Genome-wide ATAC-seq on Arabidopsis for studying the regulatory chromatin landscape of PTI and ETI

Initially from time-course RNAseq (Sohn et al 2014 PLoS genetics), we identified ETI-specific early elevated genes in comparison to PTI with PTI plus ETI. In order to study how the early response genes activated by ETI, we performed ATACseq at early timepoint using Pf0-1 to deliver effector and activate ETI in the presence of PTI, as well as using SETI (Ngou et al 2019 JXB), an inducible ETI system to activate ETI in the absence of PTI. We have also included mutant effector of AvrRps4 (KRVY135-138AAAA) as a control for wild-type (WT) AvrRps4, which induce ETI via recognition by two paired R proteins RPS4 and RRS1. We included gh (sard1 cbp60g) double mutant of two functionally redundant transcription factors (TFs) in this study, to address the function relevance of TF and changes in chromatin accessibility in response to PTI and ETI at early time points of immune activation.