ArticleGenome biology2013
DNA methylation dynamics during intestinal stem cell differentiation reveals enhancers driving gene expression in the villus.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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Who cites it
74 citing papers in PubMed, 1 synthesis or guideline pooled it, 118 citations in OpenAlex.
- Genome-wide association study identifies variation at 6q25.1 associated with survival in multiple myeloma.Nature communications · 2016Pooled it
- Current Status of Intestinal Stem Cell Research: Mechanisms, Intestinal Diseases, and Organoid Development.Cells · 2026Review
- Iron homeostasis and cell clonality drive cancer-associated intestinal DNA methylation drift in aging.Nature aging · 2025Article
- Epigenetic conservation infers that colorectal cancer progenitors retain the phenotypic plasticity of normal colon.Scientific reports · 2025Article
- Late-Life Short-Term Dietary Restriction Improves Intestinal Stem Cell Function and Alters Intestinal Stem Cell Deoxyribonucleic Acid Methylation in Mice.The Journal of nutrition · 2025Article
- H3K36 methylation regulates cell plasticity and regeneration in the intestinal epithelium.Nature cell biology · 2025Article
- Modeling DNA methyltransferase function to predict epigenetic correlation patterns in healthy and cancer cells.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Intestinal stem cells in intestinal homeostasis and colorectal tumorigenesis.Life medicine · 2024Review
- Dynamic RNA polymerase II occupancy drives differentiation of the intestine under the direction of HNF4.Cell reports · 2024Article
- The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer.Stem cells (Dayton, Ohio) · 2024Review
- Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4.bioRxiv : the preprint server for biology · 2023Article
- Retrospective analysis of enhancer activity and transcriptome history.Nature biotechnology · 2023Article
- Advanced Progression for the Heterogeneity and Homeostasis of Intestinal Stem Cells.Stem cell reviews and reports · 2023Review
- Identification of key modules and driving genes in nonalcoholic fatty liver disease by weighted gene co-expression network analysis.BMC genomics · 2023Article
- Intestinal stem cells and gut microbiota therapeutics: hype or hope?Frontiers in medicine · 2023Review
- Gut microbiota-stem cell niche crosstalk: A new territory for maintaining intestinal homeostasis.iMeta · 2022Review
- DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon.Nature communications · 2022Article
- Article
- Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential.NPJ Regenerative medicine · 2022Article
- Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues.Nature biotechnology · 2022Article
14 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundDNA methylation is of pivotal importance during development. Previous genome-wide studies identified numerous differentially methylated regions upon differentiation of stem cells, many of them associated with transcriptional start sites.
resultsWe present the first genome-wide, single-base-resolution view into DNA methylation dynamics during differentiation of a mammalian epithelial stem cell: the mouse small intestinal Lgr5+ stem cell. Very little change was observed at transcriptional start sites and our data suggest that differentiation-related genes are already primed for expression in the stem cell. Genome-wide, only 50 differentially methylated regions were identified. Almost all of these loci represent enhancers driving gene expression in the differentiated part of the small intestine. Finally, we show that binding of the transcription factor Tcf4 correlates with hypo-methylation and demonstrate that Tcf4 is one of the factors contributing to formation of differentially methylated regions.
conclusionsOur results reveal limited DNA methylation dynamics during small intestine stem cell differentiation and an impact of transcription factor binding on shaping the DNA methylation landscape during differentiation of stem cells in vivo.
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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.