Open chromatin in defense gene priming and systemic plant immunity

当被病原体局部侵染时，植物在感染部位远端的叶片在二次侵染时能够更快、更强地表达防御基因。这一过程通常与一种称为系统获得性抵抗(SAR)的免疫反应的诱导有关。在拟南芥中，防御基因的启动和合成需要休眠信号酶(如MPK3和MPK6)的积累和热激转录因子HsfB1的活性。基因启动和SAR还与防御基因启动子上特定的组蛋白修饰(如甲基化和乙酰化)相关。然而，参与系统基因启动和获得性免疫的其他调控DNA元件(如启动子-远端DNA位点、增强子)在很大程度上仍然难以捉摸。为了鉴定这些DNA元件，以及从长远来看，它们的结合蛋白(例如转录共激活因子、染色质修饰物)，我们建立了甲醛辅助分离拟南芥叶片染色质调节元件(FAIRE)。首先，我们将利用FAIRE-SEQ技术对拟南芥防御基因启动过程中开放染色质进行全基因组鉴定。然后，FIRE-SEQ数据将与细菌挑战感染前后启动和未启动叶片的同步全基因组基因表达分析的数据相一致。通过这样做，我们将识别新的调控DNA元件(例如增强子序列)，这些元件对防御基因启动和SAR非常重要。它们的重要性将在几个选定的基因座上得到例证。这些研究是使用重要的调控DNA元件对新的染色质结合蛋白(如转录共激活物、染色质重塑酶)进行无偏分析的绝对要求，这些蛋白对启动和反向染色质免疫沉淀的SAR至关重要。

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.