ArticleGenome biology2018
A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- EpiATLAS - a reference for human epigenomic research.bioRxiv : the preprint server for biology · 2026Article
- Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation.Nucleic acids research · 2026Article
- Flanking DNA sequences determine DNA methylation maintenance in proliferation, cancer and aging.bioRxiv : the preprint server for biology · 2026Article
- DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A.PLoS genetics · 2026Article
- Multi-omic analysis of hepatocellular carcinoma reveals aberrant cis-regulatory changes and dysregulated retrotransposons with prognostic potential.Communications biology · 2025Article
- Interrogating subclonal heterogeneity of liver cancer with single-cell multi-omics analysis.Scientific reports · 2025Article
- Epigenetically Controlled ZEB2 Expression Promotes the Cytotoxic Potential of CMV-Specific CD8European journal of immunology · 2025Article
- Genome-wide profiling of unmodified DNA using methyltransferase-directed tagging and enrichment.Cell reports methods · 2025Article
- Structural DNMT-nucleosome contacts are related to DNA methylation patterns.Epigenetics & chromatin · 2025Article
- Direct genetic transformation bypasses tumor-associated DNA methylation alterations.Genome biology · 2025Article
- Comprehensive analysis of H3K27me3 LOCKs under different DNA methylation contexts reveal epigenetic redistribution in tumorigenesis.Epigenetics & chromatin · 2025Article
- DNA methylation in mammalian development and disease.Nature reviews. Genetics · 2025Review
- On correlative and causal links of replicative epimutations.Trends in genetics : TIG · 2025Review
- Methylomes of human CD4 and CD8 memory T lymphocytes reveal tissue-specific epigenetic signatures for maintenance and recall function.Immunity & inflammation · 2025Article
- UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation.Nucleic acids research · 2024Article
- MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets.Nucleic acids research · 2024Article
- Epigenetic dynamics of partially methylated domains in human placenta and trophoblast stem cells.BMC genomics · 2024Article
- Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes.Life science alliance · 2024Article
- CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses.Science advances · 2024Article
- TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells.Nature aging · 2023Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
15 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPartially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them.
resultsPartially methylated domains are present in up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Each cell type has a distinct set of partially methylated domains, and genes expressed in such domains show a strong cell type effect. The methylation level varies between cell types with a more pronounced effect in differentiating and replicating cells. The lowest level of methylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA methylation within partially methylated domains tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expression. Characteristic combinations of heterochromatic signatures in partially methylated domains are linked to domains of early and middle S-phase and late S-G2 phases of DNA replication.
conclusionsPartially methylated domains are prominent signatures of long-range epigenomic organization. Integrative analysis identifies them as important general, lineage- and cell type-specific topological features. Changes in partially methylated domains are hallmarks of cell differentiation, with decreased methylation levels and increased heterochromatic marks being linked to enhanced cell proliferation. In combination with broad histone marks, partially methylated domains demarcate distinct domains of late DNA replication.
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