Analysis of plant DNA methylation profiles using R

Marco Catoni, Nicolae Radu Zabet

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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.

Original languageEnglish
Pages (from-to)219-238
Number of pages20
JournalMethods in molecular biology
Publication statusPublished - 27 Apr 2021


  • Cytosine methylation
  • Plant epigenetics
  • ifferentially methylated regions


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