Valproic acid-induced changes in transcription at specific genes are not consistently linked to changes in histone acetylation. Modified histones were assayed at selected regions of genes showing increased expression (H1f0, Egr1, Ndrg4), or decreased expression (Nanog) in response to valproic acid (VPA). Chromatin was prepared from CCE/R embryonic stem (ES) cells before (white bars) and after (black bars) VPA treatment (1 mM, 8 h) and immunoprecipitated with antibodies against H3K9ac, H3K4me3, H4K8ac and H3K27me3, as indicated. DNA extracted from bound (B) and unbound (UB) fractions was analysed by real time-quantitative (RT-q)PCR using region-specific primers (Additional file 1: Table S7 shows both the sequences and positions relative to the transcription start site of each primer pair). Relative enrichment in each modification was calculated as the B/UB ratio; a region can be considered enriched in a particular modification if B/UB exceeds 1.0 (dashed lines). Error bars represent the standard error of the mean of independent experiments (n = 2): apparent absence of error bars occurs where the error is too low to be visible at this scale.