We next examined the localization of broad differences in H3K9 acetylation, DNA methylation (i.e., RDac and RDme) and transcription with respect to the physical anatomy of genes within the locus. Gene regulatory elements, including transcription start sites, 5′ and 3′ gene ends, and CpG islands are typical regions of interest in studies of gene regulation by epigenetic mechanisms. We found no evidence of a relationship between CpG density and the presence of RDme (P = 0.53 by Wilcoxon rank sum test), indicating there is no difference between CpG islands and other regions with respect to the presence of RDme. RDme/ac overlapped the transcription start sites of some but not all genes, indicating specificity in epigenetic signaling within the locus. Seventy-seven transcription start sites in 69 genes contain RDme while 127 transcript start sites in 94 genes do not contain RDme. Similarly, 37 transcription start sites in 32 genes contain RDac while 167 transcription start sites in 131 genes do not contain RDac. There was a significant enrichment of hyperacetylated RDac (regions in which the high maternal care group has higher
