ReviewEpigenetics & chromatin2016
Profiling genome-wide DNA methylation.
Review in Epigenetics & chromatin, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
161 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- The applications of DNA methylation as a biomarker in kidney transplantation: a systematic review.Clinical epigenetics · 2022Pooled it
- Epigenetic alterations induced by genotoxic occupational and environmental human chemical carcinogens: An update of a systematic literature review.Mutation research. Reviews in mutation researchPooled it
- Tumor and serum DNA methylation in women receiving preoperative chemotherapy with or without vorinostat in TBCRC008.Breast cancer research and treatment · 2018Trial
- Whole-genome 5-hydroxymethylation profiling of human neurons for regulatory and biological insight.Epigenetics & chromatin · 2026Article
- From epigenetic mark detection to rational design of epigenetic editing strategies.Molecular therapy. Advances · 2026Review
- The Impact of Nutrition on DNA Methylation: Methodological Challenges in Understanding Cause and Effect.Nutrients · 2026Review
- Methylation biomarkers in non-regressive cervical intraepithelial neoplasia grade 2 lesions: an epigenome wide association study.British journal of cancer · 2026Article
- Uncovering alterations in cancer epigenetics via trans-dimensional Markov chain Monte Carlo and hidden Markov models.Journal of the Royal Statistical Society. Series C, Applied statistics · 2026Article
- Estimating population structure using epigenome-wide methylation data.Briefings in bioinformatics · 2026Article
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis.Bio-protocol · 2025Article
- Transgenerational diabetogenic effects of preconception exposure to inorganic arsenic in C57BL/6 mice are associated with dysregulation of DNA methylation and gene expression in G1 and G2 offspring.Archives of toxicology · 2025Article
- Review
- Estimating population structure using epigenome-wide methylation data.medRxiv : the preprint server for health sciences · 2025Article
- Unleashing the potential of urine DNA methylation detection: Advancements in biomarkers, clinical applications, and emerging technologies.Current urology · 2025Article
- A comprehensive guide to genomeZhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences · 2025Review
- Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics.Molecular ecology resources · 2025Article
- Methylation risk score of C-reactive protein associates sleep health with related health outcomes.Communications biology · 2025Article
- Molecular regulation of whole genome DNA methylation in heat stress response of dairy cows.BMC genomics · 2025Article
- Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia.International journal of molecular sciences · 2025Review
101 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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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.