Cited by 814Epigenetics and DNA MethylationGenomics and Chromatin DynamicsPluripotent Stem Cells Research

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Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

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Pastor, William A., Pape, Utz J., Huang, Yun, Henderson, Hope R., Lister, Ryan, Ko, Myunggon, McLoughlin, Erin M., Brudno, Yevgeny, Mahapatra, Sahasransu, Kapranov, Philipp, Tahiliani, Mamta, Daley, George Q., Liu, X. Shirley, Ecker, Joseph R., Milos, Patrice M., Agarwal, Suneet, Rao, Anjana·2011·Nature

DOI 10.1038/nature10102PMC PMC3124347

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Abstract

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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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: Pastor, William A.
Pape, Utz J.
Huang, Yun
Henderson, Hope R.
Lister, Ryan
Ko, Myunggon
Brudno, Yevgeny
Mahapatra, Sahasransu
Kapranov, Philipp
Tahiliani, Mamta
Daley, George Q.
Ecker, Joseph R.
Agarwal, Suneet
Rao, Anjana
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2011-05-08
Volume: 473
Issue: 7347
Pages: 394-397
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature10102
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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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