ArticleBMC genomics2014
5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 42 citations in OpenAlex.
- Combined epigenomic landscapes of 5mC, 5hmC, and 6mA modifications in papillary thyroid carcinogenesis.Communications biology · 2026Article
- Profiling of 5-hydroxymethylcytosine in blood reveals preferential enrichment at exon-intron junctions and predictive value for Parkinson's disease.NPJ Parkinson's disease · 2026Article
- Integrative epigenomic landscape of Alzheimer's Disease brains reveals oligodendrocyte molecular perturbations associated with tau.Nature communications · 2026Article
- Loss of ten-eleven translocation 2 (TET2) facilitates aggressive behaviour in cutaneous melanoma by inducing peroxisome proliferator-activated receptor-γ coactivator 1α expression and oxidative phosphorylation.The British journal of dermatology · 2026Article
- Article
- Binding Affinity Quantifications of the Bacteriophage Mu DNA Modification Protein Mom Using Microscale Thermophoresis (MST).Bio-protocol · 2022Article
- Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors.Journal of biochemistry · 2022Article
- The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine.Frontiers in cell and developmental biology · 2022Review
- Emergence of a novel immune-evasion strategy from an ancestral protein fold in bacteriophage Mu.Nucleic acids research · 2020Article
- Human Muscle Progenitor Cells Overexpressing Neurotrophic Factors Improve Neuronal Regeneration in a Sciatic Nerve Injury Mouse Model.Frontiers in neuroscience · 2019Article
- Exploring the genetic basis of human population differences in DNA methylation and their causal impact on immune gene regulation.Genome biology · 2018Article
- Epigenetics and Trained Immunity.Antioxidants & redox signaling · 2018Review
- Epigenetic regulation of neuroblastoma development.Cell and tissue research · 2018Review
- Comprehensive Evaluation of Commercial Bisulfite-Based DNA Methylation Kits and Development of an Alternative Protocol With Improved Conversion Performance.Genetics & epigenetics · 2018Article
- A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline.Frontiers in cell and developmental biology · 2018Review
- Epigenetics in formation, function, and failure of the endocrine pancreas.Molecular metabolism · 2017Review
- Prenatal Exposure to Mercury: Associations with Global DNA Methylation and Hydroxymethylation in Cord Blood and in Childhood.Environmental health perspectives · 2017Article
- Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation.Genes & development · 2016Article
- Epigenetic Changes in Diabetes and Cardiovascular Risk.Circulation research · 2016Review
- Genome-wide alteration of 5-hydroxymenthylcytosine in a mouse model of Alzheimer's disease.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
backgroundRecent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especially at enhancers.
resultsWe found a group of distal transcription factor binding sites highly enriched for 5-hdroxymethylcytosine (5hmC), but lacking any known activating histone marks and being depleted for nascent transcripts, suggesting a repressive role for 5hmC in mouse embryonic stem cells (mESCs). 5-formylcytosine (5fC), which is known to mark poised enhancers where H3K4me1 is enriched, is also observed at these sites. Furthermore, the 5hmC levels were inversely correlated with RNA polymerase II (PolII) occupancy in mESCs as well as in fully differentiated adipocytes. Interestingly, activating H3K4me1/2 histone marks were enriched at these sites when the associated genes become activated following lineage specification. These putative enhancers were shown to be functional in embryonic stem cells when unmethylated. Together, these data suggest that 5hmC suppresses the activity of this group of enhancers, which we termed "silenced enhancers".
conclusionsOur findings indicate that 5hmC has a repressive role at specific proximal and distal regulatory regions in mESCs, and suggest that 5hmC is a new epigenetic mark for silenced enhancers.
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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.