ArticlePLoS genetics2015
Genome-wide negative feedback drives transgenerational DNA methylation dynamics in Arabidopsis.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 69 citations in OpenAlex.
- Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana.Nature plants · 2025Article
- Dynamic evolution of the heterochromatin sensing histone demethylase IBM1.PLoS genetics · 2024Article
- H3K9 methylation regulates heterochromatin silencing through incoherent feedforward loops.Science advances · 2024Article
- The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.G3 (Bethesda, Md.) · 2024Article
- The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis.BMC genomics · 2024Article
- Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants.Plants (Basel, Switzerland) · 2023Review
- Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin.Seminars in cell & developmental biology · 2023Review
- DDM1-Mediated TE Silencing in Plants.Plants (Basel, Switzerland) · 2023Review
- Local and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis.Nature communications · 2022Article
- Lymphoid-specific helicase in epigenetics, DNA repair and cancer.British journal of cancer · 2022Review
- Molecular properties of epimutation hotspots.Nature plants · 2022Article
- Article
- Heterochromatin is a quantitative trait associated with spontaneous epiallele formation.Nature communications · 2021Article
- Pathway conversion enables a double-lock mechanism to maintain DNA methylation and genome stability.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Article
- Transgenerational effect of mutants in the RNA-directed DNA methylation pathway on the triploid block in Arabidopsis.Genome biology · 2021Article
- Chromatin-based mechanisms to coordinate convergent overlapping transcription.Nature plants · 2021Article
- RNA interference-independent reprogramming of DNA methylation in Arabidopsis.Nature plants · 2020Article
- 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
- Role of Chromatin Architecture in Plant Stress Responses: An Update.Frontiers in plant science · 2020Review
Corrections and comments
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Authors and funding
12 authors at 7 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epigenetic variations of phenotypes, especially those associated with DNA methylation, are often inherited over multiple generations in plants. The active and inactive chromatin states are heritable and can be maintained or even be amplified by positive feedback in a transgenerational manner. However, mechanisms controlling the transgenerational DNA methylation dynamics are largely unknown. As an approach to understand the transgenerational dynamics, we examined long-term effect of impaired DNA methylation in Arabidopsis mutants of the chromatin remodeler gene DDM1 (Decrease in DNA Methylation 1) through whole genome DNA methylation sequencing. The ddm1 mutation induces a drastic decrease in DNA methylation of transposable elements (TEs) and repeats in the initial generation, while also inducing ectopic DNA methylation at hundreds of loci. Unexpectedly, this ectopic methylation can only be seen after repeated self-pollination. The ectopic cytosine methylation is found primarily in the non-CG context and starts from 3' regions within transcription units and spreads upstream. Remarkably, when chromosomes with reduced DNA methylation were introduced from a ddm1 mutant into a DDM1 wild-type background, the ddm1-derived chromosomes also induced analogous de novo accumulation of DNA methylation in trans. These results lead us to propose a model to explain the transgenerational DNA methylation redistribution by genome-wide negative feedback. The global negative feedback, together with local positive feedback, would ensure robust and balanced differentiation of chromatin states within the genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.