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 pluripotency [1][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 E coli, and in the mouse are expressed in tissues in which demethylation occurs 10 . Here we profiled DNA methylation throughout the genome by unbiased bisulfite Next Generation Sequencing 11-13 (BS-Seq) in wildtype and Aid deficient PGCs at E13.5. Wildtype PGCs revealed dramatic genome-wide erasure of methylation to a level below that of methylation deficient (Np95-/-) ES cells, with female PGCs being less methylated than male ones. By contrast, Aid deficient PGCs were up to three times more methylated than wildtype 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, suggesting that Aid has a critical function in epigenetic reprogramming and potentially in restricting the inheritance of epimutations in mammals.In plants active demethylation occurs widely (including in imprinted genes) and is carried out by 5meC glycosylases such as Demeter and Demeter like proteins [14][15][16] . This class of enzymes does not appear to exist in mammalian genomes, but instead we found that the cytosine Correspondence and requests for materials should be addressed to S.E. J. (jacobsen@ucla.edu) or W.R. (wolf.reik@bbsrc.ac.uk). * These authors contributed equally to this work Supplementary Information is linked to the online version of the paper at www.nature.com/nature.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 and determined weights of mouse pups. S.F. constructed bisulfite 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. deaminases Aid and Apobec1 can deaminate 5meC both in vitro and in E coli 10 , suggesting deamination of 5meC followed by T:G base excision repair by glycosylases such as Tdg or Mbd4 as an equivalent pathway for demethylation of DNA. Recently it has been shown that co-expression of Aid and Mbd4 in Zebrafish embryos ca...

When is incomplete epigenetic resetting in germ cells favoured by natural selection?

“…Such effects are increasingly observed in animals and, in particular, plants (reviews in [4,5,17,19,42]), where studies of experimental lines suggest that induced patterns of DNA methylation are readily inherited [11]. Similarly, in mammals, DNA sequences can resist reprogramming [43,44], and the extent of demethylation is regulated by the methylation machinery [45,46]. Thus, although we often expect transgenerational epigenetic inheritance to be maladaptive (or fitness neutral), the extent of resetting could evolve in response to selection.…”

Parental epigenetic control of embryogenesis: a balance between inheritance and reprogramming?

“…It was hypothesized that, following a paradigm established in plants [21], deamination and subsequent DNA repair might be involved in DNA demethylation. Deletion of the cytidine deaminase Aid in the mouse provided some support for this model as PGCs in these animals display modest DNA hypermethylation [20]. Further support was provided by the observation that PGC demethylation is also associated with the presence of DNA single stranded breaks [22].…”

“…During the same time period levels of 5mC in germ cells also begin to decrease [18]. PGC DNA demethylation continues after their arrival in the gonad and effects around 80-90% of the genome [20]. The mechanism behind this demethylation has been the subject of many years of research.…”

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“…These heritable epigenetic changes persisted for multiple generations, and could be fully reversed (Nelson et al, 2012). Aberrant epigenetic reprogramming in the germ line would cause the inheritance of epimutations, that may have consequences for human diseases (Hajkova et al, 2002, Popp et al, 2010. The same is true for histone modifications.…”