The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was 
recently established as a method to profile open chromatin, which overcomes the 
sample size limitations of the alternative methods DNase/MNase-seq. To 
investigate the role of Piwi in heterochromatin formation around transposable 
element loci, we have used ATAC-seq to examine chromatin accessibility at target 
transposable elements in a Drosophila cultured cell line, ovarian somatic cells 
(OSCs). In this chapter, we describe our method to profile open chromatin 
structure in OSCs using ATAC-seq.