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Series GSE171198 Query DataSets for GSE171198
Status Public on Jun 01, 2021
Title Repression of CHROMOMETHYLASE 3 Prevents Epigenetic Collateral Damage in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. Here, we report that microRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features that CMT3 prefers help prevent ectopic methylation of thousands of genes during embryogenesis that can persist for weeks afterwards. Moreover, CMT3-induced ectopic methylation of genes undergoing transcriptional activation can reduce their corresponding transcript levels. Therefore, the repression of CMT3 prevents epigenetic collateral damage on endogenous genes. We also provide a model that may help reconcile conflicting viewpoints regarding the functions of gene-body methylation that occurs in nearly all flowering plants.
 
Overall design Methyl cytosine sequencing libraries were generated from 2-4 biological replicates of bent cotyledon stage embryos or seedlings from four genotypes. mRNA-seq libraries were generated from 9 biological replicates of bent cotyledon embryos from three genotypes.
 
Contributor(s) Nodine M, Papareddy R
Citation(s) 34296996
Submission date Mar 30, 2021
Last update date Aug 18, 2021
Contact name Michael D Nodine
E-mail(s) michael.nodine@wur.nl
Organization name Wageningen University & Research
Department Plant Sciences
Lab Molecular Biology
Street address Radix West
City Wageningen
State/province Gelderland
ZIP/Postal code 6708 PB
Country Netherlands
 
Platforms (2)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (35)
GSM5220623 Col-0 methylC-seq bent cotyledon (biorep #1)
GSM5220624 Col-0 methylC-seq bent cotyledon (biorep #2)
GSM5220625 cCMT3 methylC-seq bent cotyledon (Line #1; biorep #1)
Relations
BioProject PRJNA718622
SRA SRP312789

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
GSE171198_WT_Bentcotyledon_BioRep_R1.genes.results.gz 582.0 Kb (ftp)(http) RESULTS
GSE171198_WT_Bentcotyledon_BioRep_R2.genes.results.gz 559.3 Kb (ftp)(http) RESULTS
GSE171198_WT_Bentcotyledon_BioRep_R3.genes.results.gz 588.9 Kb (ftp)(http) RESULTS
GSE171198_allC_WT_BentCotyledon2020.tsv.gz 135.6 Mb (ftp)(http) TSV
GSE171198_allC_WT_Seedling.tsv.gz 132.5 Mb (ftp)(http) TSV
GSE171198_allC_gCMT3_L1_BentCotyledon.tsv.gz 150.9 Mb (ftp)(http) TSV
GSE171198_allC_gCMT3_L1_Seedling.tsv.gz 131.7 Mb (ftp)(http) TSV
GSE171198_allC_gCMT3_L3_BentCotyledon.tsv.gz 125.1 Mb (ftp)(http) TSV
GSE171198_allC_gCMT3_L3_Seedling.tsv.gz 127.6 Mb (ftp)(http) TSV
GSE171198_allC_miR823_L1_BentCotyledon2020.tsv.gz 124.1 Mb (ftp)(http) TSV
GSE171198_allC_miR823_L2_BentCotyledon2020.tsv.gz 62.2 Mb (ftp)(http) TSV
GSE171198_allC_rCMT3_L1_BentCotyledon.tsv.gz 138.7 Mb (ftp)(http) TSV
GSE171198_allC_rCMT3_L1_Seedling.tsv.gz 131.1 Mb (ftp)(http) TSV
GSE171198_allC_rCMT3_L3_BentCotyledon.tsv.gz 135.0 Mb (ftp)(http) TSV
GSE171198_allC_rCMT3_L3_Seedling.tsv.gz 145.2 Mb (ftp)(http) TSV
GSE171198_rCMT3_L1_Bentcotyledon_BioRep_R1.genes.results.gz 605.0 Kb (ftp)(http) RESULTS
GSE171198_rCMT3_L1_Bentcotyledon_BioRep_R2.genes.results.gz 612.0 Kb (ftp)(http) RESULTS
GSE171198_rCMT3_L1_Bentcotyledon_BioRep_R3.genes.results.gz 581.7 Kb (ftp)(http) RESULTS
GSE171198_rCMT3_L3_Bentcotyledon_BioRep_R1.genes.results.gz 588.1 Kb (ftp)(http) RESULTS
GSE171198_rCMT3_L3_Bentcotyledon_BioRep_R2.genes.results.gz 587.1 Kb (ftp)(http) RESULTS
GSE171198_rCMT3_L3_Bentcotyledon_BioRep_R3.genes.results.gz 587.6 Kb (ftp)(http) RESULTS
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