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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.

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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.

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Gene Expression Omnibus

Data deposits

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

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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.

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Correspondence to Steven E. Jacobsen or Wolf Reik.

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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

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