使用 Illumina MethylationEPIC BeadChip 微阵列区分主动和被动 DNA 去甲基化。
Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays.
机构信息
Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
出版信息
Methods Mol Biol. 2021;2272:97-140. doi: 10.1007/978-1-0716-1294-1_7.
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.
基因组 DNA（CpG）中鸟嘌呤前的胞嘧啶核苷酸的 5-碳位是 DNA 甲基化（5mC）的常见靶点。DNA 甲基化的去除可以通过主动和被动机制发生。十-十一易位酶（TET）逐步氧化 5mC 生成 5-羟甲基胞嘧啶（5hmC）、5-甲酰胞嘧啶（5fC）和 5-羧基胞嘧啶（5caC）。在没有 DNA 甲基化维持的情况下，5mC 也可以通过连续的细胞分裂被动去除。在本章中，我们描述了将 TET 辅助亚硫酸氢盐（TAB）和氧化亚硫酸氢盐（OxBS）转化与 Illumina MethylationEPIC BeadChIP（EPIC 阵列）相结合的方法，并展示了如何使用这些技术来区分主动和被动 DNA 去甲基化。我们还描述了集成的生物信息学管道来促进这种分析。
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