, Y. et al. Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein. Nat. Commun. 8, 16026 (2017).

  264. 264.

    Stepper, P. et al. Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Res. 45, 1703–1713 (2017).

  265. 265.

    Huang, Y.-H. et al. DNA epigenome editing using CRISPR-Cas SunTag-directed DNMT3A. Genome Biol. 18, 176 (2017).

  266. 266.

    Pflueger, C. et al. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Res. 28, 1193–1206 (2018).

  267. 267.

    Morita, S. et al. Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions. Nat. Biotechnol. 34, 1060–1065 (2016).

  268. 268.

    Amabile, A. et al. Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing. Cell 167, 219–232 (2016).

  269. 269.

    Saunderson, E. A. et al. Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors. Nat. Commun. 8, 1450 (2017).

Download references

Acknowledgements

The laboratory of D.B. is part of the Laboratoire d’Excellence (LABEX) entitled DEEP (11-LBX0044) and is supported by the European Research Council (ERC) (grant ERC-Cog EpiRepro).

Author information

The authors contributed equally to all aspects of the article.

Correspondence to Deborah Bourc’his.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information

Nature Reviews Molecular Cell Biology thanks G. Kelsey, R. Lister and T. Nakano for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Glossary

Pericentromeric satellite repeats

Tandem repeats enriched in heterochromatin modifications such as DNA methylation and histone H3 Lys9 trimethylation.

Retrotransposons

Transposable elements that propagate in the genome through RNA intermediates and reverse transcription.

Whole-genome bisulfite sequencing

Sodium bisulfite treatment converts unmodified cytosines — but not (hydroxy)methylated cytosines — into uracils (thymines following PCR). Paired with next-generation sequencing, this technique generates genome-wide, single-nucleotide resolution maps of DNA methylation.

Intergenerational epigenetic inheritance

Epigenetic information that is inherited from the parents (for example, genomic imprinting).

Transgenerational epigenetic inheritance

Epigenetic information that is inherited from generations that were not exposed to the initial cue that caused the epigenetic change.

Inner cell mass

Refers to the pluripotent cells in the blastocyst of preimplantation embryos, which can be derived and cultured as embryonic stem cells.

Neomorphic mutations

Typically, dominant mutations, which confer altered expression or novel function for the protein product.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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). https://doi.org/10.1038/s41580-019-0159-6

Download citation

Further reading