ArticleScientific reports2017
Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
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- SOPA and SIMPA: normalized single-sample integrated multiomics pathway analysis of tumor heterogeneity in solid cancers.Briefings in bioinformatics · 2026Article
- Genome-wide analysis of strand-specific transcription and DNA methylation inFrontiers in microbiology · 2026Article
- Tracing the Origin of Cell-Free DNA Molecules through Tissue-Specific Epigenetic Signatures.Diagnostics (Basel, Switzerland) · 2022Review
- Gene Set Enrichment Analysis Detected Immune Cell-Related Pathways Associated with Primary Sclerosing Cholangitis.BioMed research international · 2022Article
- The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals.Mammalian genome : official journal of the International Mammalian Genome Society · 2021Review
- Epigenome-scale comparison of DNA methylation between blood leukocytes and bronchial epithelial cells.Epigenomics · 2021Article
- Deconvolution of cellular subsets in human tissue based on targeted DNA methylation analysis at individual CpG sites.BMC biology · 2020Article
- A Novel Early-Stage Lung Adenocarcinoma Prognostic Model Based on Feature Selection With Orthogonal Regression.Frontiers in cell and developmental biology · 2020Article
- HMST-Seq-Analyzer: A new python tool for differential methylation and hydroxymethylation analysis in various DNA methylation sequencing data.Computational and structural biotechnology journal · 2020Article
- Review
- HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation.Genomics, proteomics & bioinformatics · 2018Article
- Inference of Crosstalk Effects between DNA Methylation and lncRNA Regulation in NSCLC.BioMed research international · 2018Article
- Spurious transcription and its impact on cell function.Transcription · 2018Article
- Review
- Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage.EpigeneticsArticle
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Despite numerous studies done on understanding the role of DNA methylation, limited work has focused on systems integration of cell type-specific interplay between DNA methylation and gene transcription. Through a genome-wide analysis of DNA methylation across 19 cell types with T-47D as reference, we identified 106,252 cell type-specific differentially-methylated CpGs categorized into 7,537 differentially (46.6% hyper- and 53.4% hypo-) methylated regions. We found 44% promoter regions and 75% CpG islands were T-47D cell type-specific methylated. Pyrosequencing experiments validated the cell type-specific methylation across three benchmark cell lines. Interestingly, these DMRs overlapped with 1,145 known tumor suppressor genes. We then developed a Bayesian Gaussian Regression model to measure the relationship among DNA methylation, genomic segment distribution, differential gene expression and tumor suppressor gene status. The model uncovered that 3'UTR methylation has much less impact on transcriptional activity than other regions. Integration of DNA methylation and 82 transcription factor binding information across the 19 cell types suggested diverse interplay patterns between the two regulators. Our integrative analysis reveals cell type-specific and genomic region-dependent regulatory patterns and provides a perspective for integrating hundreds of various omics-seq data together.
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