ArticleGenetics2021
Gene body methylation is under selection in Arabidopsis thaliana.
Article in Genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 41 citations in OpenAlex.
- Mapping genetic modifiers of epimutation rates identifies VIM2/4 as dosage-sensitive negative regulators of CG methylation maintenance.Nature plants · 2026Article
- Nonadditive gene expression and reduced homoeolog expression bias in an intraspecific hexaploid wheat hybrid.BMC plant biology · 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
- Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana.Genome biology · 2026Article
- Genome-wide and gene-specific DNA methylation across developmental stages in Pogonomyrmex californicus: A socially polymorphic ant.Insect molecular biology · 2026Article
- Adaptation beyond the DNA sequence.Nature plants · 2025Article
- Epigenetic regulation modulates seasonal temperature-dependent growth of soybean in southern China.Plant biotechnology journal · 2025Article
- Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations.Nature plants · 2025Article
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- Molecular mechanisms and biological functions of active DNA demethylation in plants.Epigenetics & chromatin · 2025Review
- Quantifying the Evolution of SNPs That Affect RNA Secondary Structure in Arabidopsis thaliana Genes.Molecular biology and evolution · 2025Article
- Methylomes Reveal Recent Evolutionary Changes in Populations of Two Plant Species.Genome biology and evolution · 2025Article
- The genomic and epigenomic landscapes of hemizygous genes across crops with contrasting reproductive systems.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Epigenetic variation in light of population genetic practice.Nature communications · 2025Review
- From juvenile to adult: investigating miRNAs, gene expression, and the juvenile cone in olive development.Frontiers in plant science · 2025Article
- Article
- Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms.Molecular biology and evolution · 2024Review
- Patterns of methylation and transcriptional plasticity during thermal acclimation in a reef-building coral.Evolutionary applications · 2024Article
- Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes.Horticulture research · 2024Article
- Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In plants, mammals and insects, some genes are methylated in the CG dinucleotide context, a phenomenon called gene body methylation (gbM). It has been controversial whether this phenomenon has any functional role. Here, we took advantage of the availability of 876 leaf methylomes in Arabidopsis thaliana to characterize the population frequency of methylation at the gene level and to estimate the site-frequency spectrum of allelic states. Using a population genetics model specifically designed for epigenetic data, we found that genes with ancestral gbM are under significant selection to remain methylated. Conversely, ancestrally unmethylated genes were under selection to remain unmethylated. Repeating the analyses at the level of individual cytosines confirmed these results. Estimated selection coefficients were small, on the order of 4 Nes = 1.4, which is similar to the magnitude of selection acting on codon usage. We also estimated that A. thaliana is losing gbM threefold more rapidly than gaining it, which could be due to a recent reduction in the efficacy of selection after a switch to selfing. Finally, we investigated the potential function of gbM through its link with gene expression. Across genes with polymorphic methylation states, the expression of gene body methylated alleles was consistently and significantly higher than unmethylated alleles. Although it is difficult to disentangle genetic from epigenetic effects, our work suggests that gbM has a small but measurable effect on fitness, perhaps due to its association to a phenotype-like gene expression.
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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.