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

William A. Pastor, Utz Pape, Yun Huang, Hope R. Henderson, Ryan Lister, Myunggon Ko, Erin M. McLoughlin, Yevgeny Brudno, Sahasransu Mahapatra, Philipp Kapranov, Mamta Tahiliani, George Q. Daley, X. Shirley Liu, Joseph R. Ecker, Patrice M. Milos, Suneet Agarwal () and Anjana Rao ()
Additional contact information
William A. Pastor: Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston
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
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
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
George Q. Daley: Children’s Hospital Boston; Dana-Farber Cancer Institute; Harvard Stem Cell 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
Anjana Rao: Harvard Medical School, Immune Disease Institute and Program in Cellular and Molecular Medicine, Children’s Hospital Boston

Nature, 2011, vol. 473, issue 7347, 394-397

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.

Date: 2011
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DOI: 10.1038/nature10102

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