Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

Abstract

Epigenetic reprogramming including demethylation of DNA occurs in mammalian primordial germ cells (PGCs) and in early embryos, and is important for the erasure of imprints and epimutations, and the return to pluripotency1,2,3,4,5,6,7,8,9. The extent of this reprogramming and its molecular mechanisms are poorly understood. We previously showed that the cytidine deaminases AID and APOBEC1 can deaminate 5-methylcytosine in vitro and in Escherichia coli, and in the mouse are expressed in tissues in which demethylation occurs10. Here we profiled DNA methylation throughout the genome by unbiased bisulphite next generation sequencing11,12,13 in wild-type and AID-deficient mouse PGCs at embryonic day (E)13.5. Wild-type PGCs revealed marked genome-wide erasure of methylation to a level below that of methylation deficient (Np95-/- , also called Uhrf1-/- ) embryonic stem cells, with female PGCs being less methylated than male ones. By contrast, AID-deficient PGCs were up to three times more methylated than wild-type ones; this substantial difference occurred throughout the genome, with introns, intergenic regions and transposons being relatively more methylated than exons. Relative hypermethylation in AID-deficient PGCs was confirmed by analysis of individual loci in the genome. Our results reveal that erasure of DNA methylation in the germ line is a global process, hence limiting the potential for transgenerational epigenetic inheritance. AID deficiency interferes with genome-wide erasure of DNA methylation patterns, indicating that AID has a critical function in epigenetic reprogramming and potentially in restricting the inheritance of epimutations in mammals.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Genome-wide BS-Seq reveals global hypomethylation in PGCs dependent on AID.
Figure 2: Erasure of DNA methylation in different genomic elements in PGCs.
Figure 3: Erasure of DNA methylation in different classes of transposable elements in PGCs.
Figure 4: Analysis of DNA methylation of individual genomic loci in E13.5 PGCs by Sequenom MassArray.

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

All sequencing files have been deposited in GEO under accession code GSE19960.

References

  1. Reik, W., Dean, W. & Walter, J. Epigenetic reprogramming in mammalian development. Science 293, 1089–1093 (2001)

    Article  CAS  Google Scholar 

  2. Sasaki, H. & Matsui, Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nature Rev. Genet. 9, 129–140 (2008)

    Article  CAS  Google Scholar 

  3. Oswald, J. et al. Active demethylation of the paternal genome in the mouse zygote. Curr. Biol. 10, 475–478 (2000)

    Article  CAS  Google Scholar 

  4. Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501–502 (2000)

    Article  ADS  CAS  Google Scholar 

  5. Dean, W. et al. Conservation of methylation reprogramming in mammalian development: aberrant reprogramming in cloned embryos. Proc. Natl Acad. Sci. USA 98, 13734–13738 (2001)

    Article  ADS  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Lee, J. et al. Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development 129, 1807–1817 (2002)

    Article  CAS  Google Scholar 

  8. Yamazaki, Y. et al. Reprogramming of primordial germ cells begins before migration into the genital ridge, making these cells inadequate donors for reproductive cloning. Proc. Natl Acad. Sci. USA 100, 12207–12212 (2003)

    Article  ADS  CAS  Google Scholar 

  9. Hajkova, P. et al. Chromatin dynamics during epigenetic reprogramming in the mouse germ line. Nature 452, 877–881 (2008)

    Article  ADS  CAS  Google Scholar 

  10. Morgan, H. D., Dean, W., Coker, H. A., Reik, W. & Petersen-Mahrt, S. K. Activation-induced cytidine deaminase deaminates 5-methylcytosine in DNA and is expressed in pluripotent tissues: implications for epigenetic reprogramming. J. Biol. Chem. 279, 52353–52360 (2004)

    Article  CAS  Google Scholar 

  11. Cokus, S. J. et al. Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008)

    Article  ADS  CAS  Google Scholar 

  12. Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008)

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  14. Gehring, M., Reik, W. & Henikoff, S. DNA demethylation by DNA repair. Trends Genet. 25, 82–90 (2009)

    Article  CAS  Google Scholar 

  15. Gehring, M., Bubb, K. L. & Henikoff, S. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324, 1447–1451 (2009)

    Article  ADS  CAS  Google Scholar 

  16. Hsieh, T. F. et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451–1454 (2009)

    Article  ADS  CAS  Google Scholar 

  17. Rai, K. et al. DNA demethylation in zebrafish involves the coupling of a deaminase, a glycosylase and gadd45. Cell 135, 1201–1212 (2008)

    Article  CAS  Google Scholar 

  18. 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)

    Article  CAS  Google Scholar 

  19. Zvetkova, I. et al. Global hypomethylation of the genome in XX embryonic stem cells. Nature Genet. 37, 1274–1279 (2005)

    Article  CAS  Google Scholar 

  20. Seki, T. et al. Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development 134, 2627–2638 (2007)

    Article  CAS  Google Scholar 

  21. Muramatsu, M. et al. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potent RNA editing enzyme. Cell 102, 553–563 (2000)

    Article  CAS  Google Scholar 

  22. Whitelaw, N. C. & Whitelaw, E. Transgenerational epigenetic inheritance in health and disease. Curr. Opin. Genet. Dev. 18, 273–279 (2008)

    Article  CAS  Google Scholar 

  23. Slotkin, R. K. et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136, 461–472 (2009)

    Article  CAS  Google Scholar 

  24. Teixeira, F. K. et al. A role for RNAi in the selective correction of DNA methylation defects. Science 323, 1600–1604 (2009)

    Article  ADS  CAS  Google Scholar 

  25. Bhutani, N. et al. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 10.1038/nature08752 (in the press)

  26. Robbiani, D. F. et al. Aid produces DNA double-strand breaks in non-Ig genes and mature B cell lymphomas with reciprocal chromosome translocations. Mol. Cell 36, 631–641 (2009)

    Article  CAS  Google Scholar 

  27. Neuberger, M. S., Harris, R. S., Di Noia, J. & Petersen-Mahrt, S. K. Immunity through DNA deamination. Trends Biochem. Sci. 28, 305–312 (2003)

    Article  CAS  Google Scholar 

  28. Larijani, M. et al. Methylation protects cytidines from Aid-mediated deamination. Mol. Immunol. 42, 599–604 (2005)

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank H. Morgan for his contributions to some of the early analysis of Aid-/- mice, A. Segonds-Pichon for help with statistical evaluation, and J. Hetzel for assisting in preparing the Illumina Solexa libraries and their sequencing. We also thank S. Petersen-Mahrt, C. Rada and F. Santos for advice and discussions. C.P. was a Boehringer-Ingelheim predoctoral Fellow. S.F. is a Howard Hughes Medical Institute Fellow of the Life Science Research Foundation. S.E.J. is an investigator of the Howard Hughes Medical Institute. This work was supported by BBSRC, MRC, EU NoE The Epigenome, and CellCentric (to W.R.), and by HHMI, NSF Plant Genome Research Programme, and NIH (to S.E.J.).

Author Contributions C.P. and W.D. isolated tissue samples and PGCs, assessed the purity of the samples and prepared DNA. C.P. undertook genetic crosses, determined weights of mouse pups and carried out Sequenom EpiTYPER analysis. S.F. constructed bisulphite libraries and did Illumina Solexa sequencing. S.J.C., S.A. and M.P. carried out mapping, base-calling and computational analyses. C.P., W.D., S.F., S.J.C., S.A., M.P., S.E.J. and W.R. analysed data. C.P., W.D., S.F., S.E.J and W.R. designed experiments; S.E.J. and W.R. designed and directed the study. C.P. and W.R. wrote the manuscript.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Steven E. Jacobsen or Wolf Reik.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S4 with Legends, Supplementary Methods and a Supplementary Reference (PDF 795 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Popp, C., Dean, W., Feng, S. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101–1105 (2010). https://doi.org/10.1038/nature08829

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature08829

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing