Genome-wide mapping of 5-hmC in epithelial samples from IMQ-treated skin versus control skin in mice.

Analysis of the tag densities showed lower 5-hmC levels in both CpG islands and genebodies in Imiquimod (IMQ)-treated epidermal samples. We looked further into loci-specific changes of 5-hmC and found a total of 364 differentially hydroxymethylated regions. Within these regions, 321 genes showed significantly lower 5-hmC levels and 67 genes had significantly higher 5-hmC levels in the IMQ-treated epidermis compared to control. We used a barcoded hydroxymethylated DNA immunoprecipitation (hMeDIP) method coupled with deep sequencing (hMeDIP-seq) for quantitative comparison of 5-hmC tag density at specific genome loci in IMQ-induced epidermal lesions compared to control non-lesional epidermis in mice.