ArticleGenome biology2022
Methylome decoding of RdDM-mediated reprogramming effects in the Arabidopsis MSH1 system.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 18 citations in OpenAlex.
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- Intragenic methylation repatterning is associated with alternative splicing and unique epigenetic phenotypes.Environmental epigenetics · 2026Article
- Epigenetic-modifications induced by plant-microbial interactions modulate plant immunity, Defense-response and mutualistic associations.Molecular biology reports · 2025Review
- Expansion of the MutS gene family in plants.The Plant cell · 2025Article
- Flipping the switch on some of the slowest mutating genomes: Direct measurements of plant mitochondrial and plastid mutation rates in msh1 mutants.PLoS genetics · 2025Article
- Short-Term High Light Stress Analysis Through Differential Methylation Identifies Root Architecture and Cell Size Responses.Plant, cell & environment · 2025Article
- Flipping the switch on some of the slowest mutating genomes: Direct measurements of plant mitochondrial and plastid mutation rates inbioRxiv : the preprint server for biology · 2025Article
- Recent advances in the use of plant growth promoting microorganisms for enhancing micropropagation efficiency.Frontiers in plant science · 2025Review
- Expansion of the MutS Gene Family in Plants.bioRxiv : the preprint server for biology · 2024Article
- Editing of ORF138 restores fertility of Ogura cytoplasmic male sterile broccoli via mitoTALENs.Plant biotechnology journal · 2024Article
- Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals.Molecular ecology · 2024Article
- Sensory plastid-associated PsbP DOMAIN-CONTAINING PROTEIN 3 triggers plant growth- and defense-related epigenetic responses.The Plant journal : for cell and molecular biology · 2023Article
- On the thermodynamics of DNA methylation process.Scientific reports · 2023Article
- Re-analysis of publicly available methylomes using signal detection yields new information.Scientific reports · 2023Article
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Authors and funding
5 authors at 1 institution in 2 countries.
Funding
Abstract
backgroundPlants undergo programmed chromatin changes in response to environment, influencing heritable phenotypic plasticity. The RNA-directed DNA methylation (RdDM) pathway is an essential component of this reprogramming process. The relationship of epigenomic changes to gene networks on a genome-wide basis has been elusive, particularly for intragenic DNA methylation repatterning.
resultsEpigenomic reprogramming is tractable to detailed study and cross-species modeling in the MSH1 system, where perturbation of the plant-specific gene MSH1 triggers at least four distinct nongenetic states to impact plant stress response and growth vigor. Within this system, we have defined RdDM target loci toward decoding phenotype-relevant methylome data. We analyze intragenic methylome repatterning associated with phenotype transitions, identifying state-specific cytosine methylation changes in pivotal growth-versus-stress, chromatin remodeling, and RNA spliceosome gene networks that encompass 871 genes. Over 77% of these genes, and 81% of their central network hubs, are functionally confirmed as RdDM targets based on analysis of mutant datasets and sRNA cluster associations. These dcl2/dcl3/dcl4-sensitive gene methylation sites, many present as singular cytosines, reside within identifiable sequence motifs. These data reflect intragenic methylation repatterning that is targeted and amenable to prediction.
conclusionsA prevailing assumption that biologically relevant DNA methylation variation occurs predominantly in density-defined differentially methylated regions overlooks behavioral features of intragenic, single-site cytosine methylation variation. RdDM-dependent methylation changes within identifiable sequence motifs reveal gene hubs within networks discriminating stress response and growth vigor epigenetic phenotypes. This study uncovers components of a methylome "code" for de novo intragenic methylation repatterning during plant phenotype transitions.
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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 Socratic graph.