ArticlePLoS genetics2011
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers, 2 of them syntheses 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
236 citing papers in PubMed, 2 syntheses or guidelines pooled it, 402 citations in OpenAlex.
- Active Demethylation of Non-CpG Moieties in Animals: A Neglected Research Area.International journal of molecular sciences · 2019Pooled it
- Incorporating DNA Methyltransferase Inhibitors (DNMTis) in the Treatment of Genitourinary Malignancies: A Systematic Review.Targeted oncology · 2018Pooled it
- Integration of polygenic risk with single cell methylation data using met-scDRS.Bioinformatics (Oxford, England) · 2026Article
- Apparent methylation of mitochondrial DNA in WGBS is dominated by technical artifacts.Epigenetics & chromatin · 2026Article
- Article
- NELFA supports naïve pluripotency and drives 8C-like state in human embryonic stem cells.Nature communications · 2026Article
- DNMT3A in cancer: from epigenetic writer to oncogenic driver.Clinical epigenetics · 2026Review
- Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana.Nature plants · 2025Article
- Do Glioma Cells Rewire Neural Circuits through Epigenetic Changes? DNA Methylation Analysis of Genes Involved in Neuron-Glioma Communication in the Human Frontal Cortex.Journal of molecular neuroscience : MN · 2025Article
- Reproductive Dysfunction and Testicular Epigenetic Alterations in Male Rats with Experimental Amebiasis: Evaluation of SPATA6 Methylation and Therapeutic Outcomes.Acta parasitologica · 2025Article
- Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression.Genome medicine · 2025Article
- Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.Brain and behavior · 2025Article
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
- Steroid hormone-mediated epigenetic programming during puberty: uncovering links to depression.Epigenomics · 2025Review
- Cryo-EM reveals evolutionarily conserved and distinct structural features of plant CG maintenance methyltransferase MET1.Nature communications · 2025Article
- Review
- Simultaneous RNA Sequencing and DNA Methylation Profiling Reveals Neural Mechanisms That Regulate Sensitive Period Behavioral Learning.Genes, brain, and behavior · 2025Article
- PlantDeepMeth: A Deep Learning Model for Predicting DNA Methylation States in Plants.Plants (Basel, Switzerland) · 2025Article
- Basic Epigenetic Mechanisms.Sub-cellular biochemistry · 2025Review
- DNA methylation in mammalian development and disease.Nature reviews. Genetics · 2025Review
176 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 2 countries.
Funding
Abstract
DNA methylation plays an important role in development and disease. The primary sites of DNA methylation in vertebrates are cytosines in the CpG dinucleotide context, which account for roughly three quarters of the total DNA methylation content in human and mouse cells. While the genomic distribution, inter-individual stability, and functional role of CpG methylation are reasonably well understood, little is known about DNA methylation targeting CpA, CpT, and CpC (non-CpG) dinucleotides. Here we report a comprehensive analysis of non-CpG methylation in 76 genome-scale DNA methylation maps across pluripotent and differentiated human cell types. We confirm non-CpG methylation to be predominantly present in pluripotent cell types and observe a decrease upon differentiation and near complete absence in various somatic cell types. Although no function has been assigned to it in pluripotency, our data highlight that non-CpG methylation patterns reappear upon iPS cell reprogramming. Intriguingly, the patterns are highly variable and show little conservation between different pluripotent cell lines. We find a strong correlation of non-CpG methylation and DNMT3 expression levels while showing statistical independence of non-CpG methylation from pluripotency associated gene expression. In line with these findings, we show that knockdown of DNMTA and DNMT3B in hESCs results in a global reduction of non-CpG methylation. Finally, non-CpG methylation appears to be spatially correlated with CpG methylation. In summary these results contribute further to our understanding of cytosine methylation patterns in human cells using a large representative sample set.
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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.