Most loci that are regulated by genomic imprinting have differentially methylated regions (DMRs). Previously, we showed that the DMRs of the mouse Snrpn and U2af1-rs1 genes have paternal allele-specific patterns of acetylation on histones H3 and H4. To investigate the maintenance of acetylation at these DMRs, we performed chromatin immuno-precipitation on Trichostatin-A (TSA) treated and control cells. In embryonic stem (ES) cells and fibroblasts, brief (6-hour) TSA treatment induces global hyperacetylation of H3 and H4. In ES cells only, TSA led to a selective increase in maternal acetylation at U2af1-rs1, at lysine-5 of H4 and at lysine-14 of H3. TSA treatment of ES cells did not affect DNA methylation or expression of U2af1-rs1, but was sufficient to increase DNase-I sensitivity along the maternal allele to a level comparable to that of the paternal allele. In fibroblasts, TSA did not alter U2af1-rs1 acetylation and the parental alleles retained their differential DNase-I sensitivity. At Snrpn, no changes in acetylation were observed in the TSA-treated cells. Our data suggest that the mechanisms regulating histone acetylation at DMRs are locus and developmental-stage specific, and are distinct from those effecting global levels of acetylation. Furthermore, it seems that the allelic U2af1-rs1 acetylation determines DNase-I sensitivity/chromatin conformation.