DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1

The relationship between DNA methylation and histone acetylation at the imp rinted mouse genes U2af1-rs1 and Snrpn is explored by chromatin immunopreci pitation (ChIP) and resolution of parental allelles using single-strand con formational polymorphisms. The U2af1-rs1 gene lies within a differentially methylated region (DMR), while Snrpn has a 5' DMR (DMR1) with sequences hom ologous to the imprinting control center of the Prader-Willi/Angelman regio n. For both DMR1 of Snrpn and the 5' untranslated region (5'-UTR) and 3'-UT R of U2af1-rs1, the methylated and nonexpressed maternal allelle was undera cetylated, relative to the paternal allele, at all H3 lysines tested (K14, K9, and K18). For H4, underacetylation of the maternal allelle was exclusiv ely (U2af1-rs1) or predominantly (Snrpn) at lysine 5. Essentially the same patterns of differential acetylation were found in embryonic stem (ES) cell s, embryo fibroblasts, and adult liver from F1 mice and in ES cells from mi ce that were dipaternall or dimaternall for U2af1-rs1. In contrast, in a re gion within Snrpn that has biallelic methylation in the cells and tissues a nalyzed, the paternal (expressed) allele showed relatively increased acetyl ation of H4 but not of H3. The methyl-CpG-binding-domain (MBD) protein MeCP 2 was found, by ChIP, to be associated exclusively with the maternal U2af1- rs1 allele. To ask whether DNA methylation is associated with histone deace tylation, we produced mice with transgene-induced methylation at the patern al allele of U2arf1-rs1. In these mice, H3 was underacetylated across both the parental U2af1-rs1 alleles whereas H4 acetylation was unaltered. Collec tively, these data are consistent with the hypothesis that CpG methylation leads to deacetylation of histone H3, but not H4, through a process that in volves selective binding of MBD proteins.