ArticleMethods in molecular biology (Clifton, N.J.)2021
Analysis of Plant DNA Methylation Profiles Using R.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 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
3 citing papers in PubMed, 8 citations in OpenAlex.
- Gene body methylation buffers noise in gene expression in plants.Nucleic acids research · 2026Article
- Developmentally regulated generation of a systemic signal for long-lasting defence priming in tomato.The New phytologist · 2025Article
- Long-Lasting Defence Priming by β-Aminobutyric Acid in Tomato Is Marked by Genome-Wide Changes in DNA Methylation.Frontiers in plant science · 2022Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is a transgenerational stable epigenetic modification able to regulate gene expression and genome stability. The analysis of DNA methylation by genome-wide bisulfite sequencing become the main genomic approach to study epigenetics in many organisms; leading to standardization of the alignment and methylation call procedures. However, subsequent steps of the computational analysis should be tailored to the biological questions and the organisms used. Since most bioinformatics tools designed for epigenetic studies are built using mammalian models, they are potentially unsuitable for organisms with substantially different epigenetic regulation, such as plants. Therefore, in this chapter we propose a computational workflow for the analysis, visualization, and interpretation of data obtained from alignment of whole genome bisulfite sequencing of plant samples. Using almost exclusively the R working environment we will examine in depth how to tackle some plant-related issues during epigenetic analysis.
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Registered trials
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