ArticleGenome research2009
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 149 papers.
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Who cites it
149 citing papers in PubMed, 282 citations in OpenAlex.
- The methylome in females with adolescent Conduct Disorder: Neural pathomechanisms and environmental risk factors.PloS one · 2022Trial
- Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain.bioRxiv : the preprint server for biology · 2026Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Machine Learning Analysis of the Impact of Silver Nitrate and Silver Nanoparticles on Wheat (Plants (Basel, Switzerland) · 2023Article
- Cost-effective DNA methylation profiling by FML-seq.Life science alliance · 2023Article
- Cost-effective DNA methylation profiling by FML-seq.bioRxiv : the preprint server for biology · 2023Article
- Technologies and applications of single-cell DNA methylation sequencing.Theranostics · 2023Review
- Advances in liquid biopsy in neuroblastoma.Fundamental research · 2022Review
- Effects of Zinc, Copper and Iron Oxide Nanoparticles on Induced DNA Methylation, Genomic Instability and LTR Retrotransposon Polymorphism in Wheat (Plants (Basel, Switzerland) · 2022Article
- Epigenomic insight of lingonberry and health-promoting traits during micropropagation.Scientific reports · 2022Article
- ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells.Database : the journal of biological databases and curation · 2022Article
- Cell-free DNA technologies for the analysis of brain cancer.British journal of cancer · 2022Review
- Glutathione and copper ions as critical factors of green plant regeneration efficiency of triticaleFrontiers in plant science · 2022Article
- Z-DNA as a Tool for Nuclease-Free DNA Methyltransferase Assay.International journal of molecular sciences · 2021Article
- Inhibition of the H3K27 demethylase UTX enhances the epigenetic silencing of HIV proviruses and induces HIV-1 DNA hypermethylation but fails to permanently block HIV reactivation.PLoS pathogens · 2021Article
- Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System.International journal of molecular sciences · 2021Review
- Introduction to Single-Cell DNA Methylation Profiling Methods.Biomolecules · 2021Review
- Performance comparison: exome sequencing as a single test replacing Sanger sequencing.Molecular genetics and genomics : MGG · 2021Article
- Simplified MethylRAD Sequencing to Detect Changes in DNA Methylation at Enhancer Elements in Differentiating Embryonic Stem Cells.Epigenomes · 2020Article
- Cell Mechanics in Embryoid Bodies.Cells · 2020Review
89 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
15 authors at 4 institutions in 1 country.
Funding
Abstract
To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives, and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2%-11%). Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation. Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains, and low density CpG promoters (LCPs), suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation. Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs. Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.
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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.