Here, the authors develop a statistical approach to identify candidate noncoding driver mutations in DNase I hypersensitive sites in breast cancer and experimentally demonstrate they are regulatory elements of known cancer genes.
Here, we use ENCODE ChIP-seq and DNase I hypersensitivity data, along with large-scale breast cancer genomic data from The Cancer Genome Atlas (TCGA) to computationally dissect the intricacies of DNA methylation in regulation of cancer transcriptomes.
Northern analyses of ErbB2-overexpressing breast cancer lines (SKBR3, BT-474, and MDA-453) showed that within 24 h of submicromolar treatment by TSA, ESX transcript levels increase while ErbB2 transcript levels rapidly decline, with no TSA effect apparent on the open chromatin configuration of either gene as monitored by DNase I hypersensitivity.
Analysis of the chromatin structure of the vimentin gene in V+ and V- breast cancer cells showed DNase I hypersensitive sites in the 5' promoter region in V+ cell lines and 3' to the start of transcription in V- cell lines.