ArticleNature communications2014
Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Decitabine-induced DNA methylation remodeling reveals targetable biological processes in gilthead seabream pituitary and liver explants.Epigenetics · 2025Article
- AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.Genomics, proteomics & bioinformatics · 2021Article
- Epigenetic Mechanisms of Paternal Stress in Offspring Development and Diseases.International journal of genomics · 2021Review
- Comparison of differential accessibility analysis strategies for ATAC-seq data.Scientific reports · 2020Article
- Review
- Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes.Scientific reports · 2019Article
- A20 and ABIN1 Suppression of a Keratinocyte Inflammatory Program with a Shared Single-Cell Expression Signature in Diverse Human Rashes.The Journal of investigative dermatology · 2019Article
- Epigenetic control in skin development, homeostasis and injury repair.Experimental dermatology · 2019Review
- Single-Cell Transcriptomics Reveals Spatial and Temporal Turnover of Keratinocyte Differentiation Regulators.Frontiers in genetics · 2019Article
- Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-β Signaling.Cell reports · 2018Article
- Heart morphogenesis gene regulatory networks revealed by temporal expression analysis.Development (Cambridge, England) · 2017Article
- Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.BMC genomics · 2017Article
- Intratumoral Heterogeneity of the Epigenome.Cancer cell · 2016Review
- Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome.G3 (Bethesda, Md.) · 2016Article
- Comparative transcriptome analysis of papilla and skin in the sea cucumber, Apostichopus japonicus.PeerJ · 2016Article
- Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos.Nature communications · 2015Article
- Article
- Cofunctional Subpathways Were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue.BioMed research international · 2015Article
Corrections and comments
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Authors and funding
15 authors at 5 institutions in 2 countries.
Funding
Abstract
Developmental history shapes the epigenome and biological function of differentiated cells. Epigenomic patterns have been broadly attributed to the three embryonic germ layers. Here we investigate how developmental origin influences epigenomes. We compare key epigenomes of cell types derived from surface ectoderm (SE), including keratinocytes and breast luminal and myoepithelial cells, against neural crest-derived melanocytes and mesoderm-derived dermal fibroblasts, to identify SE differentially methylated regions (SE-DMRs). DNA methylomes of neonatal keratinocytes share many more DMRs with adult breast luminal and myoepithelial cells than with melanocytes and fibroblasts from the same neonatal skin. This suggests that SE origin contributes to DNA methylation patterning, while shared skin tissue environment has limited effect on epidermal keratinocytes. Hypomethylated SE-DMRs are in proximity to genes with SE relevant functions. They are also enriched for enhancer- and promoter-associated histone modifications in SE-derived cells, and for binding motifs of transcription factors important in keratinocyte and mammary gland biology. Thus, epigenomic analysis of cell types with common developmental origin reveals an epigenetic signature that underlies a shared gene regulatory network.
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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.