DNA methylation inhibitors such as
5-aza-2'-deoxycytidine (5-Aza-CdR) are currently used for the treatment of
myelodysplastic syndrome. Although global DNA demethylation has been observed
after treatment, it is unclear to what extent demethylation induces changes in
nucleosome occupancy, a key determinant of gene expression. We use the
colorectal cancer cell line HCT116 as a model to address this question and determine that <2% of regions demethylated by 5-Aza-CdR treatment assume an open configuration. Consolidating our findings, we detect
nucleosome retention at sites of global DNA methylation loss in DKO1, an HCT116-derived non-tumorigenic cell-line engineered for
DNA methyltransferase disruption. Notably, regions that are open in both HCT116 cells
after treatment and in DKO1 cells include promoters belonging to
tumor suppressors and genes under-expressed in
colorectal cancers. Our results indicate that only a minority of demethylated promoters are associated with
nucleosome remodeling, and these could potentially be the epigenetic drivers causing the loss of tumorigenicity. Furthermore, we show that the
chromatin opening induced by the
histone deacetylase inhibitor suberoylanilide hydroxamic acid has strikingly distinct targets compared with those of 5-Aza-CdR, providing a mechanistic explanation for the importance of combinatorial
therapy in eliciting maximal de-repression of the
cancer epigenome.