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Series GSE197718 Query DataSets for GSE197718
Status Public on Feb 17, 2023
Title A balance of de novo and maintenance activities governs epigenetic inheritance of CG methylation in Arabidopsis transposons
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Dnmt1/MET1 methyltransferases mediate the epigenetic inheritance of cytosine methylation within CG dinucleotides (mCG). These enzymes use a semiconservative mechanism previously expected to produce binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is quantitatively associated with transposon expression and is stably inherited across many generations. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamical balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that mCG epigenetic inheritance in plant heterochromatin is highly dynamic, with CG sites frequently switching methylation states.
Overall design Bisulfite sequencing was carried out on inbred h1ddm1 mutants and compound methyltransferase mutants to monitor changes in methylation over transgenerational time. RNA-seq was carried out on an early generation (F3) set of h1ddm1 and control sibling cohort to measure differences in transposon transcription.
Contributor(s) Lyons DB
Citation(s) 36827183
Submission date Mar 01, 2022
Last update date May 19, 2023
Contact name David B. Lyons
Organization name John Innes Centre
Department Cell and Developmental Biology
Lab Daniel Zilberman
Street address Colney Lane
City Norwich
State/province Norfolk
ZIP/Postal code NR47UH
Country United Kingdom
Platforms (2)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (80)
GSM5928674 ddm1.f2_1.bsseq
GSM5928675 ddm1.f3_1.bsseq
GSM5928676 ddm1.f4_1.bsseq
BioProject PRJNA811960

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Supplementary file Size Download File type/resource
GSE197718_RAW.tar 17.9 Gb (http)(custom) TAR (of TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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