Gene promoter associated histone H4 becomes deacetylated following optic nerve crush (ONC). Two gene sets were examined by chromatin immunoprecipitation for acetylated H4. The first was comprised of genes whose expression had been documented to decrease during ganglion cell apoptosis (grey bars), including Thy1, Brn3b, Fem1c, Nrn1, and BclX (see text). The second set consisted of a pair of genes (Bim and cJun) whose expression has been documented to increase during apoptosis (black bars). The data is shown as a ratio of crush (OS)/control (OD) and has been normalized to day 0 levels (dashed line) (n = 6 samples at each time point). (A) At 1 day post ONC, there was a significant decrease in promoter H4 acetylation of most of the genes examined (range of P values was 9.9 × 10-5 for Thy1 to 0.04 for Bim). Promoter acetylation for cJun was decreased, but this was not significant compared to day 0 levels (*P = 0.08). (B) At 3 days post ONC, the decrease in promoter acetylation persisted for down-regulated genes. Conversely, the promoters of genes that are typically up-regulated exhibited a detectable increase in H4 acetylation to normal or above-normal levels. All changes were significantly different compared to day 0 levels, with the exceptions of Nrn1 and cJun (*P > 0.08). (C) The general pattern of H4 acetylation observed at 3 days post ONC, remained consistent through 5 days post ONC. Promoters for BclX and cJun exhibited no statistical change from day 0 histone acetylation levels at this stage (*P > 0.1).