To index broad epigenetic changes observed across the locus, we defined a Regional Difference in DNA methylation and a Regional Difference H3K9 acetylation (RDme and RDac, respectively) as a statistically significant difference between High LG and Low LG offspring of at least 1000 bp containing at least one statistically significant probe per 1000 bp (see Methods S1 for details). Across the entire locus, we identified 723 RDme of which 373 are significantly hypermethylated and 350 are hypomethylated in High relative to Low LG offspring. We similarly identified 471 RDac of which 204 are hyperacetylated and 267 are hypoacetylated. We found that these broad epigenetic differences associated with maternal care are significantly co-localized within the locus, and were positively correlated at distances over 100 Kb ( Fig. 3a ). The data suggest that clustering of differentially methylated and acetylated regions is not exclusive to pathological responses under extreme selection as is the case in cancer but includes epigenetic responses to natural variations in maternal care, and may be characteristic of naturally occurring epigenetic responses.
