ArticleGenome biology2022
DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis.
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 35 papers.
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Who cites it
35 citing papers in PubMed, 68 citations in OpenAlex.
- AI-Augmented Multi-Omics for Abiotic Stress Responses: A New Frontier in Plant Hormone Systems Biology.Plants (Basel, Switzerland) · 2026Review
- Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana.Genome biology · 2026Article
- Heterochromatin reorganization associated with the transcriptional reprogramming under viral infection in Arabidopsis.Nucleic acids research · 2026Article
- Occupancy-based mechanism is the chief mode of ROS1 function in preventing DNA hypermethylation.Nature plants · 2026Article
- DNA methylation around transcription start sites is not globally associated with transcription in the grain of natural and synthetic hexaploid wheat.BMC plant biology · 2026Article
- The mirage of DNA methylation in transcriptional regulation of plants.The plant genome · 2026Review
- Genome-wide profiling and functional characterization of N4-acetyldeoxycytosine reveals conserved epigenetic roles in rice and Arabidopsis.BMC genomics · 2026Article
- Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation.bioRxiv : the preprint server for biology · 2026Article
- Plant-specific function of H3K9me3 as a permissive chromatin mark during Arabidopsis seed germination.Frontiers in plant science · 2026Article
- Bivalent Histone Modifications Orchestrate Temporal Regulation of Glucosinolate Biosynthesis During Wound-Induced Stress Responses in Arabidopsis.Plant, cell & environment · 2026Article
- Multifactorial and multiplexed epigenomic profiling of five DNA modifications in plants with mDIP-seq.Science China. Life sciences · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- A chromatin-linked CPL2-PHD2/3 module sustains multiple DNA methylation pathways and Polycomb silencing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The arabidopsis GyraseB3 contributes to transposon silencing by promoting histone deacetylation.Nucleic acids research · 2025Article
- Genome-wide profiling and functional study of short N-terminal H2B variants in Arabidopsis.Journal of advanced research · 2025Article
- Dynamic changes in DNA methylation play a regulatory role in gene expression during the formation of callus from immature barley embryos.BMC plant biology · 2025Article
- Article
- Epigenetic gene regulation in plants and its potential applications in crop improvement.Nature reviews. Molecular cell biology · 2025Review
- DNMT3a promotes LUAD cell proliferation and metastasis by activating the HDAC7 signalling pathway.International journal of biological sciences · 2025Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt is challenging to determine the effect of DNA methylation on the epigenetic landscape and the function in higher organisms due to the lack of DNA methylation-free mutants.
resultsHere, the analysis of a recently generated Arabidopsis mutant completely devoid of DNA methylation reveals that DNA methylation underpins the genome-wide landscape of histone modifications. Complete loss of DNA methylation causes an upheaval of the histone modification landscape, including complete loss of H3K9me2 and widespread redistribution of active and H3K27me3 histone marks, mostly owing to the role of DNA methylation in initiating H3K9me2 deposition and excluding active marks and repressive mark H3K27me3; CG and non-CG methylation can act independently at some genomic regions while they act cooperatively at many other regions. The transcriptional reprogramming upon loss of all DNA methylation correlates with the extensive redistribution or switches of the examined histone modifications. Histone modifications retained or gained in the DNA methylation-free mutant serve as DNA methylation-independent transcriptional regulatory signals: active marks promote genome transcription, whereas the repressive mark H3K27me3 compensates for the lack of DNA hypermethylation/H3K9me2 at multiple transposon families.
conclusionsOur results show that an intact DNA methylome constitutes the scaffolding of the epigenomic landscape in Arabidopsis and is critical for controlled genome transcription and ultimately for proper growth and development.
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