Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

Chromatin structure plays a pivotal role in facilitating proper control of gene expression. The ability of transcription factors (TF) to bind cis-elements is often associated with accessible chromatin regions. Therefore, identification of these accessible regions throughout plant genomes is important to understanding the relationship between TF binding, chromatin status and the regulation of gene expression. Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) is a recently developed technique used to map open chromatin zones in animal genomes. However, in plants, the existence of cell walls, subcellular organelles and the lack of stable cell lines have prevented routine application of this technique. Here, we describe an assay combining ATAC-seq with Fluorescence-Activated Nuclei Sorting (FANS) to identify and map open chromatin and TF-binding sites in plant genomes. FANS-ATAC-seq compares favorably with published DNaseI sequencing (DNase-seq) results and it only requires 500-50,000 nuclei for accurate identification of open chromatin states. Chromatin accessibility profiling (FANS-ATAC-seq) data collected from Arabidopsis 7-day old Col-0 whole seedlings, roots, 35S:H2AX-GFP/Col-0 whole seedlings, or 10-day old maize B73 overground parts. Replicates are included when available. Please note that the *1million_reads raw data were used to generate the percentage of nuclear and organelle reads data, which is included in the associated manuscript as supplementary data table (therefore not included in the GEO records).