ArticleGenome biology2017
Proximal methylation features associated with nonrandom changes in gene body methylation.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- A VIM2/4 deletion, and premature truncations of CMT2 and FBX5, drive DNA methylation changes after colonization of a novel habitat.Nature plants · 2026Article
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Genome-wide CG hypomethylation of theProceedings of the National Academy of Sciences of the United States of America · 2026Article
- The 5-methylcytosine DNA glycosylase ROS1 prevents paternal genome hypermethylation in Arabidopsis endosperm.Genome biology · 2025Article
- A modulatory role of CG methylation on gene expression in soybean implicates its potential utility in breeding.Plant biotechnology journal · 2025Article
- Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants.Genome biology · 2023Article
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- Epigenetic Regulation During Plant Development and the Capacity for Epigenetic Memory.Annual review of plant biology · 2023Review
- Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughoutFrontiers in plant science · 2023Article
- Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time.The Plant cell · 2022Article
- Molecular properties of epimutation hotspots.Nature plants · 2022Article
- An Optimized Method for the Construction of a DNA Methylome from Small Quantities of Tissue or Purified DNA fromMolecules and cells · 2021Article
- Epimutations Define a Fast-Ticking Molecular Clock in Plants.Trends in genetics : TIG · 2021Review
- Article
- CRISPR-based targeting of DNA methylation inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Natural variation in DNA methylation homeostasis and the emergence of epialleles.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Classroom as Genome: Using the Tools of Genomics and Bioinformatics to Illuminate Classroom Observation Data.CBE life sciences education · 2019Article
- Article
- Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit.Nature communications · 2017Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundGene body methylation at CG dinucleotides is a widely conserved feature of methylated genomes but remains poorly understood. The Arabidopsis thaliana strain Cvi has depleted gene body methylation relative to the reference strain Col. Here, we leverage this natural epigenetic difference to investigate gene body methylation stability.
resultsRecombinant inbred lines derived from Col and Cvi were used to examine the transmission of distinct gene body methylation states. The vast majority of genic CG methylation patterns are faithfully transmitted over nine generations according to parental genotype, with only 1-4% of CGs either losing or gaining methylation relative to the parent. Genic CGs that fail to maintain the parental methylation state are shared among independent lines, suggesting that these are not random occurrences. We use a logistic regression framework to identify features that best predict sites that fail to maintain parental methylation state. Intermediate levels of CG methylation around a dynamic CG site and high methylation variability across many A. thaliana strains at that site are the strongest predictors. These data suggest that the dynamic CGs we identify are not specific to the Col-Cvi recombinant inbred lines but have an epigenetic state that is inherently less stable within the A. thaliana species. Extending this, variably methylated genic CGs in maize and Brachypodium distachyon are also associated with intermediate local CG methylation.
conclusionsThese results provide new insights into the features determining the inheritance of gene body methylation and demonstrate that two different methylation equilibria can be maintained within single individuals.
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