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The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine

Nature Cell Biology volume 17, pages 545557 (2015) | Download Citation

Abstract

How embryonic stem cells (ESCs) commit to specific cell lineages and yield all cell types of a fully formed organism remains a major question. ESC differentiation is accompanied by large-scale histone and DNA modifications, but the relations between these epigenetic categories are not understood. Here we demonstrate the interplay between the histone deacetylase sirtuin 6 (SIRT6) and the ten-eleven translocation enzymes (TETs). SIRT6 targets acetylated histone H3 at Lys 9 and 56 (H3K9ac and H3K56ac), while TETs convert 5-methylcytosine into 5-hydroxymethylcytosine (5hmC). ESCs derived from Sirt6 knockout (S6KO) mice are skewed towards neuroectoderm development. This phenotype involves derepression of OCT4, SOX2 and NANOG, which causes an upregulation of TET-dependent production of 5hmC. Genome-wide analysis revealed neural genes marked with 5hmC in S6KO ESCs, thereby implicating TET enzymes in the neuroectoderm-skewed differentiation phenotype. We demonstrate that SIRT6 functions as a chromatin regulator safeguarding the balance between pluripotency and differentiation through Tet-mediated production of 5hmC.

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Acknowledgements

This work was supported in part by NIH grants GM093072-01, DK088190-01A1 (R.M.), 5R01HD058013-05 (to K.H.) and HD065812, CA151535 (to A.R.). R.M. is the Kristine and Bob Higgins MGH Research Scholar, the Warshaw Institute Fellow, and a Howard Goodman Awardee. L.C. was the recipient of a Feodor Lynen Research Fellowship from the Alexander von Humboldt Foundation. Y.H. was supported by a postdoctoral fellowship from the Leukemia and Lymphoma Society. C.A.S. is the recipient of the Evans Center Fellow Award. A.Gladden and A.Goren were the recipient of the Broad Institute SPARC (Scientific Projects to Accelerate Research and Collaboration) program. We thank O. Bar-Nur and S. Cheloufi for advice on the reprogramming of neural progenitor cells, and E. Kelliher for setting up the automation of the ChIP-Seq experiments.

Author information

Author notes

    • Lukas Chavez
    •  & Yun Huang

    Present addresses: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany (L.C.); Institute of Biosciences & Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA (Y.H.).

    • Lukas Chavez
    •  & Yun Huang

    These authors contributed equally to this work.

Affiliations

  1. The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts 02114, USA

    • Jean-Pierre Etchegaray
    • , Kenneth N. Ross
    • , Jiho Choi
    • , Barbara Martinez-Pastor
    • , Ryan M. Walsh
    • , Sita Kugel
    • , Sridhar Ramaswamy
    • , Konrad Hochedlinger
    •  & Raul Mostoslavsky
  2. The MGH Center for Regenerative Medicine, Harvard Medical School, Boston, Massachusetts 02114, USA

    • Jean-Pierre Etchegaray
    • , Kenneth N. Ross
    • , Jiho Choi
    • , Barbara Martinez-Pastor
    • , Ryan M. Walsh
    • , Sita Kugel
    • , Sridhar Ramaswamy
    • , Konrad Hochedlinger
    •  & Raul Mostoslavsky
  3. La Jolla Institute for Allergy and Immunology, Sanford Consortium for Regenerative Medicine, UCSD Department of Pharmacology, UCSD Moores Cancer Center, La Jolla, California 92037, USA

    • Lukas Chavez
    • , Yun Huang
    • , Matthias Lienhard
    •  & Anjana Rao
  4. The Center for Regenerative Medicine (CReM), Boston Medical Center, Boston University School of Medicine, Boston, Massachusetts 02118, USA

    • Cesar A. Sommer
    •  & Gustavo Mostoslavsky
  5. Broad Technology Labs (BTL), The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA

    • Adrianne Gladden
    •  & Alon Goren
  6. Department of Human Biochemistry, Medical School, CEFyBO-UBA-CONICET, Buenos Aires, CP1121, Argentina

    • Dafne M. Silberman
  7. Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA

    • Konrad Hochedlinger

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Contributions

J-P.E. conceived and designed most of the experiments, collected and analysed data, and wrote the manuscript; L.C., M.L. and K.N.R. performed computational analyses; Y.H. performed ChIP-Seq experiments; J.C. performed human ESC experiments; C.A.S. and G.M. performed iPSC experiments; B.M-P. performed and analysed immunofluorescence experiments; R.M.W. performed neurogenesis and immunofluorescence experiments; A.Gladden performed ChIP-Seq experiments; S.K. performed cloning of human SIRT6 expression system; D.M.S. performed in vitro experiments; S.R. supervised computational analyses; K.H. supervised the human ESC experiments; A.Goren conceived, supervised and analysed all the ChIP-Seq experiments and their computational analysis; A.R. supervised computational analyses, 5hMeC Chip-Seq experiments and edited the manuscript; R.M. conceived and supervised the study, analysed the data and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Jean-Pierre Etchegaray or Alon Goren or Raul Mostoslavsky.

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DOI

https://doi.org/10.1038/ncb3147

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