Elf18-induced long noncoding RNA associates with Mediator to enhance expression of innate immune response genes in Arabidopsis

Plant immune response is a complex process involving both transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis long-noncoding (lnc) RNA, designated elf18-induced long noncoding RNA 1 (ELENA1), as a factor enhancing resistance against Pseudomonas syringe pv. tomato DC3000. ELENA1 knock-down plants show a decreased expression of PR1 and the plants are susceptible to pathogens. By contrast, plants over-expressing ELENA1 show elevated Pathogenesis-Related gene 1 (PR1) expression after elf18 treatment and display pathogen resistance phenotype. RNA-seq analysis of ELENA1 overexpressing plants after elf18 treatment confirms increased expression of defense-related genes compared to WT. ELENA1 directly interacts with Mediator subunit 19a (MED19a) and affects enrichment of MED19a on PR1 promoter. These results show that ELENA1 is a novel lncRNA that regulates PR1 expression through MED19a. Our findings uncover an additional layer of complexity implicating lncRNA in the transcriptional regulation of plant innate immunity. Overall design: To investigate the role of ELENA1 in regulating immune response, we performed strand-specific RNA-seq (ssRNA-seq) on WT and ELENA1 OX plants grown under normal (0 h) and elf18-treated conditions (1 h, 6 h and 12 h). For each condition we used three biological replicates.

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Seo JS, Sun HX, Park BS, Huang CH, Yeh SD, Jung C, Chua NH