ArticlePloS one2020
A cost-effective approach to DNA methylation detection by Methyl Sensitive DArT sequencing.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 22 citations in OpenAlex.
- Repeatome Dynamics and Sex Chromosome Differentiation in the XY and XYInternational journal of molecular sciences · 2025Article
- DNA Methylation Changes Reflect Aluminum Stress in Triticale and Epigenetic Control of the Trait.International journal of molecular sciences · 2025Article
- β-glucans, SAM, and GSH fluctuations in barley anther tissue culture conditions affect regenerants' DNA methylation and GPRE.BMC plant biology · 2024Article
- Unravelling DNA methylation dynamics during developmental stages in Quercus ilex subsp. ballota [Desf.] Samp.BMC plant biology · 2024Article
- Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat (Plants (Basel, Switzerland) · 2023Article
- Epigenomics in stress tolerance of plants under the climate change.Molecular biology reports · 2023Review
- Effects of Zinc, Copper and Iron Oxide Nanoparticles on Induced DNA Methylation, Genomic Instability and LTR Retrotransposon Polymorphism in Wheat (Plants (Basel, Switzerland) · 2022Article
- Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine.Diagnostics (Basel, Switzerland) · 2022Review
- Glutathione and copper ions as critical factors of green plant regeneration efficiency of triticaleFrontiers in plant science · 2022Article
- Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions.Frontiers in cell and developmental biology · 2022Review
- Article
- Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System.International journal of molecular sciences · 2021Review
- Challenges and Perspectives in the Epigenetics of Climate Change-Induced Forests Decline.Frontiers in plant science · 2021Review
- Epigenetic Analysis through MSAP-NGS Coupled Technology: The Case Study of White Poplar Monoclonal Populations/Stands.International journal of molecular sciences · 2020Article
- Copper Ions Induce DNA Sequence Variation in Zygotic Embryo Culture-Derived Barley Regenerants.Frontiers in plant science · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).
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