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Global hypomethylation of the genome in XX embryonic stem cells

Abstract

Embryonic stem (ES) cells are important tools in the study of gene function and may also become important in cell therapy applications1. Establishment of stable XX ES cell lines from mouse blastocysts is relatively problematic owing to frequent loss of one of the two X chromosomes. Here we show that DNA methylation is globally reduced in XX ES cell lines and that this is attributable to the presence of two active X chromosomes. Hypomethylation affects both repetitive and unique sequences, the latter including differentially methylated regions that regulate expression of parentally imprinted genes. Methylation of differentially methylated regions can be restored coincident with elimination of an X chromosome in early-passage parthenogenetic ES cells, suggesting that selection against loss of methylation may provide the basis for X-chromosome instability. Finally, we show that hypomethylation is associated with reduced levels of the de novo DNA methyltransferases Dnmt3a and Dnmt3b and that ectopic expression of these factors restores global methylation levels.

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Figure 1: Hypomethylation of major satellite sequences in XX ES cells.
Figure 2: Global hypomethylation of the genome in XX ES cells.
Figure 3: Hypomethylation of imprinted DMRs in XX ES cells.
Figure 4: Progressive hypomethylation of the Igf2r-Air DMR correlates with X chromosome number in parthenogenetic ES cells.
Figure 5: Reduced levels of de novo methyltransferases in XX ES cells.
Figure 6: Ectopic expression of de novo methyltransferases restores methylation in XX ES cells.

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Acknowledgements

We thank members of the Developmental Epigenetics laboratory for discussions. This work was supported by a grant from the Human Frontier Science Program and by the Medical Research Council, UK. R.F. is supported by grant funding from the Association pour la Recherche contre de Cancer.

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Correspondence to Neil Brockdorff.

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PCR primers. (PDF 10 kb)

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Zvetkova, I., Apedaile, A., Ramsahoye, B. et al. Global hypomethylation of the genome in XX embryonic stem cells. Nat Genet 37, 1274–1279 (2005). https://doi.org/10.1038/ng1663

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