ArticlePLoS genetics2019
Common alleles of CMT2 and NRPE1 are major determinants of CHH methylation variation in Arabidopsis thaliana.
Article in PLoS genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 101 citations in OpenAlex.
- A VIM2/4 deletion, and premature truncations of CMT2 and FBX5, drive DNA methylation changes after colonization of a novel habitat.Nature plants · 2026Article
- Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana.Nature plants · 2025Article
- Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations.Nature plants · 2025Article
- DNA Methylation in Rice: Mechanisms, Regulatory Roles, and Beyond.International journal of molecular sciences · 2025Review
- Beyond the Standard GWAS-A Guide for Plant Biologists.Plant & cell physiology · 2025Review
- Epigenetic variation in light of population genetic practice.Nature communications · 2025Review
- Article
- Substrate specificity and protein stability drive the divergence of plant-specific DNA methyltransferases.Science advances · 2024Article
- The evolutionary consequences of interactions between the epigenome, the genome and the environment.Evolutionary applications · 2024Review
- Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize.Plant physiology · 2024Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- Forces driving transposable element load variation during Arabidopsis range expansion.The Plant cell · 2024Article
- Population epigenetics: DNA methylation in the plant omics era.Plant physiology · 2024Article
- Epiallelic variation of non-coding RNA genes and their phenotypic consequences.Nature communications · 2024Article
- Transposon dynamics in the emerging oilseed crop Thlaspi arvense.PLoS genetics · 2024Article
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 2023Article
- Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development.Current opinion in plant biology · 2023Review
- New insights into the regulation of plant metabolism by O-acetylserine: sulfate and beyond.Journal of experimental botany · 2023Article
- Comparative genetic and epigenetic of the Sphagneticola trilobata (L.) Pruski from different regions in China.BMC plant biology · 2023Article
- On the causes of gene-body methylation variation in Arabidopsis thaliana.PLoS genetics · 2023Article
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA cytosine methylation is an epigenetic mark associated with silencing of transposable elements (TEs) and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have previously shown that CMT2 and NRPE1 are major determinants of genome-wide patterns of TE CHH methylation. Here we instead focus on CHH methylation of individual TEs and TE-families, allowing us to identify the pathways involved in CHH methylation simply from natural variation and confirm the associations by comparing them with mutant phenotypes. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected by CMT2 variation, but is strongly affected by variation at NRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection.
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