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

Author

Listed:
  • William A. Pastor

    (Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston
    La Jolla Institute for Allergy & Immunology)

  • Utz J. Pape

    (Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston
    Dana-Farber Cancer Institute and Harvard School of Public Health)

  • Yun Huang

    (La Jolla Institute for Allergy & Immunology)

  • Hope R. Henderson

    (Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston
    La Jolla Institute for Allergy & Immunology)

  • Ryan Lister

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Myunggon Ko

    (La Jolla Institute for Allergy & Immunology)

  • Erin M. McLoughlin

    (Children’s Hospital Boston; Dana-Farber Cancer Institute; Harvard Stem Cell Institute
    Dana-Farber Cancer Institute)

  • Yevgeny Brudno

    (Harvard University)

  • Sahasransu Mahapatra

    (La Jolla Institute for Allergy & Immunology)

  • Philipp Kapranov

    (Helicos BioSciences Corporation)

  • Mamta Tahiliani

    (Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston
    Present address: Department of Biochemistry, New York University Langone Medical Centre, New York, New York 10016, USA.)

  • George Q. Daley

    (Children’s Hospital Boston; Dana-Farber Cancer Institute; Harvard Stem Cell Institute
    Dana-Farber Cancer Institute)

  • X. Shirley Liu

    (Dana-Farber Cancer Institute and Harvard School of Public Health)

  • Joseph R. Ecker

    (Genomic Analysis Laboratory, The Salk Institute for Biological Studies)

  • Patrice M. Milos

    (Helicos BioSciences Corporation)

  • Suneet Agarwal

    (Children’s Hospital Boston; Dana-Farber Cancer Institute; Harvard Stem Cell Institute
    Dana-Farber Cancer Institute)

  • Anjana Rao

    (Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston
    La Jolla Institute for Allergy & Immunology)

Abstract

Fine-tuning DNA methylation by Tet proteins The modified DNA base 5-hydroxymethylcytosine (5hmC), sometimes called the sixth base, is present in the mammalian genome where it is generated by oxidation of 5-methylcytosine (5mC; the fifth base) by enzymes of the Tet family. Four papers in this issue, from the Helin, Zhang, Rao and Reik laboratories, respectively, report on the genome-wide distribution of Tet1 and/or 5hmC in mouse embryonic stem cells using the ChIP-seq technique. Links between Tet1 and transcription regulation — both activation and repression — are revealed. Anjana Rao and colleagues also describe two alternative methods with increased sensitivity for mapping single 5hmC bases. In the associated News & Views, Nathalie Véron and Antoine H. F. M. Peters discuss what these and other recent papers reveal about the role of Tet proteins in regulating DNA methylation and gene expression.

Suggested Citation

  • William A. Pastor & Utz J. Pape & Yun Huang & Hope R. Henderson & Ryan Lister & Myunggon Ko & Erin M. McLoughlin & Yevgeny Brudno & Sahasransu Mahapatra & Philipp Kapranov & Mamta Tahiliani & George Q, 2011. "Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells," Nature, Nature, vol. 473(7347), pages 394-397, May.
    • Handle: RePEc:nat:nature:v:473:y:2011:i:7347:d:10.1038_nature10102
    DOI: 10.1038/nature10102
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