Genome-wide identification of transcribed enhancer candidates during pattern triggered immunity in Arabidopsis

Proper transcriptional reprogramming is central for hosts to launch an effective defense response upon pathogen attack. Relatively short DNA sequences known as enhancers play a key role in gene regulation by increasing the amount of transcription from associated genes. Here, we investigate the Arabidopsis thaliana distal enhancers involved in early innate immunity. Using an integrated computational pipeline, a class of low abundant transcripts that are transcribed uni- or bidirectionally from putative distal enhancers are identified based on intergenic open chromatin. Most of them may be non-polyadenylated, which are in concert with the enhancer RNAs (eRNAs) found in mammalian cells. The production of eRNAs at distal enhancers is strongly correlated with open chromatin architecture, low DNA methylation, as well as the enrichment of RNA poly II and acetylated histone marks. Immune transcription factors are enriched in the PTI-induced enhancers, such as WRKYs and SARD1, and up-regulated enhancers significantly associated with early immune gene regulation. Moreover, a subset of core patterns induced-enhancers was defined which up-regulated by multiple patterns from diverse pathogens. Genome-wide dynamic correlation of transcribed enhancer activity to gene transcription.