NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE174350 Query DataSets for GSE174350
Status Public on Jul 04, 2023
Title Methylome dynamic upon proteasome inhibition by the pseudomonas virulence factor Syringolin A
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary DNA methylation is an important epigenetic mark required for proper gene expression and silencing of transposable elements. DNA methylation patterns can be modified by environmental factors such as pathogen infection, where modification of DNA methylation can be associated with plant resistance. To counter the plant defense pathways, pathogens produce effectors molecule, several of which act as proteasome inhibitors. Here we investigated the effect of proteasome inhibition by the bacterial virulence factor Syringolin A on genome-wide DNA methylation. We show that Syringolin A treatment results in an increase of DNA methylation at centromeric and pericentromeric regions of Arabidopsis chromosomes. We identify several CHH DMRs that are enriched in the proximity of transcriptional start sites. Syringolin A treatment does not result in significant changes in small RNA composition. However, significant changes in genome transcriptional activity can be observed, including a strong upregulation of resistance genes that are located on chromosomal arms. We hypothesize that DNA methylation changes could be linked to the upregulation of some atypical members of the de novo DNA methylation pathway: AGO3, AGO9 and DRM1. Our data suggests that modification of genome-wide DNA methylation resulting from an inhibition of the proteasome by bacterial effectors could be part of a epi-genomic arms race against pathogens.
 
Overall design GWBS, mRNA and sRNA sequencing of wildtype Arabidopsis plantlets treated or not with SyringolinA
 
Contributor(s) Jullien PE, Grob S
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date May 12, 2021
Last update date Jul 05, 2023
Contact name Stefan Grob
E-mail(s) sgrob@botinst.uzh.ch
Organization name University of Zurich
Department Institute of Plant Biology
Lab Grossniklaus Lab
Street address Zollikerstrasse 107
City Zurich
ZIP/Postal code 8008
Country Switzerland
 
Platforms (1)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (8)
GSM5292513 SM1
GSM5292514 SM2
GSM5292515 SP1
Relations
BioProject PRJNA729499
SRA SRP319525

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
GSE174350_RAW.tar 179.3 Mb (http)(custom) TAR (of TXT)
GSE174350_RNAseq_counts.txt.gz 2.7 Mb (ftp)(http) TXT
GSE174350_frags_100bp_bySize.txt.gz 13.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap