ArticleBMC genomics2015
DNA methylation and gene expression in Mimulus guttatus.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
- Variations inGenes · 2023Article
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- Exploiting Epigenetic Variations for Crop Disease Resistance Improvement.Frontiers in plant science · 2021Review
- On the Use of Blood Samples for Measuring DNA Methylation in Ecological Epigenetic Studies.Integrative and comparative biology · 2020Review
- Article
- Epigenetics: possible applications in climate-smart crop breeding.Journal of experimental botany · 2020Review
- Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees.Epigenomes · 2020Article
- Empirical patterns of environmental variation favor adaptive transgenerational plasticity.Ecology and evolution · 2020Article
- Transgenerational effects of parental light environment on progeny competitive performance and lifetime fitness.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Parental experience modifies the Mimulus methylome.BMC genomics · 2018Article
- The DNA Methylome and Association of Differentially Methylated Regions with Differential Gene Expression during Heat Stress inInternational journal of molecular sciences · 2018Article
- Context-Dependent Developmental Effects of Parental Shade Versus Sun Are Mediated by DNA Methylation.Frontiers in plant science · 2018Article
- Transgenerational effects alter plant defence and resistance in nature.Journal of evolutionary biology · 2017Article
- Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.BMC genomics · 2017Article
- Putting DNA methylation in context: from genomes to gene expression in plants.Biochimica et biophysica acta. Gene regulatory mechanisms · 2017Review
- Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing.Nature communications · 2016Article
- Genome-Wide Differences in DNA Methylation Changes in Two Contrasting Rice Genotypes in Response to Drought Conditions.Frontiers in plant science · 2016Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThe presence of methyl groups on cytosine nucleotides across an organism's genome (methylation) is a major regulator of genome stability, crossing over, and gene regulation. The capacity for DNA methylation to be altered by environmental conditions, and potentially passed between generations, makes it a prime candidate for transgenerational epigenetic inheritance. Here we conduct the first analysis of the Mimulus guttatus methylome, with a focus on the relationship between DNA methylation and gene expression.
resultsWe present a whole genome methylome for the inbred line Iron Mountain 62 (IM62). DNA methylation varies across chromosomes, genomic regions, and genes. We develop a model that predicts gene expression based on DNA methylation (R(2) = 0.2). Post hoc analysis of this model confirms prior relationships, and identifies novel relationships between methylation and gene expression. Additionally, we find that DNA methylation is significantly depleted near gene transcriptional start sites, which may explain the recently discovered elevated rate of recombination in these same regions.
conclusionsThe establishment here of a reference methylome will be a useful resource for the continued advancement of M. guttatus as a model system. Using a model-based approach, we demonstrate that methylation patterns are an important predictor of variation in gene expression. This model provides a novel approach for differential methylation analysis that generates distinct and testable hypotheses regarding gene expression.
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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.