DNA Methylation Is Linked to Deacetylation of Histone H3, but Not H4, on the Imprinted Genes Snrpnand U2af1-rs1

Abstract

The relationship between DNA methylation and histone acetylation at the imprinted mouse genes U2af1-rs1 and Snrpnis explored by chromatin immunoprecipitation (ChIP) and resolution of parental alleles using single-strand conformational polymorphisms. TheU2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5′ DMR (DMR1) with sequences homologous to the imprinting control center of the Prader-Willi/Angelman region. For both DMR1 of Snrpn and the 5′ untranslated region (5′-UTR) and 3′-UTR ofU2af1-rs1, the methylated and nonexpressed maternal allele was underacetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allele was exclusively (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cells, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mice that were dipaternal or dimaternal for U2af1-rs1. In contrast, in a region within Snrpn that has biallelic methylation in the cells and tissues analyzed, the paternal (expressed) allele showed relatively increased acetylation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP2 was found, by ChIP, to be associated exclusively with the maternal U2af1-rs1 allele. To ask whether DNA methylation is associated with histone deacetylation, we produced mice with transgene-induced methylation at the paternal allele of U2af1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collectively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that involves selective binding of MBD proteins.

ACKNOWLEDGMENTS

We thank Wolf Reik, Peter Fraser, and Gavin Kelsey for critical reading of the manuscript.

This work was supported by the Biotechnology and Biological Sciences Research Council (Studentship to R.I.G.), the Wellcome Trust (grant 045030/Z/95 to B.M.T.), the Human Frontier Science Program (grant RG0083/1999 to R.F., I.H., and Neil Brockdorff), the Centre National de la Recherche Scientifique (ATIPE grant to R.F.), the Fondation pour la Recherche Médicale (to R.F.), and the Royal Society (Fellowship 516002 to L.P.O.).