Application of a low cost array-based technique — TAB-Array — for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells

Nazor, Kristopher L.; Boland, Michael J.; Bibikova, Marina; Klotzle, Brandy; Yu, Miao; Glenn-Pratola, Victoria; Schell, John P.; Coleman, R.L.; Cabral-da-Silva, Mauricio Castro; Schmidt, Ulrich; Peterson, Suzanne E.; He, Chuan; Loring, Jeanne F.; Fan, Jian‐Bing

doi:10.1016/j.ygeno.2014.08.014

Cited by 33 publications

(40 citation statements)

References 34 publications

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“…Highly active TET proteins are required for the efficient conversion of 5mC to 5caC (more than 96 %), or else the incomplete conversion of 5mC might lead to false identification as 5hmC sites [ 81 ]. Both oxidative bisulfite conversion and TET-assisted bisulfite conversion are compatible with microarray and sequencing platforms to generate the 5hmC methylation profile for a whole genome or targeted regions [ 82 ]. The relatively low levels of 5hmC and the subtraction step demand an increase in the sequencing coverage and the number of replicates.…”

Section: Experimental Techniques For Dna Methylation Profilingmentioning

confidence: 99%

Profiling genome-wide DNA methylation

Yong

Hsu

Chen

2016

Epigenetics & Chromatin

303

225

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DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques. The advances in microarray and sequencing technologies make genome-wide profiling possible at a single-nucleotide or even a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods. We first introduce the biological background of DNA methylation and its pattern in plants, animals and fungi. We present an overview of major experimental approaches to profiling genome-wide DNA methylation and hydroxymethylation and then extend to the single-cell methylome. To evaluate these methods, we outline their strengths and weaknesses and perform comparisons across the different platforms. Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples. Overall, this review provides researchers useful guidance for the selection of a profiling method suited to specific research questions.

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Section: Experimental Techniques For Dna Methylation Profilingmentioning

confidence: 99%

Profiling genome-wide DNA methylation

Yong

Hsu

Chen

2016

Epigenetics & Chromatin

303

225

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“…An emerging issue relates to the inability of sodium bisulfite conversion, which is the commonly used method for determination of 5-mC at single-base resolution, to distinguish 5-mC from its oxidative derivative 5-hydroxymethylcytosine (5-hmC) [ 131 ]. It has been reported that 5-hmC is enriched in intergenic regions, including LINE-1 elements and gene body regions [ 132 - 134 ]. In studies evaluating the association of DNA methylation and environmental chemicals using bisulfite conversion based methods for DNA methylation assessment, residual measurement error by 5-hmC content is, thus, possible.…”

Section: Reviewmentioning

confidence: 99%

Environmental chemicals and DNA methylation in adults: a systematic review of the epidemiologic evidence

et al. 2015

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Current evidence supports the notion that environmental exposures are associated with DNA-methylation and expression changes that can impact human health. Our objective was to conduct a systematic review of epidemiologic studies evaluating the association between environmental chemicals with DNA methylation levels in adults. After excluding arsenic, recently evaluated in a systematic review, we identified a total of 17 articles (6 on cadmium, 4 on lead, 2 on mercury, 1 on nickel, 1 on antimony, 1 on tungsten, 5 on persistent organic pollutants and perfluorinated compounds, 1 on bisphenol A, and 3 on polycyclic aromatic hydrocarbons). The selected articles reported quantitative methods to determine DNA methylation including immunocolorimetric assays for total content of genomic DNA methylation, and microarray technologies, methylation-specific quantitative PCR, Luminometric Methylation Assay (LUMA), and bisulfite pyrosequencing for DNA methylation content of genomic sites such as gene promoters, LINE-1, Alu elements, and others. Considering consistency, temporality, strength, dose-response relationship, and biological plausibility, we concluded that the current evidence is not sufficient to provide inference because differences across studies and limited samples sizes make it difficult to compare across studies and to evaluate sources of heterogeneity. Important questions for future research include the need for larger and longitudinal studies, the validation of findings, and the systematic evaluation of the dose-response relationships. Future studies should also consider the evaluation of epigenetic marks recently in the research spotlight such as DNA hydroxymethylation and the role of underlying genetic variants.Electronic supplementary materialThe online version of this article (doi:10.1186/s13148-015-0055-7) contains supplementary material, which is available to authorized users.

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“…Different from 5-mC, 5-hmC has an abundance within the genome 10-100-fold lower than that of 5-mC, and the abundances of 5-foC and 5-caC are about 40-1000-fold higher than that of 5-hmC [70][71][72]. These C modifications are a hot spot, and the analytical methods have been developed significantly, and mainly involve the application of LC, CE, bioaffinity or chemical derivatization, such as recombinant β-glucosyltransferase analysis [73], selective chemical labeling [74], combined glycosylation restriction analysis [75], and TAB-array [76].…”

Section: Discussionmentioning

confidence: 99%