Comparison of the overlap of DNA methylation probes with epigenetic marks showed the outcome of DIM-mediated alteration in DNA methylation may be influenced by local histone modifications.

<p>(A) The genomic region coordinates of DNA methylation probes that had decreased methylation (black bar) or increased methylation (white bar) in DIM-treated LnCAP cells were uploaded into EpiExplorer to determine potential overlap with various histone modifications from the ENCODE database. A randomized control set was generated by reshuffling the genomic positions of each dataset (light and dark gray bars for decreased methylation and increased methylation, respectively). Data summarize the percent overlap of DNA methylation probes and their respective randomized control to histone methylation mark H3K4me3, and histone acetylation marks H3K9ac. (B) ChIP assays for H3K4me3 at the TGFBR1 and CYR61 promoters in LnCAP cells after vehicle (DMSO) or 15 µM DIM treatments for 48 h. ChIP-qPCR data were expressed as % input. Results represent the mean % input fold-change ± SEM compared to DMSO vehicle control of two independent experiments. *p-value <0.05.