Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays

Rochelle L. Tiedemann, Hope E. Eden, Zhijun Huang, Keith D. Robertson, Scott B. Rothbart

Research output: Chapter in Book/Report/Conference proceedingChapter


The 5-carbon positions on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). DNA methylation removal can occur through both active and passive mechanisms. Ten-eleven translocation enzymes (TETs) oxidize 5mC in a stepwise manner to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. In this chapter, we describe approaches that couple TET-assisted bisulfite (TAB) and oxidative bisulfite (OxBS) conversion to the Illumina MethylationEPIC BeadChIP (EPIC array) and show how these technologies can be used to distinguish active versus passive DNA demethylation. We also describe integrative bioinformatics pipelines to facilitate this analysis.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages44
StatePublished - 2021

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • Active demethylation
  • DNA hydroxymethylation
  • DNA methylation
  • DNMTs
  • Epigenetics
  • Illumina MethylationEPIC BeadChip
  • Oxidative bisulfite (OxBS)
  • Passive demethylation
  • TETs
  • Tet-assisted bisulfite (TAB)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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