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Series GSE93560 Query DataSets for GSE93560
Status Public on May 19, 2017
Title Elf18-induced long noncoding RNA associates with Mediator to enhance expression of innate immune response genes in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Contributor(s) Seo JS, Sun H, Park B, Huang C, Yeh S, Jung C, Chua N
Citation(s) 28400491
Submission date Jan 12, 2017
Last update date May 15, 2019
Contact name Nam-Hai Chua
Organization name The Rockefeller University
Lab Lab of Plant Molecular Biology
Street address 1230 York Avenue
City NEW YORK
State/province New York
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (24)
GSM2454694 WT_0hr_rep1
GSM2454695 WT_0hr_rep2
GSM2454696 WT_0hr_rep3
Relations
BioProject PRJNA361118
SRA SRP096695

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE93560_TranscriptsFPKM.txt.gz 1.2 Mb (ftp)(http) TXT
GSE93560_TranscriptsReadCounts.txt.gz 1.4 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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