Chromatin Modification at Imprinting Control Centres

Robert Feil
Institute of Molecular Genetics

Most imprinted loci have differentially methylated regions (DMRs) and several of these were shown to be essential in the control of parental allele-specific gene expression. DNA methylation does not, however, provide a complete explanation for the somatic maintenance of imprints. To explore the relationship between methylation of DNA and covalent modification of histories at the DMRs of the mouse Snrpn and U2afl-rsl genes, we performed chromatin immuno-precipitation on embryonic cells and adult tissues. At both these imprinted genes, the methylated and repressed maternal allele was under-acetylated relative to the active paternal allele, at histories H3 (at all lysines analysed) and H4 (predominantly at lysine 5). To explore whether DNA methylation is associated with deacetylation along U2afl-rsl, we studied mice with transgene-induced methylation on the paternal allele (in addition to that on the maternal allele). This established that CpG methylation is linked to deacetylation of histone H3, but not H4, and this may involve selective binding of MBD proteins. Compared to bulk chromatin, which became hyper-acetylated, we found the Snrpn and U2afl-rsl loci to be highly resistant to the effects of the HDAC-inhibitor Trichostatin-A. One explanation for this finding might be that other histone modifications are required to facilitate gain of acetylation at these imprinted loci. Intriguingly, the DMRs of Snrpn and U2afl-rsl both displayed high levels of methylation at lysine 4 of histone 3 on the paternal allele, in all tissues analysed. Our data suggest a complex interplay between CpG methylation, histone acetylation, histone methylation, and non-histone protein binding at imprinting control centres.


  1. Gregory, R. et al. DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2afJ-rsl. Mol. Cell. Biol. 21: 5426-5436, 2001.

  2. Gregory, R. et al. Inhibition of histone deacetylases alters allelic chromatin conformation at the imprinted U2af1-rsl locus in mouse embryonic stem cells. J. Biol. Chem., (in press), 2002.