The Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) is a powerful technique that enables the genome-wide analysis of chromatin accessibility. At the level of individual loci this allows an understanding of the positional relationship between chromatin, transcriptional regulators and gene expression whilst on a global level can provide an understanding of how large areas of the genome are regulated.
ATAC-seq relies upon the engineered activity of the hyperactive transposase Tn5, which both cleaves accessible DNA and anneals specific adaptors to either end of the resulting fragments. These DNA fragments can be isolated, amplified and analysed by NGS. ATAC-seq requires a clean nuclear extraction that has limited contamination from, in particular, chloroplast DNA.
This article outlines a consensus methodology for ATAC-seq that includes descriptions of a crude nuclear extraction, cleavage by Tn5 and amplification of DNA fragments in preparation for NGS
