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The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming

Nature volume 488, pages 409–413 (2012)Cite this article

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Abstract

Induced pluripotent stem cells (iPSCs) can be derived from somatic cells by ectopic expression of different transcription factors, classically Oct4 (also known as Pou5f1), Sox2, Klf4 and Myc (abbreviated as OSKM)1. This process is accompanied by genome-wide epigenetic changes2,3,4,5, but how these chromatin modifications are biochemically determined requires further investigation. Here we show in mice and humans that the histone H3 methylated Lys 27 (H3K27) demethylase Utx6,7,8,9 (also known as Kdm6a) regulates the efficient induction, rather than maintenance, of pluripotency. Murine embryonic stem cells lacking Utx can execute lineage commitment and contribute to adult chimaeric animals; however, somatic cells lacking Utx fail to robustly reprogram back to the ground state of pluripotency. Utx directly partners with OSK reprogramming factors and uses its histone demethylase catalytic activity to facilitate iPSC formation. Genomic analysis indicates that Utx depletion results in aberrant dynamics of H3K27me3 repressive chromatin demethylation in somatic cells undergoing reprogramming. The latter directly hampers the derepression of potent pluripotency promoting gene modules (including Sall1, Sall4 and Utf1), which can cooperatively substitute for exogenous OSK supplementation in iPSC formation. Remarkably, Utx safeguards the timely execution of H3K27me3 demethylation observed in embryonic day 10.5–11 primordial germ cells (PGCs)10, and Utx-deficient PGCs show cell-autonomous aberrant epigenetic reprogramming dynamics during their embryonic maturation in vivo. Subsequently, this disrupts PGC development by embryonic day 12.5, and leads to diminished germline transmission in mouse chimaeras generated from Utx-knockout pluripotent cells. Thus, we identify Utx as a novel mediator with distinct functions during the re-establishment of pluripotency and germ cell development. Furthermore, our findings highlight the principle that molecular regulators mediating loss of repressive chromatin during in vivo germ cell reprogramming can be co-opted during in vitro reprogramming towards ground state pluripotency.

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Figure 1: Utx promotes the re-establishment of pluripotency in somatic cells.
Figure 2: Genomic dissection of reprogramming in Utx-knockout cells.
Figure 3: Downstream effectors of Utx that promote iPSC reprogramming.
Figure 4: Utx regulates epigenetic reprogramming and development of PGCs.

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Gene Expression Omnibus

Data deposits

Microarray data are available at the National Center for Biotechnology Information Gene Expression Omnibus database under the series accession number GSE37822.

Change history

  • 30 July 2012

    The second supplementary information file (Supplementary Tables 1-5) was incorrect and has been updated.

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Acknowledgements

J.H.H. is supported by a generous gift from Ilana and Pascal Mantoux, The Sir Charles Clore Research Prize, an ERC starting investigator grant (StG-2011-281906), the Israel Science Foundation Regular and Bikura research grants, the ICRF Foundation, Fritz Thyssen Stiftung, the Alon Foundation scholar award, a grant from E. A. and R. Drake, and the Leona M. and Harry B. Helmsley Charitable Trust. N.N. and A.P. are supported by Weizmann Dean fellowship awards. We thank A. Smith, H. Niwa and M. Saitou for reagents. We thank the Weizmann Institute management for providing critical financial and infrastructural support.

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Author notes

  1. Abed AlFatah Mansour, Ohad Gafni and Noa Novershtern: These authors contributed equally to this work.

Authors and Affiliations

  1. The Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel,

    Abed AlFatah Mansour, Ohad Gafni, Leehee Weinberger, Asaf Zviran, Yoach Rais, Vladislav Krupalnik, Mirie Zerbib, Itay Maza, Shay Geula, Sergey Viukov, Liad Holtzman, Ariel Pribluda, Noa Novershtern & Jacob H. Hanna

  2. The Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel,

    Muneef Ayyash

  3. The Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel,

    Daniela Amann-Zalcenstein & Ido Amit

  4. The Department of Biological Services—Genomics Unit, Weizmann Institute of Science, Rehovot 76100, Israel,

    Daniela Amann-Zalcenstein & Shirley Horn-Saban

  5. The Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel,

    Eli Canaani

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Contributions

O.G., A.A.M., N.N. and J.H.H. concieved the idea for this project, designed and conducted experiments and wrote the manuscript. L.W. conducted PGC differentiation. A.Z. conducted computational simulations. N.N. conducted bioinformatics analysis. O.G., I.A., D.A.-Z., S.H.-S. and E.C. conducted genomic and chromatin immunoprecipiation experiments. A.A.M., A.P., L.H. and I.M. conducted teratoma and embryo analysis. O.G. and S.V. generated knockout cells. J.H.H., O.G., V.K. and Y.R. conducted reprogramming experiments. M.Z. conducted microinjections. S.G. conducted pre-implantation analysis. M.A. provided critical technical advice.

Corresponding authors

Correspondence to Noa Novershtern or Jacob H. Hanna.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This fie contains Supplementary Figures 1-21 and legends for Supplementary Tables 1-5 (see separate zipped file for tables). (PDF 4398 kb)

Supplementary Tables

This file contains Supplementary Tables 1-5 (see Supplementary Information file for legends). The original incorrect zipped file was replaced on 30 July 2012. (ZIP 2005 kb)

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Mansour, A., Gafni, O., Weinberger, L. et al. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 488, 409–413 (2012). https://doi.org/10.1038/nature11272

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