@inbook{146667343f7c412991a9eae4149db043,
title = "Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays",
abstract = "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.",
keywords = "Active demethylation, DNA hydroxymethylation, DNA methylation, DNMTs, Epigenetics, Illumina MethylationEPIC BeadChip, Oxidative bisulfite (OxBS), Passive demethylation, TETs, Tet-assisted bisulfite (TAB)",
author = "Tiedemann, {Rochelle L.} and Eden, {Hope E.} and Zhijun Huang and Robertson, {Keith D.} and Rothbart, {Scott B.}",
note = "Funding Information: This work was supported in part by grants from the American Cancer Society—Michigan Cancer Research Fund to R.L.T. (PF-16-245-01-DMC) and the National Institutes of Health to S.B.R. (R35GM124736). We also acknowledge Julie Koeman and Marie Adams from the Van Andel Institute Genomics Core for their expertise with OxBS treatments and processing of the EPIC arrays. Finally, we would like to thank Dr. Alison Bernstein at Michigan State University for her guidance on processing OxBS array data. Publisher Copyright: {\textcopyright} 2021, Springer Science+Business Media, LLC, part of Springer Nature.",
year = "2021",
doi = "10.1007/978-1-0716-1294-1_7",
language = "English (US)",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "97--140",
booktitle = "Methods in Molecular Biology",
}