ArticlePLoS genetics2016
Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
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Who cites it
59 citing papers in PubMed, 121 citations in OpenAlex.
- Response of DNA methylation and gene expression to light treatments in Norway spruce [Picea abies (L.) Karst.].BMC genomics · 2026Article
- Differential methylation analysis of floral buds between two morphs unravels the contributions of key genes to flowering time in heterodichogamousHorticulture research · 2026Article
- Regulation of gene expression by 5mC DNA methylation during the bolting process of cabbage (Frontiers in plant science · 2026Article
- Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.The Plant journal : for cell and molecular biology · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- Gene body methylation regulates gene expression and mediates phenotypic diversity in natural Arabidopsis populations.Nature plants · 2025Article
- The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing in Drosophila.Genome biology · 2025Article
- DNA methylation and hydroxymethylation combined with transcriptional profiling identify key regulators of hyperoxia-induced bronchopulmonary dysplasia.Clinical epigenetics · 2025Article
- Beyond the Standard GWAS-A Guide for Plant Biologists.Plant & cell physiology · 2025Review
- A modulatory role of CG methylation on gene expression in soybean implicates its potential utility in breeding.Plant biotechnology journal · 2025Article
- Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.Cell research · 2024Article
- Single-Base Methylome Analysis of Sweet Cherry (International journal of molecular sciences · 2024Article
- Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids.Life science alliance · 2024Article
- Article
- CG hypermethylation of theHorticulture research · 2023Article
- Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.Genome biology · 2022Article
- DNA hypermethylation promotes the flowering of orchardgrass during vernalization.Plant physiology · 2022Article
- Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes.PLoS genetics · 2022Article
- Species-specific chromatin landscape determines how transposable elements shape genome evolution.eLife · 2022Article
- Methylome and transcriptome analyses of three different degrees of albinism in apple seedlings.BMC genomics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
The extent to which epigenetic variation affects complex traits in natural populations is not known. We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A. thaliana accessions. Across individuals, expression was significantly associated with cis-methylation for hundreds of genes, and many of these associations remained significant after taking SNP effects into account. The pattern of correlations differed markedly between gene body methylation and transposable element methylation. The former was usually positively correlated with expression, and the latter usually negatively correlated, although exceptions were found in both cases. Finally, we developed graphical models of causality that adapt to a sample with heavy population structure, and used them to show that while methylation appears to affect gene expression more often than expression affects methylation, there is also strong support for both being independently controlled. In conclusion, although we find clear evidence for epigenetic regulation, both the number of loci affected and the magnitude of the effects appear to be small compared to the effect of SNPs.
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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.