Assessing chromatin accessibility in maize using ATAC-seq

The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. We demonstrate a streamlined ATAC-seq protocol for maize in which nuclei purification can be achieved without cell sorting, and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, provides a precise and efficient assessment of the maize chromatin landscape. Overall design: We perform the Maize seedling ATAC-Seq using only 2500 and 5000 nuclei, as well as the naked gDNA as control, in a total of three samples with two biological replicates, providing a new way to study the role of chromatin accessibility.