Integration of ATAC-seq and DAP-seq Data to Uncover Gene Regulatory Networks in Soybean

Chromatin structure plays a pivotal role in enabling proper control of gene expression. The abilities of transcription factors (TF) to bind cis-elements are often associated with accessible chromatin zones, in which chromatin is decondensed, exposing the DNA. Therefore, identification of these accessible regions throughout plant genomes is important to understanding the relationship between TF binding, chromatin status and thus the regulation of gene expression. Assay for Transposase Accessible Chromatin (ATAC-seq) is a recently developed and widely used technique to map open chromatin zones in animal and human genomes. Furthermore, this technique can be carried out on samples containing hundreds to thousands of cells. However, in plants, the existence of cell walls, robust cell types and numerous subcellular organelles have prevented the application of this technique. Here, we describe an assay combing ATAC-seq with Fluorescence-Activated Nuclei Sorting (FANS) to identify and map accessible chromatin, as a rapid and sensitive method for integrative chromatin status analysis in plant genomes. We are furthering development of this methodology by combining ATAC-seq with FANS and with samples collected from laser capture as this will enable cell-type specific analysis of chromatin states in any plant genome.