The 18,023 genes form the expression dataset were ranked by level table 5 of expression in FC com pared to na ve controls and plotted against the average coverage of H4K5ac 5 kb relative to the TSS. The level of gene expression was found to correlate to H4K5ac enrichment such that the highest expressed genes had the highest coverage for H4K5ac, while the least expressed genes had the lowest coverage. This applied to both groups regardless of training, suggesting that H4K5ac is a general feature of expressed genes. We also confirmed that H4K12ac correlated with the level of gene expression. There was no correlation between gene expression and IgG IP coverage. These results indicate a clear association between both H4K5ac and H4K12ac and gene expression.

We then identified genes acetylated above average and performed a cross wise comparison between experimental groups. Based on the average promoter read count of 45 in our dataset, we considered genes with more than 50 reads in the promoter as above average. From a total of 23,235 genes in the dataset, 7,103 genes were identified in the FC group, and 7,708 genes in the control. Using this criteria, 742 genes were specific for FC, 1,273 genes were specific for control, and 6,029 genes were common to both groups. We then looked at whether genes with above average H4K5ac after 2 days of CFC were also associated with H4K12ac after one session of CFC. Using an adjusted threshold of 10 reads in promoter due to the lower aver age coverage, approximately 9 reads in promoter, in the H4K12ac dataset, we identified 4,259 unique genes with above average H4K12ac, of which 2,772 genes over lapped with genes with above average H4K5ac in FC, and 2,846 genes with above average H4K5ac in controls.

2,440 genes over lapped all three groups using this criteria. The results of these analyses extend our findings that in control conditions most nucleosomes are not only acety lated for H4K5 above the average of all genes, but are also acetylated for H4K12. Batimastat Interestingly, nearly two thirds of genes with above average H4K12ac after one session of CFC was found to overlap with above average H4K5ac after 2 days of CFC or context. This suggests that the same set of genes, associated with H4K12ac and induced imme diately after CFC, may be upregulated following reinforced training, regardless of the associated histone acetylation used to identify the genes. It also suggests that the same set of genes may be activated after initial learning, during the formation of contextual fear memory, and after memory re trieval, independently of the CFC paradigm.