We found non-random patterns of epigenetic and transcriptional alterations in a number of genes in association with differences in maternal care ( Fig. 2 ). The specificity of this pattern is further underscored by the fact that both increased and decreased peaks of acetylation and DNA methylation are observed throughout the region. However, the response is gene-specific, as not all genes appear to respond to differences in maternal care (Table S1). Differences in broad epigenetic marks co-cluster over large distances ( Fig. 3a ), supporting previous work in cancer cells and suggesting the possibility of widespread epigenetic effects on multiple genes in the same genomic regions in response to maternal care. Analysis of our data with respect to protein-coding genes reveals expected relationships between epigenetic marks and gene expression levels. Increased transcription is associated with decreased 5′ DNA methylation and increased exonic H3K9 acetylation and DNA methylation ( Fig. 3b–c ). Previous studies have examined the relationships between differences in DNA methylation and histone acetylation and gene expression in on/off states of gene expression activity, as seen in cancer and
