ArticleNucleic acids research2016
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 2 of them syntheses that pooled it.
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Who cites it
36 citing papers in PubMed, 2 syntheses or guidelines pooled it, 83 citations in OpenAlex.
- DNA methylation in monozygotic twins discordant for acute lymphoblastic leukemia: a case report and systematic review.Clinical epigenetics · 2025Pooled it
- Prenatal medication exposure and epigenetic outcomes: a systematic literature review and recommendations for prenatal pharmacoepigenetic studies.Epigenetics · 2022Pooled it
- Recurrent mechanisms of biallelic epigenetic inactivation reveal new putative tumour suppressor genes in prostate cancer.Nature communications · 2026Article
- metileneNature communications · 2026Article
- cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers.Genomics, proteomics & bioinformatics · 2026Article
- Pan-cancer differentially methylated regions are promising biomarkers for non-invasive diagnosis in multiple cancers.iScience · 2026Article
- Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA.Genome biology · 2024Article
- HBCR_DMR: A Hybrid Method Based on Beta-Binomial Bayesian Hierarchical Model and Combination of Ranking Method to Detect Differential Methylation Regions in Bisulfite Sequencing Data.Journal of personalized medicine · 2024Article
- MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.Nucleic acids research · 2024Article
- Cancer signature ensemble integrating cfDNA methylation, copy number, and fragmentation facilitates multi-cancer early detection.Experimental & molecular medicine · 2023Article
- Article
- Integrated chromatin accessibility and DNA methylation analysis to reveal the critical epigenetic modification and regulatory mechanism in gonadal differentiation of the sequentially hermaphroditic fish, Monopterus albus.Biology of sex differences · 2022Article
- Association between cancer genes and germ layer specificity.Medical oncology (Northwood, London, England) · 2022Article
- A multi-tissue atlas of regulatory variants in cattle.Nature genetics · 2022Article
- Epigenetic control of ataxin-1 in multiple sclerosis.Annals of clinical and translational neurology · 2022Article
- Whole-genome bisulfite sequencing analysis of circulating tumour DNA for the detection and molecular classification of cancer.Clinical and translational medicine · 2022Article
- Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation.Nature metabolism · 2022Article
- DiseaseMeth version 3.0: a major expansion and update of the human disease methylation database.Nucleic acids research · 2022Article
- DNA methylation signatures of adolescent victimization: analysis of a longitudinal monozygotic twin sample.Epigenetics · 2021Article
- Hypermethylation and global remodelling of DNA methylation is associated with acquired cisplatin resistance in testicular germ cell tumours.Epigenetics · 2021Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation.
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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.