Open chromatin in defense gene priming and systemic plant immunity

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Upon localized foliar infection by a pathogen plant leaves distal to the infection site become primed for faster and stronger defense gene expression upon secondary infection. This process is often associated with the induction of an immune response called systemic acquired resistance (SAR). In Arabidopsis thaliana defense gene priming and SAR require accumulation of dormant signaling enzymes (e.g. MPK3 and MPK6) and activity of heat-shock transcription factor HsfB1. Gene priming and SAR also correlate with specific histone modifications (e.g. methylation and acetylation) on defense gene promoters. Other regulatory DNA elements (e.g. promoter-distal DNA sites, enhancers) involved in systemic gene priming and acquired immunity, however, remained largely elusive. To identify such DNA elements and, in the long run, their binding proteins (e.g. transcription coactivators, chromatin modifiers) we developed formaldehyde-assisted isolation of regulatory elements (FAIRE) from Arabidopsis leaf chromatin. First, using FAIRE-seq we will perform genome-wide identification of open chromatin during defense gene priming and SAR in Arabidopsis. FAIRE-seq data will then be aligned to data of a synchronous genome-wide gene expression analysis of primed vs. nonprimed leaves before and after bacterial challenge infection. By doing so we will identify novel regulatory DNA elements (e.g. enhancer sequences) important to defense gene priming and SAR. Their importance will be exemplified for a few selected loci. These investigations are an absolute requirement for using important regulatory DNA elements for the unbiased analysis of novel chromatin-binding proteins (e.g. transcription coactivators, chromatin remodeling enzymes) important to priming and SAR by reverse chromatin immunoprecipitation.