Pathways of DNA Demethylation

  • Wendy DeanEmail author
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 945)


The regulation of the genome relies on the epigenome to instruct, define and restrict the activities of growth and development. Among the cohort of epigenetic instructions, DNA methylation is perhaps the best understood. In most mammals, cycles of the addition and removal of DNA methylation constitute phases of reprogramming when the developing embryo must negotiate lineage defining and developmental commitment events. In these instances, the DNA methylation instruction is often removed, thereby allowing a change in permission for future development and a return to a more plastic and pluripotent state. Because of this, the germ line, upon demethylation, can give rise to gametes that are fully functional across generations and poised for totipotency. This return to a less differentiated state can also be achieved experimentally. The loss of DNA methylation constitutes one of the significant barriers to induced pluripotency and is a prerequisite for the generation of iPS cells. Taking fully differentiated cells, such as skin cells, and turning back the developmental clock heralded a technological breakthrough discovery in 2006 (Takahashi and Yamanaka 2006) with unprecedented promise in regenerative medicine. In this chapter, the mechanistic possibilities for DNA demethylation will be described in the context of natural and experimentally induced epigenetic reprogramming. The balance of the maintenance of this heritable mark together with its timely removal is essential for lifelong health and may be a key in our understanding of ageing.


Active demethylation Passive demethylation Deamination Dnmt1 Uhfr1 













Activation-induced deaminase


Activation-induced cytosine deaminase


Apurinic/apyrimidinic (AP) endonuclease 1


Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like


Base excision repair




Cytosine–adenosine dinucleotide


Cytosine–guanosine dinucleotide


CpG islands


Zinc finger protein-binding domain to non-methylated CpG


Asymmetric DNA methylation


Deoxyribonucleic acid

ES cells

Embryonic stem cells


DNA methyltransferases, Dnmt1, DNA (cytosine-5)-methyltransferase 1; Dnmt1o, DNA (cytosine-5)-methyltransferase 1 oocyte form; Dnmt1s, DNA (cytosine-5)-methyltransferase 1 somatic form; Dnmt3a, DNA (cytosine-5)-methyltransferase 3a


DNA (cytosine-5)-methyltransferase 3b


DNA (cytosine-5)-methyltransferase 3-like, E6.5, embryonic day 6.5


Embryonic day thirteen


Enhanced green fluorescent protein


Elongator complex protein 1


Elongator complex protein 3


Elongator complex protein 4


Germinal vesicle


Germinal vesicle oocytes


Gonad-specific expression




Intracisternal A particles, IF, immunofluorescence

iPS cells

Induced pluripotent stem cells


Histone H3 lysine 9 dimethylation


Knockout, MBD2, methyl-CpG-binding domain 2


Methyl-CpG-binding domain 4


Next-generation sequencing


Nucleotide excision repair


Nuclear protein 95


Replication foci targeting domain


Poly-ADP-ribose polymerase 1


Polycomb repressive complex


Primordial germ cells


Reduced representational bisulphite sequencing


Ribonucleic acid


RNA interference




Small interfering RNA


Single-strand selective monofunctional uracil DNA glycosylase 1


Somatic nuclear transfer




Thymine DNA glycosylase


Ten-eleven translocation 1, 2 or 3




Zygotic genome activation


  1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. DNA repair. In: Molecular biology of the cell. 4th ed. New York: Garland Science; 2002.Google Scholar
  2. Amouroux R, Nashun B, Shirane K, Nakagawa S, Hill PW, D’Souza Z, Nakayama M, Matsuda M, Turp A, Ndjetehe E, Encheva V, Kudo NR, Koseki H, Sasaki H, Hajkova P. De novo DNA methylation drives 5hmC accumulation in mouse zygotes. Nat Cell Biol. 2016;18(2):225–33. doi: 10.1038/ncb3296.PubMedPubMedCentralCrossRefGoogle Scholar
  3. Barnetova I, Fulka H, Fulka Jr J. Epigenetic characteristics of paternal chromatin in interspecies zygotes. J Reprod Dev. 2010;56(6):601–6.PubMedCrossRefGoogle Scholar
  4. Beaujean N, Taylor JE, McGarry M, Gardner JO, Wilmut I, Loi P, Ptak G, Galli C, Lazzari G, Bird A, Young LE, Meehan RR. The effect of interspecific oocytes on demethylation of sperm DNA. Proc Natl Acad Sci U S A. 2004;101(20):7636–40. doi: 10.1073/pnas.0400730101.PubMedPubMedCentralCrossRefGoogle Scholar
  5. Bestor TH. The host defence function of genomic methylation patterns. Novartis Found Symp. 1998;214:187–95; discussion 195–189, 228–132.PubMedGoogle Scholar
  6. Bhattacharya SK, Ramchandani S, Cervoni N, Szyf M. A mammalian protein with specific demethylase activity for mCpG DNA. Nature. 1999;397(6720):579–83. doi: 10.1038/17533.PubMedCrossRefGoogle Scholar
  7. Bird AP. DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res. 1980;8(7):1499–504.PubMedPubMedCentralCrossRefGoogle Scholar
  8. Blaschke K, Ebata KT, Karimi MM, Zepeda-Martinez JA, Goyal P, Mahapatra S, Tam A, Laird DJ, Hirst M, Rao A, Lorincz MC, Ramalho-Santos M. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature. 2013;500(7461):222–6. doi: 10.1038/nature12362.PubMedPubMedCentralCrossRefGoogle Scholar
  9. Boeke J, Ammerpohl O, Kegel S, Moehren U, Renkawitz R. The minimal repression domain of MBD2b overlaps with the methyl-CpG-binding domain and binds directly to Sin3A. J Biol Chem. 2000;275(45):34963–7. doi: 10.1074/jbc.M005929200.PubMedCrossRefGoogle Scholar
  10. Bouniol-Baly C, Hamraoui L, Guibert J, Beaujean N, Szollosi MS, Debey P. Differential transcriptional activity associated with chromatin configuration in fully grown mouse germinal vesicle oocytes. Biol Reprod. 1999;60(3):580–7.PubMedCrossRefGoogle Scholar
  11. Bourc’his D, Le Bourhis D, Patin D, Niveleau A, Comizzoli P, Renard JP, Viegas-Pequignot E. Delayed and incomplete reprogramming of chromosome methylation patterns in bovine cloned embryos. Curr Biol. 2001;11(19):1542–6.PubMedCrossRefGoogle Scholar
  12. Braun RE. Packaging paternal chromosomes with protamine. Nat Genet. 2001;28(1):10–2. doi: 10.1038/88194.PubMedGoogle Scholar
  13. Brewer LR, Corzett M, Balhorn R. Protamine-induced condensation and decondensation of the same DNA molecule. Science. 1999;286(5437):120–3.PubMedCrossRefGoogle Scholar
  14. Broderick JB, Duffus BR, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev. 2014;114(8):4229–317. doi: 10.1021/cr4004709.PubMedPubMedCentralCrossRefGoogle Scholar
  15. Cardoso MC, Leonhardt H. DNA methyltransferase is actively retained in the cytoplasm during early development. J Cell Biol. 1999;147(1):25–32.PubMedPubMedCentralCrossRefGoogle Scholar
  16. Carlson LL, Page AW, Bestor TH. Properties and localization of DNA methyltransferase in preimplantation mouse embryos: implications for genomic imprinting. Genes Dev. 1992;6(12B):2536–41.PubMedCrossRefGoogle Scholar
  17. Cedar H, Solage A, Glaser G, Razin A. Direct detection of methylated cytosine in DNA by use of the restriction enzyme MspI. Nucleic Acids Res. 1979;6(6):2125–32.PubMedPubMedCentralCrossRefGoogle Scholar
  18. Cheng X, Roberts RJ, AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 2001;29:3784–95.Google Scholar
  19. Chen T, Ueda Y, Dodge JE, Wang Z, Li E. Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol Cell Biol. 2003;23(16):5594–605.PubMedPubMedCentralCrossRefGoogle Scholar
  20. Chen J, Guo L, Zhang L, Wu H, Yang J, Liu H, Wang X, Hu X, Gu T, Zhou Z, Liu J, Liu J, Wu H, Mao SQ, Mo K, Li Y, Lai K, Qi J, Yao H, Pan G, Xu GL, Pei D. Vitamin C modulates TET1 function during somatic cell reprogramming. Nat Genet. 2013;45(12):1504–9. doi: 10.1038/ng.2807.PubMedCrossRefGoogle Scholar
  21. Chiu YL, Greene WC. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol. 2008;26:317–53. doi: 10.1146/annurev.immunol.26.021607.090350.PubMedCrossRefGoogle Scholar
  22. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994;22(15):2990–7.PubMedPubMedCentralCrossRefGoogle Scholar
  23. Constantinides PG, Jones PA, Gevers W. Functional striated muscle cells from non-myoblast precursors following 5-azacytidine treatment. Nature. 1977;267(5609):364–6.PubMedCrossRefGoogle Scholar
  24. Conticello SG, Thomas CJ, Petersen-Mahrt SK, Neuberger MS. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol Biol Evol. 2005;22(2):367–77. doi: 10.1093/molbev/msi026.PubMedCrossRefGoogle Scholar
  25. Dean W. DNA methylation and demethylation: a pathway to gametogenesis and development. Mol Reprod Dev. 2014;81(2):113–25. doi: 10.1002/mrd.22280.PubMedCrossRefGoogle Scholar
  26. Dean W, Santos F, Stojkovic M, Zakhartchenko V, Walter J, Wolf E, Reik W. Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc Natl Acad Sci U S A. 2001;98(24):13734–8. doi: 10.1073/pnas.241522698.PubMedPubMedCentralCrossRefGoogle Scholar
  27. Derijck AA, van der Heijden GW, Giele M, Philippens ME, van Bavel CC, de Boer P. gammaH2AX signalling during sperm chromatin remodelling in the mouse zygote. DNA Repair (Amst). 2006;5(8):959–71. doi: 10.1016/j.dnarep.2006.05.043.CrossRefGoogle Scholar
  28. Derijck A, van der Heijden G, Giele M, Philippens M, de Boer P. DNA double-strand break repair in parental chromatin of mouse zygotes, the first cell cycle as an origin of de novo mutation. Hum Mol Genet. 2008;17(13):1922–37. doi: 10.1093/hmg/ddn090.PubMedCrossRefGoogle Scholar
  29. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res. 1982;10(8):2709–21.PubMedPubMedCentralCrossRefGoogle Scholar
  30. Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature. 1983;301(5895):89–92.PubMedCrossRefGoogle Scholar
  31. Ficz G, Hore TA, Santos F, Lee HJ, Dean W, Arand J, Krueger F, Oxley D, Paul YL, Walter J, Cook SJ, Andrews S, Branco MR, Reik W. FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell. 2013;13(3):351–9. doi: 10.1016/j.stem.2013.06.004.PubMedPubMedCentralCrossRefGoogle Scholar
  32. Franchini DM, Chan CF, Morgan H, Incorvaia E, Rangam G, Dean W, Santos F, Reik W, Petersen-Mahrt SK. Processive DNA demethylation via DNA deaminase-induced lesion resolution. PLoS One. 2014;9(7):e97754. doi: 10.1371/journal.pone.0097754.PubMedPubMedCentralCrossRefGoogle Scholar
  33. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992;89(5):1827–31.PubMedPubMedCentralCrossRefGoogle Scholar
  34. Gama-Sosa MA, Slagel VA, Trewyn RW, Oxenhandler R, Kuo KC, Gehrke CW, Ehrlich M. The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res. 1983;11(19):6883–94.PubMedPubMedCentralCrossRefGoogle Scholar
  35. Grippo P, Iaccarino M, Parisi E, Scarano E. Methylation of DNA in developing sea urchin embryos. J Mol Biol. 1968;36(2):195–208.PubMedCrossRefGoogle Scholar
  36. Gu TP, Guo F, Yang H, Wu HP, Xu GF, Liu W, Xie ZG, Shi L, He X, Jin SG, Iqbal K, Shi YG, Deng Z, Szabo PE, Pfeifer GP, Li J, Xu GL. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature. 2011;477(7366):606–10. doi: 10.1038/nature10443.PubMedCrossRefGoogle Scholar
  37. Guenatri M, Bailly D, Maison C, Almouzni G. Mouse centric and pericentric satellite repeats form distinct functional heterochromatin. J Cell Biol. 2004;166(4):493–505. doi: 10.1083/jcb.200403109.PubMedPubMedCentralCrossRefGoogle Scholar
  38. Guibert S, Forne T, Weber M. Global profiling of DNA methylation erasure in mouse primordial germ cells. Genome Res. 2012;22(4):633–41. doi: 10.1101/gr.130997.111.PubMedPubMedCentralCrossRefGoogle Scholar
  39. Guo F, Li X, Liang D, Li T, Zhu P, Guo H, Wu X, Wen L, Gu TP, Hu B, Walsh CP, Li J, Tang F, Xu GL. Active and passive demethylation of male and female pronuclear DNA in the mammalian zygote. Cell Stem Cell. 2014;15(4):447–58. doi: 10.1016/j.stem.2014.08.003.PubMedCrossRefGoogle Scholar
  40. Hackett JA, Zylicz JJ, Surani MA. Parallel mechanisms of epigenetic reprogramming in the germline. Trends Genet. 2012;28(4):164–74. doi: 10.1016/j.tig.2012.01.005.PubMedCrossRefGoogle Scholar
  41. Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, Surani MA. Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science. 2013;339(6118):448–52. doi: 10.1126/science.1229277.PubMedCrossRefGoogle Scholar
  42. Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev. 2002;117(1–2):15–23.PubMedCrossRefGoogle Scholar
  43. Hajkova P, Jeffries SJ, Lee C, Miller N, Jackson SP, Surani MA. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science. 2010;329(5987):78–82. doi: 10.1126/science.1187945.PubMedCrossRefGoogle Scholar
  44. Herman JG, Merlo A, Mao L, Lapidus RG, Issa JP, Davidson NE, Sidransky D, Baylin SB. Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers. Cancer Res. 1995;55(20):4525–30.PubMedGoogle Scholar
  45. Hirasawa R, Sasaki H. Dynamic transition of Dnmt3b expression in mouse pre- and early post-implantation embryos. Gene Expr Patterns. 2009;9(1):27–30. doi: 10.1016/j.gep.2008.09.002.PubMedCrossRefGoogle Scholar
  46. Hotchkiss RD. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J Biol Chem. 1948;175(1):315–32.PubMedGoogle Scholar
  47. Howell CY, Bestor TH, Ding F, Latham KE, Mertineit C, Trasler JM, Chaillet JR. Genomic imprinting disrupted by a maternal effect mutation in the Dnmt1 gene. Cell. 2001;104(6):829–38.PubMedCrossRefGoogle Scholar
  48. Howlett SK, Reik W. Methylation levels of maternal and paternal genomes during preimplantation development. Development. 1991;113(1):119–27.PubMedGoogle Scholar
  49. Ichiyanagi K, Li Y, Watanabe T, Ichiyanagi T, Fukuda K, Kitayama J, Yamamoto Y, Kuramochi-Miyagawa S, Nakano T, Yabuta Y, Seki Y, Saitou M, Sasaki H. Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development. Genome Res. 2011;21(12):2058–66. doi: 10.1101/gr.123679.111.PubMedPubMedCentralCrossRefGoogle Scholar
  50. Inoue A, Zhang Y. Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science. 2011;334(6053):194. doi: 10.1126/science.1212483.PubMedPubMedCentralCrossRefGoogle Scholar
  51. Inoue A, Shen L, Dai Q, He C, Zhang Y. Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development. Cell Res. 2011;21(12):1670–6. doi: 10.1038/cr.2011.189.PubMedPubMedCentralCrossRefGoogle Scholar
  52. Inoue A, Shen L, Matoba S, Zhang Y. Haploinsufficiency, but not defective paternal 5mC oxidation, accounts for the developmental defects of maternal Tet3 knockouts. Cell Rep. 2015;10(4):463–70. doi: 10.1016/j.celrep.2014.12.049.PubMedCrossRefGoogle Scholar
  53. Iqbal K, Jin SG, Pfeifer GP, Szabo PE. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci U S A. 2011;108(9):3642–7. doi: 10.1073/pnas.1014033108.PubMedPubMedCentralCrossRefGoogle Scholar
  54. Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010;466(7310):1129–33. doi: 10.1038/nature09303.PubMedPubMedCentralCrossRefGoogle Scholar
  55. Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003;33(Suppl):245–54. doi: 10.1038/ng1089.PubMedCrossRefGoogle Scholar
  56. Kaneda M, Hirasawa R, Chiba H, Okano M, Li E, Sasaki H. 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. 2010;15(3):169–79. doi: 10.1111/j.1365-2443.2009.01374.x.PubMedCrossRefGoogle Scholar
  57. Kangaspeska S, Stride B, Metivier R, Polycarpou-Schwarz M, Ibberson D, Carmouche RP, Benes V, Gannon F, Reid G. Transient cyclical methylation of promoter DNA. Nature. 2008;452(7183):112–5. doi: 10.1038/nature06640.PubMedCrossRefGoogle Scholar
  58. Kishigami S, Van Thuan N, Hikichi T, Ohta H, Wakayama S, Mizutani E, Wakayama T. Epigenetic abnormalities of the mouse paternal zygotic genome associated with microinsemination of round spermatids. Dev Biol. 2006;289(1):195–205. doi: 10.1016/j.ydbio.2005.10.026.PubMedCrossRefGoogle Scholar
  59. Ko M, Huang Y, Jankowska AM, Pape UJ, Tahiliani M, Bandukwala HS, An J, Lamperti ED, Koh KP, Ganetzky R, Liu XS, Aravind L, Agarwal S, Maciejewski JP, Rao A. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature. 2010;468(7325):839–43. doi: 10.1038/nature09586.PubMedPubMedCentralCrossRefGoogle Scholar
  60. Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, Sato S, Nakabayashi K, Hata K, Sotomaru Y, Suzuki Y, Kono T. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet. 2012;8(1):e1002440. doi: 10.1371/journal.pgen.1002440.PubMedPubMedCentralCrossRefGoogle Scholar
  61. Kothari RM, Shankar V. 5-Methylcytosine content in the vertebrate deoxyribonucleic acids: species specificity. J Mol Evol. 1976;7(4):325–9.PubMedCrossRefGoogle Scholar
  62. Kriaucionis S, Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science. 2009;324(5929):929–30. doi: 10.1126/science.1169786.PubMedPubMedCentralCrossRefGoogle Scholar
  63. Kurimoto K, Yabuta Y, Ohinata Y, Shigeta M, Yamanaka K, Saitou M. Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice. Genes Dev. 2008;22(12):1617–35. doi: 10.1101/gad.1649908.PubMedPubMedCentralCrossRefGoogle Scholar
  64. Lane N, Dean W, Erhardt S, Hajkova P, Surani A, Walter J, Reik W. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis. 2003;35(2):88–93. doi: 10.1002/gene.10168.PubMedCrossRefGoogle Scholar
  65. Lehnertz B, Ueda Y, Derijck AA, Braunschweig U, Perez-Burgos L, Kubicek S, Chen T, Li E, Jenuwein T, Peters AH. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr Biol. 2003;13(14):1192–200.PubMedCrossRefGoogle Scholar
  66. Leitch HG, McEwen KR, Turp A, Encheva V, Carroll T, Grabole N, Mansfield W, Nashun B, Knezovich JG, Smith A, Surani MA, Hajkova P. Naive pluripotency is associated with global DNA hypomethylation. Nat Struct Mol Biol. 2013;20(3):311–6. doi: 10.1038/nsmb.2510.PubMedPubMedCentralCrossRefGoogle Scholar
  67. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462(7271):315–22. doi: 10.1038/nature08514.PubMedPubMedCentralCrossRefGoogle Scholar
  68. Longerich S, Basu U, Alt F, Storb U. AID in somatic hypermutation and class switch recombination. Curr Opin Immunol. 2006;18(2):164–74. doi: 10.1016/j.coi.2006.01.008.PubMedCrossRefGoogle Scholar
  69. Lucifero D, La Salle S, Bourc’his D, Martel J, Bestor TH, Trasler JM. Coordinate regulation of DNA methyltransferase expression during oogenesis. BMC Dev Biol. 2007;7:36. doi: 10.1186/1471-213X-7-36.PubMedPubMedCentralCrossRefGoogle Scholar
  70. Maatouk DM, Kellam LD, Mann MR, Lei H, Li E, Bartolomei MS, Resnick JL. DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. Development. 2006;133(17):3411–8. doi: 10.1242/dev.02500.PubMedCrossRefGoogle Scholar
  71. Mayer W, Niveleau A, Walter J, Fundele R, Haaf T. Demethylation of the zygotic paternal genome. Nature. 2000;403(6769):501–2. doi: 10.1038/35000654.PubMedCrossRefGoogle Scholar
  72. McLay DW, Clarke HJ. Remodelling the paternal chromatin at fertilization in mammals. Reproduction. 2003;125(5):625–33.PubMedCrossRefGoogle Scholar
  73. Metivier R, Gallais R, Tiffoche C, Le Peron C, Jurkowska RZ, Carmouche RP, Ibberson D, Barath P, Demay F, Reid G, Benes V, Jeltsch A, Gannon F, Salbert G. Cyclical DNA methylation of a transcriptionally active promoter. Nature. 2008;452(7183):45–50. doi: 10.1038/nature06544.PubMedCrossRefGoogle Scholar
  74. 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. 1987;99(3):371–82.PubMedGoogle Scholar
  75. Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL, Stivers JT, Zhang Y, Kohli RM. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat Chem Biol. 2012;8(9):751–8. doi: 10.1038/nchembio.1042.PubMedPubMedCentralCrossRefGoogle Scholar
  76. Nakamura T, Arai Y, Umehara H, Masuhara M, Kimura T, Taniguchi H, Sekimoto T, Ikawa M, Yoneda Y, Okabe M, Tanaka S, Shiota K, Nakano T. PGC7/Stella protects against DNA demethylation in early embryogenesis. Nat Cell Biol. 2007;9(1):64–71. doi: 10.1038/ncb1519.PubMedCrossRefGoogle Scholar
  77. Nakamura T, Liu YJ, Nakashima H, Umehara H, Inoue K, Matoba S, Tachibana M, Ogura A, Shinkai Y, Nakano T. PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos. Nature. 2012;486(7403):415–9. doi: 10.1038/nature11093.PubMedGoogle Scholar
  78. Ng HH, Zhang Y, Hendrich B, Johnson CA, Turner BM, Erdjument-Bromage H, Tempst P, Reinberg D, Bird A. MBD2 is a transcriptional repressor belonging to the MeCP1 histone deacetylase complex. Nat Genet. 1999;23(1):58–61. doi: 10.1038/12659.PubMedCrossRefGoogle Scholar
  79. Ohno R, Nakayama M, Naruse C, Okashita N, Takano O, Tachibana M, Asano M, Saitou M, Seki Y. A replication-dependent passive mechanism modulates DNA demethylation in mouse primordial germ cells. Development. 2013;140(14):2892–903. doi: 10.1242/dev.093229.PubMedCrossRefGoogle Scholar
  80. Okada Y, Yamagata K, Hong K, Wakayama T, Zhang Y. A role for the elongator complex in zygotic paternal genome demethylation. Nature. 2010;463(7280):554–8. doi: 10.1038/nature08732.PubMedPubMedCentralCrossRefGoogle Scholar
  81. Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T. Genome-wide analysis of DNA methylation dynamics during early human development. PLoS Genet. 2014;10(12):e1004868. doi: 10.1371/journal.pgen.1004868.PubMedPubMedCentralCrossRefGoogle Scholar
  82. Okamoto Y, Yoshida N, Suzuki T, Shimozawa N, Asami M, Matsuda T, Kojima N, Perry AC, Takada T. DNA methylation dynamics in mouse preimplantation embryos revealed by mass spectrometry. Sci Rep. 2016;6:19134. doi: 10.1038/srep19134.PubMedPubMedCentralCrossRefGoogle Scholar
  83. Oswald J, Engemann S, Lane N, Mayer W, Olek A, Fundele R, Dean W, Reik W, Walter J. Active demethylation of the paternal genome in the mouse zygote. Curr Biol. 2000;10(8):475–8.PubMedCrossRefGoogle Scholar
  84. Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W. Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation. Cell Rep. 2014;9(6):1990–2000. doi: 10.1016/j.celrep.2014.11.034.PubMedPubMedCentralCrossRefGoogle Scholar
  85. Pfaffeneder T, Spada F, Wagner M, Brandmayr C, Laube SK, Eisen D, Truss M, Steinbacher J, Hackner B, Kotljarova O, Schuermann D, Michalakis S, Kosmatchev O, Schiesser S, Steigenberger B, Raddaoui N, Kashiwazaki G, Muller U, Spruijt CG, Vermeulen M, Leonhardt H, Schar P, Muller M, Carell T. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol. 2014;10(7):574–81. doi: 10.1038/nchembio.1532.PubMedCrossRefGoogle Scholar
  86. Polanski Z, Motosugi N, Tsurumi C, Hiiragi T, Hoffmann S. Hypomethylation of paternal DNA in the late mouse zygote is not essential for development. Int J Dev Biol. 2008;52(2–3):295–8. doi: 10.1387/ijdb.072347zp.PubMedCrossRefGoogle Scholar
  87. Popp C, Dean W, Feng S, Cokus SJ, Andrews S, Pellegrini M, Jacobsen SE, Reik W. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature. 2010;463(7284):1101–5. doi: 10.1038/nature08829.PubMedPubMedCentralCrossRefGoogle Scholar
  88. Probst AV, Santos F, Reik W, Almouzni G, Dean W. Structural differences in centromeric heterochromatin are spatially reconciled on fertilisation in the mouse zygote. Chromosoma. 2007;116(4):403–15. doi: 10.1007/s00412-007-0106-8.PubMedCrossRefGoogle Scholar
  89. Ratnam S, Mertineit C, Ding F, Howell CY, Clarke HJ, Bestor TH, Chaillet JR, Trasler JM. Dynamics of Dnmt1 methyltransferase expression and intracellular localization during oogenesis and preimplantation development. Dev Biol. 2002;245(2):304–14. doi: 10.1006/dbio.2002.0628.PubMedCrossRefGoogle Scholar
  90. Razin A, Webb C, Szyf M, Yisraeli J, Rosenthal A, Naveh-Many T, Sciaky-Gallili N, Cedar H. Variations in DNA methylation during mouse cell differentiation in vivo and in vitro. Proc Natl Acad Sci U S A. 1984;81(8):2275–9.PubMedPubMedCentralCrossRefGoogle Scholar
  91. Reik W, Dean W, Walter J. Epigenetic reprogramming in mammalian development. Science. 2001;293(5532):1089–93. doi: 10.1126/science.1063443.PubMedCrossRefGoogle Scholar
  92. Riggs AD, Jones PA. 5-methylcytosine, gene regulation, and cancer. Adv Cancer Res. 1983;40:1–30.PubMedCrossRefGoogle Scholar
  93. Rougier N, Bourc’his D, Gomes DM, Niveleau A, Plachot M, Paldi A, Viegas-Pequignot E. Chromosome methylation patterns during mammalian preimplantation development. Genes Dev. 1998;12(14):2108–13.PubMedPubMedCentralCrossRefGoogle Scholar
  94. Russell GJ, Walker PM, Elton RA, Subak-Sharpe JH. Doublet frequency analysis of fractionated vertebrate nuclear DNA. J Mol Biol. 1976;108(1):1–23.PubMedCrossRefGoogle Scholar
  95. Saksouk N, Barth TK, Ziegler-Birling C, Olova N, Nowak A, Rey E, Mateos-Langerak J, Urbach S, Reik W, Torres-Padilla ME, Imhof A, Dejardin J, Simboeck E. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Mol Cell. 2014;56(4):580–94. doi: 10.1016/j.molcel.2014.10.001.PubMedCrossRefGoogle Scholar
  96. Sanford J, Forrester L, Chapman V, Chandley A, Hastie N. Methylation patterns of repetitive DNA sequences in germ cells of Mus musculus. Nucleic Acids Res. 1984;12(6):2823–36.PubMedPubMedCentralCrossRefGoogle Scholar
  97. Santos F, Hendrich B, Reik W, Dean W. Dynamic reprogramming of DNA methylation in the early mouse embryo. Dev Biol. 2002;241(1):172–82. doi: 10.1006/dbio.2001.0501.PubMedCrossRefGoogle Scholar
  98. Santos F, Peters AH, Otte AP, Reik W, Dean W. Dynamic chromatin modifications characterise the first cell cycle in mouse embryos. Dev Biol. 2005;280(1):225–36. doi: 10.1016/j.ydbio.2005.01.025.PubMedCrossRefGoogle Scholar
  99. Santos F, Peat J, Burgess H, Rada C, Reik W, Dean W. Active demethylation in mouse zygotes involves cytosine deamination and base excision repair. Epigenetics Chromatin. 2013;6(1):39. doi: 10.1186/1756-8935-6-39.PubMedPubMedCentralCrossRefGoogle Scholar
  100. Seisenberger S, Andrews S, Krueger F, Arand J, Walter J, Santos F, Popp C, Thienpont B, Dean W, Reik W. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell. 2012;48(6):849–62. doi: 10.1016/j.molcel.2012.11.001.PubMedPubMedCentralCrossRefGoogle Scholar
  101. Seki Y, Hayashi K, Itoh K, Mizugaki M, Saitou M, Matsui Y. Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Biol. 2005;278(2):440–58. doi: 10.1016/j.ydbio.2004.11.025.PubMedCrossRefGoogle Scholar
  102. Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y, Saga Y, Tachibana M, Shinkai Y, Saitou M. Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development. 2007;134(14):2627–38. doi: 10.1242/dev.005611.PubMedCrossRefGoogle Scholar
  103. Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet. 2013;9(4):e1003439. doi: 10.1371/journal.pgen.1003439.PubMedPubMedCentralCrossRefGoogle Scholar
  104. Smallwood SA, Tomizawa S, Krueger F, Ruf N, Carli N, Segonds-Pichon A, Sato S, Hata K, Andrews SR, Kelsey G. Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat Genet. 2011;43(8):811–4. doi: 10.1038/ng.864.PubMedPubMedCentralCrossRefGoogle Scholar
  105. Smith ZD, Chan MM, Mikkelsen TS, Gu H, Gnirke A, Regev A, Meissner A. A unique regulatory phase of DNA methylation in the early mammalian embryo. Nature. 2012;484(7394):339–44. doi: 10.1038/nature10960.PubMedPubMedCentralCrossRefGoogle Scholar
  106. Szabo PE, Pfeifer GP. H3K9me2 attracts PGC7 in the zygote to prevent Tet3-mediated oxidation of 5-methylcytosine. J Mol Cell Biol. 2012;4(6):427–9. doi: 10.1093/jmcb/mjs038.PubMedCrossRefGoogle Scholar
  107. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324(5929):930–5. doi: 10.1126/science.1170116.PubMedPubMedCentralCrossRefGoogle Scholar
  108. Takahashi K, Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006;126(4):663–76. doi: 10.1016/j.cell.2006.07.024.PubMedCrossRefGoogle Scholar
  109. Tomizawa S, Kobayashi H, Watanabe T, Andrews S, Hata K, Kelsey G, Sasaki H. Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development. 2011;138(5):811–20. doi: 10.1242/dev.061416.PubMedPubMedCentralCrossRefGoogle Scholar
  110. Tsukada Y, Akiyama T, Nakayama KI. Maternal TET3 is dispensable for embryonic development but is required for neonatal growth. Sci Rep. 2015;5:15876. doi: 10.1038/srep15876.PubMedPubMedCentralCrossRefGoogle Scholar
  111. van der Heijden GW, Dieker JW, Derijck AA, Muller S, Berden JH, Braat DD, van der Vlag J, de Boer P. Asymmetry in histone H3 variants and lysine methylation between paternal and maternal chromatin of the early mouse zygote. Mech Dev. 2005;122(9):1008–22. doi: 10.1016/j.mod.2005.04.009.PubMedCrossRefGoogle Scholar
  112. Vincent JJ, Huang Y, Chen PY, Feng S, Calvopina JH, Nee K, Lee SA, Le T, Yoon AJ, Faull K, Fan G, Rao A, Jacobsen SE, Pellegrini M, Clark AT. Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell Stem Cell. 2013;12(4):470–8. doi: 10.1016/j.stem.2013.01.016.PubMedPubMedCentralCrossRefGoogle Scholar
  113. Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet. 1999;23(1):62–6. doi: 10.1038/12664.PubMedCrossRefGoogle Scholar
  114. Wossidlo M, Arand J, Sebastiano V, Lepikhov K, Boiani M, Reinhardt R, Scholer H, Walter J. Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes. EMBO J. 2010;29(11):1877–88. doi: 10.1038/emboj.2010.80.PubMedPubMedCentralCrossRefGoogle Scholar
  115. Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M, Arand J, Nakano T, Reik W, Walter J. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat Commun. 2011;2:241. doi: 10.1038/ncomms1240.PubMedCrossRefGoogle Scholar
  116. Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell. 2014;156(1–2):45–68. doi: 10.1016/j.cell.2013.12.019.PubMedPubMedCentralCrossRefGoogle Scholar
  117. Xue JH, Xu GF, Gu TP, Chen GD, Han BB, Xu ZM, Bjoras M, Krokan HE, Xu GL, Du YR. Uracil-DNA Glycosylase UNG Promotes Tet-mediated DNA Demethylation. J Biol Chem. 2016;291(2):731–8. doi: 10.1074/jbc.M115.693861.PubMedCrossRefGoogle Scholar
  118. Yamaji M, Ueda J, Hayashi K, Ohta H, Yabuta Y, Kurimoto K, Nakato R, Yamada Y, Shirahige K, Saitou M. PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells. Cell Stem Cell. 2013;12(3):368–82. doi: 10.1016/j.stem.2012.12.012.PubMedCrossRefGoogle Scholar
  119. Young LE, Beaujean N. DNA methylation in the preimplantation embryo: the differing stories of the mouse and sheep. Anim Reprod Sci. 2004;82–83:61–78. doi: 10.1016/j.anireprosci.2004.05.020.PubMedCrossRefGoogle Scholar
  120. Zheng P, Schramm RD, Latham KE. Developmental regulation and in vitro culture effects on expression of DNA repair and cell cycle checkpoint control genes in rhesus monkey oocytes and embryos. Biol Reprod. 2005;72(6):1359–69. doi: 10.1095/biolreprod.104.039073.PubMedCrossRefGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Epigenetics Programme, The Babraham InstituteCambridgeUK

Personalised recommendations