DNA methylation analysis in plants: review of computational tools and future perspectives

We provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data

Jimmy Omony; Thomas Nussbaumer; Ruben Gutzat


Scholarcy highlights

  • Methylation of cytosine at carbon position 5 is a hallmark of an epigenetic modification and 5-meC has been described as the 5th base of DNA
  • Computational tools are instrumental for bridging the gap between mapping of sequenced reads, the accurate prediction of methylated sites, and their statistical analysis this effort is hampered by variations in the size of epigenomic marks and the complexity associated with normalizing peaks
  • Most computational tools for analyzing epigenomic data perform well for datasets from organisms with a genome size that is smaller than the human genome
  • For much larger and complex genomes, more computational resources are required and the genome structure and repetitive nature of the genome has to be taken into consideration during mapping to a reference genome
  • This is demonstrated in our example where we compared the mapping efficiency for Arabidopsis and a wheat chromosome; the complexity in genome structure, the presence of transposable elements, and the lack of consistent gene annotations for some plants remain a major obstacle to advancing epigenetic research

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