Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine
Epigenetic Controls
Germ cells in mammals give rise to sperm and eggs. During their development, germ cells undergo extensive epigenetic reprogramming, including global DNA demethylation, which is vital for the totipotency of the developing embryo. Hackett et al. (p. 448) show that the enzymes Tet1 and Tet2 are involved in the demethylation of individual genes and in imprinted gametic differentially methylated regions. The enzymes were also responsible for the global conversion of CpG methylation to 5-hydroxymethylcytosine, which then progressively declines. The findings suggest that demethylation can occur by replication-coupled dilution, although active mechanisms cannot be excluded. A small number of loci escape demethylation, providing a possible mechanistic basis for transgenerational inheritance.
Abstract
Mouse primordial germ cells (PGCs) undergo sequential epigenetic changes and genome-wide DNA demethylation to reset the epigenome for totipotency. Here, we demonstrate that erasure of CpG methylation (5mC) in PGCs occurs via conversion to 5-hydroxymethylcytosine (5hmC), driven by high levels of TET1 and TET2. Global conversion to 5hmC initiates asynchronously among PGCs at embryonic day (E) 9.5 to E10.5 and accounts for the unique process of imprint erasure. Mechanistically, 5hmC enrichment is followed by its protracted decline thereafter at a rate consistent with replication-coupled dilution. The conversion to 5hmC is an important component of parallel redundant systems that drive comprehensive reprogramming in PGCs. Nonetheless, we identify rare regulatory elements that escape systematic DNA demethylation in PGCs, providing a potential mechanistic basis for transgenerational epigenetic inheritance.
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Supplementary Material
Summary
Materials and Methods
Figs. S1 to S24
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References and Notes
1
Surani M. A., Hayashi K., Hajkova P., Genetic and epigenetic regulators of pluripotency. Cell 128, 747 (2007).
2
Hajkova P., et al., Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452, 877 (2008).
3
Hackett J. A., Zylicz J. J., Surani M. A., Parallel mechanisms of epigenetic reprogramming in the germline. Trends Genet. 28, 164 (2012).
4
Tahiliani M., et al., Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930 (2009).
5
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 (2010).
6
Ficz G., et al., Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473, 398 (2011).
7
Ito S., et al., Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300 (2011); 10.1126/science.1210597.
8
Maatouk D. M., et al., DNA methylation is a primary mechanism for silencing postmigratory primordial germ cell genes in both germ cell and somatic cell lineages. Development 133, 3411 (2006).
9
Hackett J. A., et al., Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline. Development 139, 3623 (2012).
10
Hayashi K., Ohta H., Kurimoto K., Aramaki S., Saitou M., Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell 146, 519 (2011).
11
Hajkova P., et al., Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 117, 15 (2002).
12
Inoue A., Zhang Y., Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos. Science 334, 194 (2011); 10.1126/science.1212483.
13
Tam P. P., Snow M. H., Proliferation and migration of primordial germ cells during compensatory growth in mouse embryos. J. Embryol. Exp. Morphol. 64, 133 (1981).
14
Popp C., et al., Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101 (2010).
15
Qin C., et al., Intracisternal A particle genes: Distribution in the mouse genome, active subtypes, and potential roles as species-specific mediators of susceptibility to cancer. Mol. Carcinog. 49, 54 (2010).
16
Smallwood S. A., et al., Dynamic CpG island methylation landscape in oocytes and preimplantation embryos. Nat. Genet. 43, 811 (2011).
17
Borgel J., et al., Targets and dynamics of promoter DNA methylation during early mouse development. Nat. Genet. 42, 1093 (2010).
18
Kurimoto K., et al., Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice. Genes Dev. 22, 1617 (2008).
19
Gu T. P., et al., The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 477, 606 (2011).
20
Wossidlo M., et al., 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. 2, 241 (2011).
21
Iqbal K., Jin S. G., Pfeifer G. P., Szabó P. E., Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. U.S.A. 108, 3642 (2011).
22
Hajkova P., et al., Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 329, 78 (2010).
23
Cortellino S., et al., Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair. Cell 146, 67 (2011).
24
Dawlaty M. M., et al., Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 9, 166 (2011).
25
Guibert S., Forné T., Weber M., Global profiling of DNA methylation erasure in mouse primordial germ cells. Genome Res. 22, 633 (2012).
26
Lao K. Q., et al., mRNA-sequencing whole transcriptome analysis of a single cell on the SOLiD system. J. Biomol. Tech. 20, 266 (2009).
Information & Authors
Information
Published In
Science
Volume 339 • Issue 6118 • 25 January 2013
Pages: 448 - 452
History
Received: 24 August 2012
Accepted: 16 November 2012
6 December 2012
Copyright
Copyright © 2013, American Association for the Advancement of Science.
