ArticleScientific reports2020
5-hydroxymethylcytosine and gene activity in mouse intestinal differentiation.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
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- Regulatory mechanisms and clinical implications of PIWI-interacting RNAs (piRNAs) in major digestive tract cancers.Cancer cell international · 2025Review
- Old mitochondria regulate niche renewal via α-ketoglutarate metabolism in stem cells.Nature metabolism · 2025Article
- Colorectal cancer progression to metastasis is associated with dynamic genome-wide biphasic 5-hydroxymethylcytosine accumulation.BMC biology · 2025Article
- TET3 regulates terminal cell differentiation at the metabolic level.Nature communications · 2024Article
- Alterations in DNA 5-hydroxymethylation patterns in the hippocampus of an experimental model of chronic epilepsy.Neurobiology of disease · 2024Article
- A hybrid residue based sequential encoding mechanism with XGBoost improved ensemble model for identifying 5-hydroxymethylcytosine modifications.Scientific reports · 2024Article
- Predicting gene expression state and prioritizing putative enhancers using 5hmC signal.Genome biology · 2024Article
- Sequence based model using deep neural network and hybrid features for identification of 5-hydroxymethylcytosine modification.Scientific reports · 2024Article
- Screening and identification of hub gene and differential gene and mutation sequence analysis of related genes in colorectal cancer based on bioinformatics analysis.Journal of gastrointestinal oncology · 2022Article
- Vitamin C epigenetically controls osteogenesis and bone mineralization.Nature communications · 2022Article
- The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome.Epigenetics · 2022Article
- The Epigenetics of Psychosis: A Structured Review with Representative Loci.Biomedicines · 2022Review
- Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors.Journal of biochemistry · 2022Article
- Effect of DNA modifications on the transition between canonical and non-canonical DNA structures in CpG islands during senescence.RSC advances · 2021Article
- ApcScientific reports · 2020Article
- Epigenetic regulation of intestinal stem cell differentiation.American journal of physiology. Gastrointestinal and liver physiology · 2020Review
- Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics.Analytical chemistry · 2020Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
Cytosine hydroxymethylation (5hmC) in mammalian DNA is the product of oxidation of methylated cytosines (5mC) by Ten-Eleven-Translocation (TET) enzymes. While it has been shown that the TETs influence 5mC metabolism, pluripotency and differentiation during early embryonic development, the functional relationship between gene expression and 5hmC in adult (somatic) stem cell differentiation is still unknown. Here we report that 5hmC levels undergo highly dynamic changes during adult stem cell differentiation from intestinal progenitors to differentiated intestinal epithelium. We profiled 5hmC and gene activity in purified mouse intestinal progenitors and differentiated progeny to identify 43425 differentially hydroxymethylated regions and 5325 differentially expressed genes. These differentially marked regions showed both losses and gains of 5hmC after differentiation, despite lower global levels of 5hmC in progenitor cells. In progenitors, 5hmC did not correlate with gene transcript levels, however, upon differentiation the global increase in 5hmC content showed an overall positive correlation with gene expression level as well as prominent associations with histone modifications that typify active genes and enhancer elements. Our data support a gene regulatory role for 5hmC that is predominant over its role in controlling DNA methylation states.
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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.