ArticlePloS one2015
Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array).
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed, 55 citations in OpenAlex.
- Comparative validation of oxidative bisulfite sequencing (oxBS) and chemical-assisted pyridine borane sequencing (CAPS) protocols for locus-specific 5-hydroxymethylcytosine quantification.Epigenetics & chromatin · 2026Article
- Whole-Genome Bisulfite Sequencing Protocol for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution.Methods in molecular biology (Clifton, N.J.) · 2024Article
- DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse.Cell genomics · 2022Article
- Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays.Epigenomics · 2022Article
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Prenatal Lead (Pb) Exposure and Peripheral Blood DNA Methylation (5mC) and Hydroxymethylation (5hmC) in Mexican Adolescents from the ELEMENT Birth Cohort.Environmental health perspectives · 2021Article
- Genome-Wide DNA Methylation and Hydroxymethylation Changes Revealed Epigenetic Regulation of Neuromodulation and Myelination in Yak Hypothalamus.Frontiers in genetics · 2021Article
- Genome-wide characterization of 5-hydoxymethylcytosine in melanoma reveals major differences with nevus.Genes, chromosomes & cancer · 2020Article
- Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue.Epigenetics · 2020Article
- Targeting epigenetic mechanisms for chronic visceral pain: A valid approach for the development of novel therapeutics.Neurogastroenterology and motility · 2019Review
- Article
- Epigenetic Applications in Adverse Outcome Pathways and Environmental Risk Evaluation.Environmental health perspectives · 2018Article
- Species-Specific 5 mC and 5 hmC Genomic Landscapes Indicate Epigenetic Contribution to Human Brain Evolution.Frontiers in molecular neuroscience · 2018Article
- Air Pollution and the Epigenome: A Model Relationship for the Exploration of Toxicoepigenetics.Current opinion in toxicology · 2017Article
- Article
- Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA.Epigenetics & chromatin · 2017Article
- TET Methylcytosine Oxidases in T Cell and B Cell Development and Function.Frontiers in immunology · 2017Review
- Elevated 5hmC levels characterize DNA of the cerebellum in Parkinson's disease.NPJ Parkinson's disease · 2017Article
- oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA.Bioinformatics (Oxford, England) · 2016Article
- 5-Hydroxymethylcytosine localizes to enhancer elements and is associated with survival in glioblastoma patients.Nature communications · 2016Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
The Infinium 450K Methylation array is an established tool for measuring methylation. However, the bisulfite (BS) reaction commonly used with the 450K array cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). The oxidative-bisulfite assay disambiguates 5mC and 5hmC. We describe the use of oxBS in conjunction with the 450K array (oxBS-array) to analyse 5hmC/5mC in cerebellum DNA. The "methylation" level derived by the BS reaction is the combined level of 5mC and 5hmC at a given base, while the oxBS reaction gives the level of 5mC alone. The level of 5hmC is derived by subtracting the oxBS level from the BS level. Here we present an analysis method that distinguishes genuine positive levels of 5hmC at levels as low as 3%. We performed four replicates of the same sample of cerebellum and found a high level of reproducibility (average r for BS = 98.3, and average r for oxBS = 96.8). In total, 114,734 probes showed a significant positive measurement for 5hmC. The range at which we were able to distinguish 5hmC occupancy was between 3% and 42%. In order to investigate the effects of multiple replicates on 5hmC detection we also simulated fewer replicates and found that decreasing the number of replicates to two reduced the number of positive probes identified by > 50%. We validated our results using qPCR in conjunction with glucosylation of 5hmC sites followed by MspI digestion and we found good concordance with the array estimates (r = 0.94). This experiment provides a map of 5hmC in the cerebellum and a robust dataset for use as a standard in future 5hmC analyses. We also provide a novel method for validating the presence of 5hmC at low levels, and highlight some of the pitfalls associated with measuring 5hmC and 5mC.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.