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Series GSE130064 Query DataSets for GSE130064
Status Public on Jul 07, 2020
Title DNA hypomethylation confers enhanced immunity against parasitic nematodes in plants
Organism Oryza sativa
Experiment type Methylation profiling by high throughput sequencing
Summary Background: Epigenetic processes play an important role in the plant response to adverse environmental conditions. A role for DNA hypomethylation has recently been suggested in the pathogenic interaction between bacteria and plants, yet it remains unclear whether this phenomenon reflects a conserved and general plant immunity response. We therefore investigated the role of DNA methylation in the plant defence against damaging parasitic nematodes.
Methods and results: Treatment of roots of rice (monocot plant) and tomato (dicot plant) by a nematode-associated molecular pattern (NAMP) from different parasitic nematodes revealed global DNA hypomethylation using ELISA based quantification, suggesting conservation among plants. Focusing on root-knot induced gall tissue in rice, the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon 5-Azacitidine treatment. Whole genome bisulfite sequencing revealed that hypomethylation was massively present in the CHH context, while absent for CpG or CHG nucleotide contexts. CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point, but rather showed a delayed effect on transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway (RdDM) and DDM1, which are known to be steering DNA methylation in CHH context.
Conclusions: We demonstrated that DNA hypomethylation confers enhanced defence in rice towards root-parasitic nematodes and is likely to be part of the basal NAMP-triggered immunity response in plants.
 
Overall design Rice plants (Oryza sativa L. cv. Nipponbare) were infected with Meloidogyne graminicola. Three replicates were made per condition (non-infected and infected). Each sample was multiplexed in four subsamples.
 
Contributor(s) Reza Atighi M, Verstraeten B, De Meyer T, Kyndt T
Citation(s) 32162327, 34284724
Submission date Apr 19, 2019
Last update date Jul 28, 2021
Contact name Jeroen Galle
Organization name Ghent University
Department Dept. Of Mathematical Modelling, Statistics and Bioinformatics
Lab Biobix, Lab of Bioinformatics and Computational Genomics
Street address Coupure Links 653
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platforms (1)
GPL21087 Illumina NextSeq 500 (Oryza sativa)
Samples (6)
GSM3731222 G1
GSM3731223 G2
GSM3731224 G3
Relations
BioProject PRJNA533778
SRA SRP193064

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
GSE130064_RAW.tar 3.6 Gb (http)(custom) TAR (of COV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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