ArticleGenome biology2023
Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
- Telomere-to-telomere genome ofHorticulture research · 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
- Photorespiration is linked to DNA methylation by formate as a one-carbon source.Nature plants · 2026Article
- Gene body methylation buffers noise in gene expression in plants.Nucleic acids research · 2026Article
- Aging drives a program of DNA methylation decay in plant organs.Science (New York, N.Y.) · 2026Article
- Productive chaos and precision engineering: decoupling discovery from manufacturing to revolutionize plant-inspired therapeutics.Frontiers in plant science · 2026Article
- Building resilience by cultivating difference: A role for noise in development.Current opinion in plant biology · 2025Review
- Molecular mechanisms and biological functions of active DNA demethylation in plants.Epigenetics & chromatin · 2025Review
- Biological Mechanisms for Allen's Rule: DNA Methylation as Mediator of the Association Between In Utero Exposure to Environmental Heat and Tibial Growth in Childhood.American journal of human biology : the official journal of the Human Biology Council · 2025Article
- Transcriptional and epigenomic changes in response to polyethylene glycol-triggered osmotic stress in Brassica napus L.Journal of experimental botany · 2025Article
- Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.Genome biology and evolution · 2025Article
- DNA methylation dynamics play crucial roles in shaping the distinct transcriptomic profiles for different root-type initiation in rice.Genome biology · 2025Article
- INCREASED DNA METHYLATION 3 forms a potential chromatin remodelling complex with HAIRPLUS to regulate DNA methylation and trichome development in tomato.The Plant journal : for cell and molecular biology · 2025Article
- DNA methylation patterns linked to salinity and geography in the American eel (Environmental epigenetics · 2025Article
- Almond Grafting for Plum Pox Virus Resistance Triggers Significant Transcriptomic and Epigenetic Shifts in Peaches.International journal of molecular sciences · 2024Article
- Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants.Genome biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear.
resultsWe report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range in drdd mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity.
conclusionsWe propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.