Dissecting the Epigenome Driving Drug Resistance by ATAC-Seq

The transcription of each gene is tightly regulated by elements like promoters, enhancers, silencers and insulators. These elements determine the temporal and tissue-specific expression in development and disease. Drug resistance is the major obstacle in successfully treating cancer patients. In the recent years, it became evident that epigenetic changes represent one of the mechanisms that contribute to the onset and progression of cancer but also to the development of therapy resistance. The assay for transposase-accessible chromatin coupled with next generation sequencing (ATAC-seq) is a fast and easy technique to track epigenetic changes that result in different opening of the chromatin in regulatory regions genome-wide. The transposase cuts DNA in regions that are open and therefore accessible for transcription factors, regulatory RNAs and proteins that alter the architectural structure of the DNA and drive or inhibit transcription through the RNA polymerase. Here we describe a detailed protocol to perform an ATAC-seq of cells from culture or tissue.