ATAC-seq stands for Assay for Transposase-Accessible Chromatin with highthroughput sequencing. It is a technique used in molecular biology for mapping chromatin accessibility sites. The ATAC-Seq method is based on the construction of a new generation sequencing library (NGS) using hyperactive Tn5 transposase. The principle of ATAC-seq is based on the mode of action of the Tn5 transposase on the genomic DNA of the sample. Transposases are enzymes that catalyse the movement of transposons to other parts of the genome. Although natural transposases have a low level of activity, ATAC-seq uses a hyperactive mutated transposase.

The principle of the method consists of incubating the chromatin in the presence of Tn5 transposomes, to simultaneously fragment and index the exposed DNA fragments.  This simple and rapid protocol must however be carried out delicately so as not to modify the structure of the chromatin and reveal sites to the transposomes.

The main advantages of ATAC-Seq over other techniques, such as FAIRE-Seq or DNase-Seq, which study similar chromatin characteristics, are the smaller number of cells required for the test and the relative simplicity of its two-step protocol.