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Series GSE178684 Query DataSets for GSE178684
Status Public on Dec 02, 2021
Title Molecular properties of epimutation hotspots
Organism Arabidopsis thaliana
Experiment type Methylation profiling by high throughput sequencing
Summary Mistakes in the maintenance of CG methylation is a source of heritable epimutations in plants. Multigenerational surveys indicate that the rate of these stochastic events varies substantially across the genome, with some regions harboring localized “epimutation hotspots”. Using Arabidopsis as a model, we show that epimutation hotspots are indexed by a specific set of chromatin states (CS) that map to sub-regions of gene body methylation genes. Although these regions comprise only ~12% of all CGs in the genome, they account for ~63% of all epimutation events per unit time. Molecular profiling revealed that these regions contain unique sequence features, harbor steady-state intermediate methylation levels, and act as putative targets of antagonistic DNA methylation pathways. We further demonstrate that experimentally-induced shifts in steady-state methylation in these hotspot regions are sufficient to significantly alter local epimutation intensities. Our work thus lays foundation for dissecting the molecular mechanisms of epimutation hotspots in plants.
 
Overall design We created two mutant lineages of MA_cmt3, and MA_suvh4/5/6 mutation accumluation lines from Col-0 that were propagated by single seed descent growth for the indicated number of generations (G#).
 
Contributor(s) Schmitz RJ, Johannes F
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Submission date Jun 22, 2021
Last update date Dec 04, 2021
Contact name Rashmi Rekha Hazarika
E-mail(s) rashmi.hazarika@tum.de
Organization name Technical University of Munich
Street address Liesel Beckmann-Str-2
City Freising
ZIP/Postal code 85354
Country Germany
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (22)
GSM5396038 CMT3-L8-G1
GSM5396039 CMT3-L10-G1
GSM5396040 CMT3-L4-G5
Relations
BioProject PRJNA740019
SRA SRP325109

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
GSE178684_RAW.tar 6.4 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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