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Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

ABSTRACT: Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

PROVIDER: PRJNA606056 | ENA |

REPOSITORIES: ENA

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Distinguishing active versus passive DNA demethylation using Illumina MethylationEPIC BeadChip microarrays

Project description:The 5-carbon position on cytosine nucleotides preceding guanines in genomic DNA (CpG) are common targets for DNA methylation (5mC). Genomic locations enriched for 5mC contribute to the regulation of chromatin structure and gene expression. While largely stable, massive waves of DNA demethylation are observed in key developmental windows in mammals. Additionally, DNA methylation is therapeutically targeted in cancer via DNA methyltransferase inhibition, in part to reverse abnormal silencing of tumor suppressor genes. 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). These oxidized cytosine forms have reported function in gene regulation and also serve as intermediates in an active 5mC removal process that involves the base excision repair pathway. 5mC can also be removed passively through sequential cell divisions in the absence of DNA methylation maintenance. Distinguishing active versus passive 5mC removal on a genome-wide scale remains a challenge. 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.

2021-01-31 | GSE145113 | GEO

Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays.

Project description: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.

| S-EPMC8265207 | biostudies-literature

Evaluating The Infinium Human MethylationEPIC v2 BeadChip

Project description:Evaluating The Infinium Human MethylationEPIC v2 BeadChip

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Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).

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Project description:We conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility.

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Project description:Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

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Illumina Infinium MethylationEPIC BeadChip (850k) data of germ cell tumor-related somatic-type maligancies

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of germ cell tumor related somati-type malignancies (STM), i. e. adenocarcinomas and rhabdomyosarcomas. As controls, yolk-sac tumors and teratoma without STM population were included.

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Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]

Project description:We performed a critical evaluation of the new Infinium MethylationEPIC BeadChip microarray. EPIC covers over 850,000 CpG sites, including >90% of the CpGs from the HumanMethylation450 (HM450) BeadChip and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58% of FANTOM5 enhancers, only 7% distal and 27% proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and whole-genome bisulphite sequencing data (WGBS) show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform.

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Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of embryonal carcinoma cell lines NCCIT and 2102EP deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Three different NCCIT and 2102EP knock out clones were analyzed.

2021-08-01 | GSE176450 | GEO

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