Genome-wide analyses of NPR1 and HAC1 direct targets in Arabidopsis

Genome-wide direct targets of Arabidopsis NPR1 and HAC1 were identified by chromain immunoprecipitation followed by sequencing (ChIP-seq). For the study, we used Arabidopsis expressing NPR1:GFP or HAC1:mCherry under native NPR1 or HAC1 promoter, respectively. To identify direct targets both under salicylic acid-treated and untreated conditions, we performed ChIP-seq by using 2,6-dichloroisonicotinc acid (INA; synthetic SA analog)-treated and untreated NPR1:GFP or HAC1:mCherry transgenic Arabidopsis plants. Overall design: For the rep1&2 NPR1:GFP ChIP-seq, chromatin was digested by sonication and immunoprecipitation (IP) was performed in condition containing 1% sodium dodecyl sulfate (SDS). For the rep3&4 NPR1:GFP ChIP-seq, chromatin was digested by micrococcal nuclease (MNase) treatment and IP was performed in condition containing 0.02% SDS. For the rep1&2 HAC1:mCherry ChIP-seq, chromatin digestion and IP were performed as described for the rep3&4 NPR1:GFP ChIP-seq. Samples were treated either with INA (+INA) or water (-INA) and incubated for 12 hours before harvesting. Columbia-0 (Col) was used as a non-transgenic wild-type control.