The ATAC-seq methodology relies on library construction using the hyperactive transposase Tn5. Tn5 is a prokaryotic transposase, which endogenously functions through the “cut and paste” mechanism, requiring sequence-specific excision of a locus containing 19 base-pair inverted repeats. The Nextera DNA Sample Preparation kit provides the Tn5 transposase reagent loaded with sequencing adapters creating an active dimeric transposome complex (Adey et al., 2010). The Nextera version of the transposase harbors specific point mutants to the Tn5 backbone which significantly increases activity (Goryshin and Reznikoff, 1998; Reznikoff, 2008). This transposase preferentially inserts sequencing adapters into unprotected regions of DNA, therefore acting as a probe for measuring chromatin accessibility genome-wide.
