ArticlePloS one2016
CG Methylation Covaries with Differential Gene Expression between Leaf and Floral Bud Tissues of Brachypodium distachyon.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 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.
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Who cites it
15 citing papers in PubMed, 31 citations in OpenAlex.
- From juvenile to adult: investigating miRNAs, gene expression, and the juvenile cone in olive development.Frontiers in plant science · 2025Article
- Detection of De Novo Mutations by Sequencing Reduced Representation Libraries.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations.Genome biology and evolution · 2024Article
- CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation.Genome biology and evolution · 2021Article
- Genome-wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white-throated sparrows.Molecular ecology · 2021Article
- Article
- Genetic and Methylome Variation in TurkishInternational journal of molecular sciences · 2020Article
- Developmental Methylome of the Medicinal PlantInternational journal of molecular sciences · 2020Article
- Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat.The plant genome · 2020Article
- The transcriptome of zinc deficient maize roots and its relationship to DNA methylation loss.BMC plant biology · 2018Article
- Reproductive Long Intergenic Noncoding RNAs Exhibit Male Gamete Specificity and Polycomb Repressive Complex 2-Mediated Repression.Plant physiology · 2018Article
- Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea.Scientific reports · 2018Article
- Massive Loss of DNA Methylation in Nitrogen-, but Not in Phosphorus-DeficientFrontiers in plant science · 2018Article
- Insights into Epigenome Evolution from Animal and Plant Methylomes.Genome biology and evolution · 2017Article
- DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.Genome research · 2016Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
DNA methylation has the potential to influence plant growth and development through its influence on gene expression. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tissues and, if so, whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq) and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud) from the model grass species Brachypodium distachyon. Our first goal was to determine whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50%) false positive rates for the inference of differentially methylated sites (DMSs) and differentially methylated regions (DMRs). Comparing methylation to gene expression, we found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.
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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.