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Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
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5-hydroxymethylcytosine (5hmC) is a modified base present at low levels in diverse cell types in mammals. 5hmC is generated by the TET family of Fe(II) and 2-oxoglutarate-dependent enzymes through oxidation of 5-methylcytosine (5mC). 5hmC and TET proteins have been implicated in stem cell biology and cancer, but information on the genome-wide distribution of 5hmC is limited. Here we describe two novel and specific approaches to profile the genomic localization of 5hmC. The first approach, termed GLIB (glucosylation, periodate oxidation, biotinylation) uses a combination of enzymatic and chemical steps to isolate DNA fragments containing as few as a single 5hmC. The second approach involves conversion of 5hmC to cytosine 5-methylenesulphonate (CMS) by treatment of genomic DNA with sodium bisulphite, followed by immunoprecipitation of CMS-containing DNA with a specific antiserum to CMS. High-throughput sequencing of 5hmC-containing DNA from mouse embryonic stem (ES) cells showed strong enrichment within exons and near transcriptional start sites. 5hmC was especially enriched at the start sites of genes whose promoters bear dual histone 3 lysine 27 trimethylation (H3K27me3) and histone 3 lysine 4 trimethylation (H3K4me3) marks. Our results indicate that 5hmC has a probable role in transcriptional regulation, and suggest a model in which 5hmC contributes to the 'poised' chromatin signature found at developmentally-regulated genes in ES cells.
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“Genome-wide enrichment studies in human and mouse embryonic stem cells (ESCs) confirms the presence of 5hmC at promoters and enhancers in addition to gene bodies (20).”
From Hepatocyte Nuclear Factor 4‐Alpha Is Essential for the Active Epigenetic State at Enhancers in Mouse Liver (2019) · cites this paper as [20]
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Metadata
- Authors
- Pastor, W. A., Pape, U. J., Huang, Y., Henderson, H. R., Lister, R., Ko, M., McLoughlin, E. M., Brudno, Y., Mahapatra, S., Kapranov, P., Tahiliani, M., Daley, G. Q., Liu, X. S., Ecker, J. R., Milos, P. M., Agarwal, S., & Rao, A.
- Affiliations
- Boston Children's Hospital (US)
- La Jolla Institute for Immunology (US)
- Salk Institute for Biological Studies (US)
- Harvard University (US)
- Helicos Biosciences (United States) (US)
- Corresponding author
- Agarwal, Suneet
- Rao, Anjana
- ORCID
- Venue
- Nature
- Published
- 2011-05-08
- Volume
- 473
- Issue
- 7347
- Pages
- 394-397
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3124347
- OpenAlex
- W1981543052
- Cited by
- 804
- References
- 28
- Citations by year
- 2026: 9 · 2025: 29 · 2024: 23 · 2023: 21 · 2022: 32 · 2021: 33 · 2020: 24 · 2019: 39 · 2018: 41 · 2017: 58 · 2016: 78 · 2015: 64 · 2014: 84 · 2013: 118 · 2012: 96
- FWCI
- 43.02
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Scholarworks@UNIST (Ulsan National Institute of Science and Technology) (submittedVersion)
- Funders
- National Science Foundation
- California Institute for Regenerative Medicine
- Leukemia and Lymphoma Society
- Harvard Catalyst (UL1-RR025758)
- California Institute of Regenerative Medicine
- National Institutes of Health
- National Heart, Lung, and Blood Institute (K08HL089150)
- National Institute on Drug Abuse (RC1DA028422)
- National Institute of Allergy and Infectious Diseases (R01AI044432)
- National Center for Research Resources (UL1RR025758)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD065812)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Keywords
- 5-hydroxymethylcytosine, TET1, mouse embryonic stem cells, DNA demethylation, DNA methylation, H3K27me3, H3K4me3, transcriptional regulation, ChIP-seq, histone modifications, gene expression regulation
- MeSH terms
- Animals, Cell Line, Cytosine, Exons, Glucose, Periodic Acid, Promoter Regions, Genetic, Transcription, Genetic, Genome, Sequence Analysis, DNA, Gene Expression Regulation, Developmental, DNA Methylation, Biotinylation, Transcription Initiation Site, 5-Methylcytosine, Mice, Embryonic Stem Cells
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