ArticleEpigenetics2022
Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons.
Article in Epigenetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
What it found
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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
79 citing papers in PubMed, 1 synthesis or guideline pooled it, 58 citations in OpenAlex.
- Schizophrenia is associated with altered DNA methylation variance.Molecular psychiatry · 2025Pooled it
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- Mapping ovarian cellular and molecular landscape across the lifespan of women: a scoping review.Human reproduction update · 2026Article
- CRISPR technologies for detecting DNA and RNA methylation: Mechanisms, platforms, and translational opportunities.Bioengineering & translational medicine · 2026Review
- Dose-Dependent Genome-Wide DNA Methylation Remodeling by Metformin Modulates Doxorubicin Sensitivity in Cardiac Cells.Epigenomes · 2026Article
- The potential of methylation signal detection in eDNA toward functional ecological monitoring.Communications biology · 2026Review
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- cyberDMR: accurate and robust identification of differentially methylated regions from WGS-derived methylomes.BMC biology · 2026Article
- APOL1 risk genotypes influence DNA methylation across multiple genomic elements in APOL1-APOL4- MYH9 region in African Americans.Clinical epigenetics · 2026Article
- Construction of a DNA Methylation Map of Argali Hybrid Sheep During Mo Infection.Microorganisms · 2026Article
- The Great Potential of DNA Methylation in Triple-Negative Breast Cancer: From Biological Basics to Clinical Application.Biomedicines · 2026Review
- Benchmarking of methods to analyse data derived from GBS-MeDIP.BMC bioinformatics · 2026Article
- Methods for Investigating the Sperm Epigenome.Advances in experimental medicine and biology · 2026Review
- Estimation of DNA Methylation in Wheat Using Reverse Phase Ultra-High-Performance Liquid Chromatography Coupled with Mass Spectrometry During Leaf Rust Pathogenesis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Weighted epigenetic site correlation network analysis of chemotherapy impacts on osteosarcoma cancer survivors' male fertility, sperm, and endocrine parameters.Environmental epigenetics · 2026Article
- Promoter hypomethylation ofFrontiers in genetics · 2026Article
- Whole-Genome Methylation Analysis of Female, Male, and Neomale Northern Pike (Animals : an open access journal from MDPI · 2025Article
- Review
- Epigenetic effects of Qixiong Formula on sperm DNA methylation in a rat model of asthenozoospermia.Translational andrology and urology · 2025Article
- ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering.bioRxiv : the preprint server for biology · 2025Article
19 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 at 1 institution in 1 country.
Funding
Abstract
Genome-wide DNA methylation analysis is one of the most common epigenetic processes analysed for genome characterization and differential DNA methylation assessment. Previous genome-wide analysis has suggested an important variable in DNA methylation methods involves CpG density. The current study was designed to investigate the CpG density in a variety of different species genomes and correlate this to various DNA methylation analysis data sets. The majority of all genomes had >90% of the genome in the low density 1-3 CpG/100 bp category, while <10% of the genome was in the higher density >5 CpG/100 bp category. Similar observations with human, rat, bird, and fish genomes were observed. The methylated DNA immunoprecipitation (MeDIP) procedure uses the anti-5-methylcytosine antibody immunoprecipitation followed by next-generation sequencing (MeDIP-Seq). The MeDIP procedure is biased to lower CpG density of <5 CpG/100 bp, which corresponds to >95% of the genome. The reduced representation bisulphite (RRBS) protocol generally identifies DMRs in higher CpG density regions of ≥3 CpG/100 bp which corresponds to approximately 20% of the genome. The whole-genome bisulphite (WGBS) analyses resulted in higher CpG densities, often greater than 10 CpG/100bp. WGBS generally identifies ≥2 CpG/100bp, which corresponds to approximately 50% of the genome. Limitations and potential optimization approaches for each method are discussed. None of the procedures can provide complete genome-wide assessment of the genome, but MeDIP-Seq provides coverage of the highest percentage. Observations demonstrate that CpG density is a critical variable in DNA methylation analysis, and different molecular techniques focus on distinct genomic regions.
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What Socratic holds
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 Socratic graph.