DNA Methylation Reprogramming in the Germ Line

  • Diane J. Lees-Murdock
  • Colum P. Walsh
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 626)


In mammals, methylation occurs almost exclusively on the CpG dinucleotide in DNA and shows no preference for sequence context surrounding this target. CpGs are found on many different sequence classes and methylation of this dinucleotide is associated with repression of transcription. Reprogramming methylation in the primordial germ cells establishes monoallelic expression of imprinted genes which exhibit monoallelic expression throughout the lifetime of an organism, maintains retrotransposons in an inactive state and inactivates one of the two X chromosomes. In addition to direct transcriptional silecing, DNA methylation is important for suppression of recombination, and resetting this information is therefore necessary for maintenance of genomic stability. In this chapter, we will review the recent progress in our understanding of the time course and extent of DNA methylation reprogramming of many different sequence classes. We focus on the mouse germline, since this has been the model system from which we have gained the most knowledge of the process. In addition we will examine some of the evidence suggesting a link between repeat methylation and methylation of epigenetically controlled single-copy genes. To do this, we will look at the temporal sequence of methylation events from the time the germ cells become recognizable as a discrete population until the mature male and female gametes fuse and form the early embryo.


Germ Cell Germ Line Imprint Gene Primordial Germ Cell Oocyte Growth 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Walsh CP, Bestor TH. Cytosine methylation and mammalian development. Genes Dev 1999; 13:26–34. Available from: Scholar
  2. 2.
    Herman JG, Umar A, Polyak K et al. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc Natl Acad Sci USA 1998; 95:6870–5. Available from: Scholar
  3. 3.
    Yoder JA, Walsh CW, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends in Genetics 1997; 13:335–340.PubMedCrossRefGoogle Scholar
  4. 4.
    Xu GL, Bestor TH, Bourc’his D et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 1999; 402:187–91.PubMedCrossRefGoogle Scholar
  5. 5.
    Hansen RS, Wijmenga C, Luo P et al. The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci USA 1999; 96:14412–7.PubMedCrossRefGoogle Scholar
  6. 6.
    Okano M, Bell DW, Haber DA et al. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999; 99:247–57.PubMedCrossRefGoogle Scholar
  7. 7.
    Gonzalo S, Jaco I, Fraga MF et al. DNA methyltransferases control telomere length and telomere recombination in mammalian cells. Nat Cell Biol 2006; 8:416–424.PubMedCrossRefGoogle Scholar
  8. 8.
    Guo G, Wang W, Bradley A. Mismatch repair genes identified using genetic screens in blm-deficient embryonic stem cells. Nature 2004; 429:891–895.PubMedCrossRefGoogle Scholar
  9. 9.
    Kim M, Trinh BN, Long TI et al. Dnmtl deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells. Nucleic Acids Res 2004; 32:5742–5749.PubMedCrossRefGoogle Scholar
  10. 10.
    Wang KY, James Shen CK. DNA methyltransferase Dnmtl and mismatch repair. Oncogene 2004; 23:7898–7902.PubMedCrossRefGoogle Scholar
  11. 11.
    Kazazian HH Jr. Mobile elements: Drivers of genome evolution. Science 2004; 303:1626–1632.PubMedCrossRefGoogle Scholar
  12. 12.
    Bourc’his D, Bestor TH. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 2004; 431:96–99.CrossRefGoogle Scholar
  13. 13.
    Webster KE, O’Bryan MK, Fletcher S et al. Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc Natl Acad Sci USA 2005; 102:4068–4073.PubMedCrossRefGoogle Scholar
  14. 14.
    Bender J. Cytosine methylation of repeated sequences in eukaryotes: The role of DNA pairing. Trends Biochem Sci 1998; 23:252–256.PubMedCrossRefGoogle Scholar
  15. 15.
    Ginsburg M, Snow MH, McLaren A. Primordial germ cells in the mouse embryo during gastrulation. Development 1990; 110:521–528.PubMedGoogle Scholar
  16. 16.
    Hajkova P, Erhardt S, Lane N et al. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev 2002; 117:15.PubMedCrossRefGoogle Scholar
  17. 17.
    Li JY, Lees-Murdock DJ, Xu GL et al. Timing of establishment of paternal methylation imprints in the mouse. Genomics 2004; 84:952–960.PubMedCrossRefGoogle Scholar
  18. 18.
    Yamazaki Y, Low EW, Marikawa Y et al. Adult mice cloned from migrating primordial germ cells. Proc Natl Acad Sci USA 2005; 102:11361–11366.PubMedCrossRefGoogle Scholar
  19. 19.
    Tam PP, Zhou SX, Tan SS. X-chromosome activity of the mouse primordial germ cells revealed by the expression of an X-linked lacZ transgene. Development 1994; 120:2925–32.PubMedGoogle Scholar
  20. 20.
    Kerjean A, Couvert P, Heams T et al. In vitro follicular growth affects oocyte impriting establishment in mice. Eur J Hum Genet 2003; 11:493–6.PubMedCrossRefGoogle Scholar
  21. 21.
    Lees-Murdock D, De Felici M, Walsh C. Methylation dynamics of repetitive DNA elements in the mouse germ cell lineage. Genomics 2003; 82:230–237.PubMedCrossRefGoogle Scholar
  22. 22.
    Mann MR, Lee SS, Doherty AS et al. Selective loss of imprinting in the placenta following preimplantation development in culture. Development 2004; 131:3727–3735.PubMedCrossRefGoogle Scholar
  23. 23.
    Schumacher A, Doerfler W. Influence of in vitro manipulation on the stability of methylation patterns in the Snurf/Snrpn-imprinting region in mouse embryonic stem cells. Nucleic Acids Res 2004; 32:1566–1576.PubMedCrossRefGoogle Scholar
  24. 24.
    Schmidt JV, Matteson PG, Jones BK et al. The Dlk1 and Gtl2 genes are linked and reciprocally imprinted. Genes Dev 2000; 14:1997–2002.PubMedGoogle Scholar
  25. 25.
    Kobayashi S, Wagatsuma H, Ono R et al. Mouse Peg9/Dlk1 and human PEG9/DLK1 are paternally expressed imprinted genes closely located to the maternally expressed imprinted genes: Mouse Meg3/Gtl2 and human MEG3. Genes Cells 2000; 5:1029–37.PubMedCrossRefGoogle Scholar
  26. 26.
    Smit AFA. The origin of interspersed repeats in the human genome. Curr Op Genet Dev 1996; 6:743–748.PubMedCrossRefGoogle Scholar
  27. 27.
    Hastie ND. Highly repeated DNA families in the genome of mus musculus. In: Lyon MF, Searle AG, eds. Genetic Variants and Strains of the Laboratory Mouse. Oxford: Oxford University Press, 1989:559–573.Google Scholar
  28. 28.
    Lucifero D, Mann MR, Bartolomei MS et al. Gene-specific timing and epigenetic memory in oocyte imprinting. Hum Mol Genet 2004; 13:839–849.PubMedCrossRefGoogle Scholar
  29. 29.
    Howlett SK, Reik W. Methylation levels of maternal and paternal genomes during preimplantation development. Development 1991; 113:119–27.PubMedGoogle Scholar
  30. 30.
    Lane N, Dean W, Erhardt S et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 2003; 35:88–93.PubMedCrossRefGoogle Scholar
  31. 31.
    Sado T, Fenner MH, Tan SS et al. X inactivation in the mouse embryo deficient for Dnmtl: Distinct effect of hypomethylation on imprinted and random X inactivation. Dev Biol 2000; 225:294–303.PubMedCrossRefGoogle Scholar
  32. 32.
    Monk M, McLaren A. X-chromosome activity in foetal germ cells of the mouse. J Embryol Exp Morphol 1981; 63:75–84.PubMedGoogle Scholar
  33. 33.
    McLaren A, Monk M. X-chromosome activity in the germ cells of sex-reversed mouse embryos. J Reprod Fertil 1981; 63:533–7.PubMedCrossRefGoogle Scholar
  34. 34.
    Boumil RM, Ogawa Y, Sun BK et al. Differential methylation of xite and CTCF sites in tsix mirrors the pattern of X-inactivation choice in mice. Mol Cell Biol 2006; 26:2109–2117.PubMedCrossRefGoogle Scholar
  35. 35.
    Wolffe AP, Jones PL, Wade PA. DNA demethylation. Proc Natl Acad Sci USA 1999; 96:5894–5896.PubMedCrossRefGoogle Scholar
  36. 36.
    Bird A. DNA methylation patterns and epigenetic memory. Genes Dev 2002; 16:6–21.PubMedCrossRefGoogle Scholar
  37. 37.
    Walsh CP, Xu GL. Cytosine methylation and DNA repair. Curr Top Microbiol Immunol 2006; 301:283–315.PubMedCrossRefGoogle Scholar
  38. 38.
    Gehring M, Huh JH, Hsieh TF et al. DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 2006; 124:495–506.PubMedCrossRefGoogle Scholar
  39. 39.
    Morgan HD, Dean W, Coker HA et al. Activation-induced cytidine deaminase deaminates 5-methyl-cytosine in DNA and is expressed in pluripotent tissues: Implications for epigenetic reprogramming. J Biol Chem 2004; 279:52353–52360.PubMedCrossRefGoogle Scholar
  40. 40.
    Ginsburg M, Snow MH, McLaren A. Primordial germ cells in the mouse embryo during gastrulation. Development 1990; 110:521–8.PubMedGoogle Scholar
  41. 41.
    Sato Y, Terada Y, Utsunomiya H et al. Immunohistochemical localization of steroidogenic enzymes in human follicle following xenotransplantation of the human ovarian cortex into NOD-SCID mice. Mol Reprod Dev 2003; 65:67–72.PubMedCrossRefGoogle Scholar
  42. 42.
    Reik W, Walter J. Evolution of imprinting mechanisms: The battle of the sexes begins in the zygote. Nat Genet 2001; 27:255–6.PubMedCrossRefGoogle Scholar
  43. 43.
    Davis TL, Trasler JM, Moss SB et al. Acquisition of the H19 methylation imprint occurs differentially on the parental alleles during spermatogenesis. Genomics 1999; 58:18–28.PubMedCrossRefGoogle Scholar
  44. 44.
    Davis TL, Yang GJ, McCarrey JR et al. The H19 methylation imprint is erased and re-established differentially on the parental alleles during male germ cell development. Hum Mol Genet 2000; 9:2885–94.PubMedCrossRefGoogle Scholar
  45. 45.
    Ueda T, Abe K, Miura A et al. The paternal methylation imprint of the mouse H19 locus is acquired in the gonocyte stage during foetal testis development. Gene Cells 2000; 5:649–659.CrossRefGoogle Scholar
  46. 46.
    Shamanski FL, Kimura Y, Lavoir MC et al. Status of genomic imprinting in mouse spermatids. Hum Reprod 1999; 14:1050–1056.PubMedCrossRefGoogle Scholar
  47. 47.
    Bao S, Obata Y, Carroll J et al. Epigenetic modifications necessary for normal development are established during oocyte growth in mice. Biol Reprod 2000; 62:616–621.PubMedCrossRefGoogle Scholar
  48. 48.
    Obata Y, Kono T. Maternal primary imprinting is established at a specific time for each gene throughout oocyte growth. J Biol Chem 2002; 277:5285–9.PubMedCrossRefGoogle Scholar
  49. 49.
    Lucifero D, Mertineit C, Clarke HJ et al. Methylation dynamics of imprinted genes in mouse germ cells. Genomics 2002; 79:530–8.PubMedCrossRefGoogle Scholar
  50. 50.
    Hiura H, Obata Y, Komiyama J et al. Oocyte growth-dependent progression of maternal imprinting in mice. Genes Cells 2006; 11:353–361.PubMedCrossRefGoogle Scholar
  51. 51.
    Walsh CP, Chaillet JR, Bestor TH. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 1998; 20:116–7.PubMedCrossRefGoogle Scholar
  52. 52.
    Lees-Murdock DJ, Walsh CP. Developmental regulation of DNA methyltransferases. Available at: Scholar
  53. 53.
    Lees-Murdock DJ, Shovlin TC, Gardiner T et al. DNA methyltransferase expression in the mouse germ line during periods of de novo methylation. Dev Dyn 2005; 232:992–1002.PubMedCrossRefGoogle Scholar
  54. 54.
    Thorvaldsen JL, Verona RI, Bartolomei MS. X-tra! X-tra! News from the mouse X chromosome. Dev Biol. In Press.Google Scholar
  55. 55.
    Nguyen DK, Disteche CM. Dosage compensation of the active X chromosome in mammals. Nat Genet 2006; 38:47–53.PubMedCrossRefGoogle Scholar
  56. 56.
    Mayer W, Niveleau A, Walter J et al. Demethylation of the zygotic paternal genome. Nature 2000; 403:501–502.PubMedCrossRefGoogle Scholar
  57. 57.
    Oswald J, Engemann S, Lane N et al. Active demethylation of the paternal genome in the mouse zygote. Curr Biol 2000; 10:475–478.PubMedCrossRefGoogle Scholar
  58. 58.
    Olek A, Walter J. The pre-implantation ontogeny of the H19 methylation imprint [letter]. Nat Genet 1997; 17:275–6.PubMedCrossRefGoogle Scholar
  59. 59.
    Howell CY, Bestor TH, Ding F et al. Genomic imprinting disrupted by a maternal effect mutation in the Dnmtl gene. Cell 2001; 104:829–38.PubMedCrossRefGoogle Scholar
  60. 60.
    Kaslow DC, Migeon BR. DNA methylation stabilizes X chromosome inactivation in eutherians but not in marsupials: Evidence for multistep maintenance of mammalian X dosage compensation. Proc Natl Acad Sci USA 1987; 84:6210–6214.PubMedCrossRefGoogle Scholar
  61. 61.
    Hansen RS. X inactivation-specific methylation of LINE-1 elements by DNMT3B: Implications for the lyon repeat hypothesis. Hum Mol Genet 2003; 12:2559–2567.PubMedCrossRefGoogle Scholar
  62. 62.
    Chen RZ, Pettersson U, Beard C et al. DNA hypomethylation leads to elevated mutation rates. Nature 1998; 395:89–93.PubMedCrossRefGoogle Scholar
  63. 63.
    Yoder JA, Soman N, Verdine GV et al. DNA methyltransferases in mouse tissues and cells: Studies with a mechanism-based probe. J Mol Biol 1997 (in press).Google Scholar
  64. 64.
    Fedoriw AM, Stein P, Svoboda P et al. Transgenic RNAi reveals essential function for CTCF in H19 gene imprinting. Science 2004; 303:238–240.PubMedCrossRefGoogle Scholar
  65. 65.
    Yoon BJ, Herman H, Sikora A et al. Regulation of DNA methylation of Rasgrf1. Nat Genet 2002; 30:92–6.PubMedCrossRefGoogle Scholar
  66. 66.
    Herman H, Lu M, Anggraini M et al. Trans allele methylation and paramutation-like effects in mice. Nat Genet 2003; 34:199–202.PubMedCrossRefGoogle Scholar
  67. 67.
    Reinhart B, Eljanne M, Chaillet JR. Shared role for differentially methylated domains of imprinted genes. Mol Cell Biol 2002; 22:2089–2098.PubMedCrossRefGoogle Scholar
  68. 68.
    Lyon MF. The lyon and the LINE hypothesis. Semin Cell Dev Biol 2003; 14:313–318.PubMedCrossRefGoogle Scholar
  69. 69.
    Lyon MF. X-chromosome inactivation: A repeat hypothesis. Cytogenet Cell Genet 1998; 80:133–137.PubMedCrossRefGoogle Scholar
  70. 70.
    Bailey JA, Carrel L, Chakravarti A et al. Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The lyon repeat hypothesis. Proc Natl Acad Sci USA 2000; 97:6634–6639.PubMedCrossRefGoogle Scholar
  71. 71.
    Parish DA, Vise P, Wichman HA et al. Distribution of LINEs and other repetitive elements in the karyotype of the bat carollia: Implications for X-chromosome inactivation. Cytogenet Genome Res 2002; 96:191–197.PubMedCrossRefGoogle Scholar
  72. 72.
    Li E, Beard C, Jaenisch R. Role for DNA methylation in genomic imprinting. Nature 1993; 366:362–365.PubMedCrossRefGoogle Scholar
  73. 73.
    Bell AC, Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 2000; 405:482–5.PubMedCrossRefGoogle Scholar
  74. 74.
    Hark AT, Schoenherr CJ, Katz DJ et al. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature 2000; 405:486–9.PubMedCrossRefGoogle Scholar
  75. 75.
    Csankovszki G, Nagy A, Jaenisch R. Synergism of xist RNA, DNA methylation and histone hypoacetylation in maintaining X chromosome inactivation. J Cell Biol 2001; 153:773–84.PubMedCrossRefGoogle Scholar

Copyright information

© Landes Bioscience and Springer Science+Business Media 2008

Authors and Affiliations

  1. 1.Stem Cells and Epigenetics Research Group, School of Biomedical Sciences, Centre for Molecular BioscienceUniversity of UlsterColeraineN. Ireland, UK

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