Identifying and characterizing highly accessible chromatin regions assists in 
determining the location of genomic regulatory elements and understanding 
transcriptional regulation. In this chapter, we describe an approach to map 
accessible chromatin features in plants using the Assay for 
Transposase-Accessible Chromatin, combined with high-throughput sequencing 
(ATAC-seq), which was originally developed for cultured animal cells. This 
technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and 
simultaneous insertion of sequencing adapters into open chromatin regions of the 
input nuclei. The application of ATAC-seq to plant tissue has been challenging 
due to the difficulty of isolating nuclei sufficiently free of interfering 
organellar DNA. Here we present two different approaches to purify plant nuclei 
for ATAC-seq: the INTACT method (Isolation of Nuclei TAgged in specific Cell 
Types) to isolate nuclei from individual cell types of the plant, and tissue 
lysis followed by sucrose sedimentation to isolate sufficiently pure total 
nuclei. We provide detailed instructions for transposase treatment of nuclei 
isolated using either approach, as well as subsequent preparation of ATAC-seq 
libraries. Sequencing-ready ATAC-seq libraries can be prepared from plant tissue 
in as little as one day. The procedures described here are optimized for 
Arabidopsis thaliana but can also be applied to other plant species.