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Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

Nature Cell Biology volume 15, pages 872882 (2013) | Download Citation

Abstract

Reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) involves a marked reorganization of chromatin. To identify post-translational histone modifications that change in global abundance during this process, we have applied a quantitative mass-spectrometry-based approach. We found that iPSCs, compared with both the starting fibroblasts and a late reprogramming intermediate (pre-iPSCs), are enriched for histone modifications associated with active chromatin, and depleted for marks of transcriptional elongation and a subset of repressive modifications including H3K9me2/me3. Dissecting the contribution of H3K9 methylation to reprogramming, we show that the H3K9 methyltransferases Ehmt1, Ehmt2 and Setdb1 regulate global H3K9me2/me3 levels and that their depletion increases iPSC formation from both fibroblasts and pre-iPSCs. Similarly, we find that inhibition of heterochromatin protein-1γ (Cbx3), a protein known to recognize H3K9 methylation, enhances reprogramming. Genome-wide location analysis revealed that Cbx3 predominantly binds active genes in both pre-iPSCs and pluripotent cells but with a strikingly different distribution: in pre-iPSCs, but not in embryonic stem cells, Cbx3 associates with active transcriptional start sites, suggesting a developmentally regulated role for Cbx3 in transcriptional activation. Despite largely non-overlapping functions and the predominant association of Cbx3 with active transcription, the H3K9 methyltransferases and Cbx3 both inhibit reprogramming by repressing the pluripotency factor Nanog. Together, our findings demonstrate that Cbx3 and H3K9 methylation restrict late reprogramming events, and suggest that a marked change in global chromatin character constitutes an epigenetic roadblock for reprogramming.

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Acknowledgements

We thank V. Pasque for critical reading of the manuscript and M. Grunstein (UCLA) for providing antibodies. K.P. is supported by the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, NIH (DP2OD001686 and P01 GM099134) and CIRM (RN1-00564); R.S. was supported by the Jonsson Comprehensive Cancer Center, C.C. by a Leukaemia and Lymphoma Research Grant (10040), G.B. by the Whitcome Pre-doctoral Training Program, B.A.G. by a National Science Foundation Early Faculty CAREER award, an NIH Innovator award (DP2OD007447) and NIH (P01 GM099134) and M.C. by the NIH (GM074701). R.S., C.C. and S.P. were supported by CIRM training grants.

Author information

Author notes

    • Rupa Sridharan

    Present address: Wisconsin Institute for Discovery, Department of Cell and Regenerative Biology, University of Wisconsin, 330 N. Orchard Street, Room 2118, Madison, Wisconsin 53715, USA

    • Michelle Gonzales-Cope
    •  & Constantinos Chronis

    These authors contributed equally to this work

Affiliations

  1. University of California Los Angeles, David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Bioinformatics Interdepartmental Degree Program, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Los Angeles, California 90095, USA

    • Rupa Sridharan
    • , Constantinos Chronis
    • , Giancarlo Bonora
    • , Robin McKee
    • , Chengyang Huang
    • , Sanjeet Patel
    • , David Lopez
    • , Matteo Pellegrini
    • , Michael Carey
    •  & Kathrin Plath
  2. Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 1009C Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104, USA

    • Michelle Gonzales-Cope
    •  & Benjamin A. Garcia
  3. Section on Rheumatology, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, USA

    • Nilamadhab Mishra

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Contributions

R.S., K.P. and B.A.G. planned the project. R.S. and K.P. wrote the manuscript. The following performed experiments, analysed and interpreted data: R.S., C.C., G.B., R.M., S.P. under K.P.’s supervision, M.G-C. under B.A.G.’s supervision, C.H. under M.C.’s supervision, and D.L. under M.P.’s supervision. N.M. generated H3K18me1 antibody.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Benjamin A. Garcia or Kathrin Plath.

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DOI

https://doi.org/10.1038/ncb2768

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