ArticleGenome research2016
DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity.
Article in Genome research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon.Genetics · 2024Article
- Single-cell multi-omics sequencing of human spermatogenesis reveals a DNA demethylation event associated with male meiotic recombination.Nature cell biology · 2023Article
- The Underlying Nature of Epigenetic Variation: Origin, Establishment, and Regulatory Function of Plant Epialleles.International journal of molecular sciences · 2021Review
- Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon.Genome biology and evolution · 2020Article
- Genetic and Methylome Variation in TurkishInternational journal of molecular sciences · 2020Article
- The impact of transposable elements on tomato diversity.Nature communications · 2020Article
- DNA methylation analysis in plants: review of computational tools and future perspectives.Briefings in bioinformatics · 2020Review
- Extending the Genotype inG3 (Bethesda, Md.) · 2020Article
- HOME: a histogram based machine learning approach for effective identification of differentially methylated regions.BMC bioinformatics · 2019Article
- Hidden variation in polyploid wheat drives local adaptation.Genome research · 2018Article
- Single-cell multi-omics sequencing of human early embryos.Nature cell biology · 2018Article
- Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon.Genome biology and evolution · 2018Article
- siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass.Biotechnology for biofuels · 2018Article
- The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress.Plant physiology · 2017Article
- Exploiting induced and natural epigenetic variation for crop improvement.Nature reviews. Genetics · 2017Review
- Proximal methylation features associated with nonrandom changes in gene body methylation.Genome biology · 2017Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.
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