ATAC-seq is the most current method for probing open chromatin, based on the ability of hyperactive Tn5 transposase [101, 102] to fragment DNA and integrate into active regulatory regions in vivo (Figure 1) [103]. During ATAC-seq, 500–50,000 unfixed nuclei are tagged in vitro with sequencing adapters by purified Tn5 transposase. Due to steric hindrance the majority of adapters are integrated into regions of accessible chromatin that are subsequently submitted to PCR for library construction followed by paired-end NGS. This method has been recently used in a eukaryotic line to uncover open chromatin, nucleosome positioning and TF footprints genome-wide [103]. Despite its limited application so far, ATAC-seq is attracting a growing interest due to its simple and fast two-step protocol, its high sensitivity with a low starting cell number (500 to 50,000 cells) and the ability to study multiple aspects of chromatin architecture simultaneously at high resolution.
