Chromatin is inherently refractory to the initiation of transcription and to the binding of regulatory factors. Nucleosomes need to be moved or destabilized from DNA sequences by processes involving remodelers. We have designed a new approach called NOME-Seq which allows us to examine DNA methylation patterns and nucleosomal positioning on individual DNA molecules thus digitizing the analysis of accessible chromatin areas. We have used this approach genome wide to analyze the precise nature and physical sizes of nucleosome depleted regions (NDRs) and examined the effects of mutations in chromatin remodelers on these accessible areas. We have also followed the alterations in chromatin accessibility immediately following drug treatment with DNA demethylation agents. Results from these studies give insights as to the mechanisms of action of the drugs and provide opportunities for future drug development.