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Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2

Nature volume 488, pages 652–655 (2012)Cite this article

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Abstract

Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by using the pluripotency factors Oct4, Sox2, Klf4 and c-Myc (together referred to as OSKM)1. iPSC reprogramming erases somatic epigenetic signatures—as typified by DNA methylation or histone modification at silent pluripotency loci—and establishes alternative epigenetic marks of embryonic stem cells (ESCs)2. Here we describe an early and essential stage of somatic cell reprogramming, preceding the induction of transcription at endogenous pluripotency loci such as Nanog and Esrrb. By day 4 after transduction with OSKM, two epigenetic modification factors necessary for iPSC generation, namely poly(ADP-ribose) polymerase-1 (Parp1) and ten-eleven translocation-2 (Tet2), are recruited to the Nanog and Esrrb loci. These epigenetic modification factors seem to have complementary roles in the establishment of early epigenetic marks during somatic cell reprogramming: Parp1 functions in the regulation of 5-methylcytosine (5mC) modification, whereas Tet2 is essential for the early generation of 5-hydroxymethylcytosine (5hmC) by the oxidation of 5mC (refs 3,4). Although 5hmC has been proposed to serve primarily as an intermediate in 5mC demethylation to cytosine in certain contexts5,6,7, our data, and also studies of Tet2-mutant human tumour cells8, argue in favour of a role for 5hmC as an epigenetic mark distinct from 5mC. Consistent with this, Parp1 and Tet2 are each needed for the early establishment of histone modifications that typify an activated chromatin state at pluripotency loci, whereas Parp1 induction further promotes accessibility to the Oct4 reprogramming factor. These findings suggest that Parp1 and Tet2 contribute to an epigenetic program that directs subsequent transcriptional induction at pluripotency loci during somatic cell reprogramming.

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Figure 1: Parp1 promotes OSKM-mediated iPSC generation.
Figure 2: Parp1 activities during iPSC reprogramming.
Figure 3: Tet2 is required for 5hmC formation at the Nanog locus.
Figure 4: Impact of Parp1 and Tet2 on chromatin state and Oct4 accessibility at the Nanog and Esrrb loci.

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Acknowledgements

We thank G. Q. Daley, A. P. Feinberg, A. Doi, R. M. Santella and M. A. Kappil for reagents and for technical assistance with pyrosequencing; A. Califano and A. Lachmann for assistance with the bioinformatics analyses; E. O. Mazzoni for assistance with the ChIP analyses; and O. Hobert for critical reading of the manuscript. This work was supported by New York State Stem Cell Science (NYSTEM) grants C024402 and C024403 and National Institutes of Health (NIH) grant RO1 NS064433 to A.A., NYSTEM Institution Development Grant N08G-071 to E.I.C., NIH grant RO1 138424 to R.L.L, and a shared NIH/National Center for Research Resources instrument grant for mass spectrometry, 1 S10 RR023680-1.

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Authors and Affiliations

  1. Departments of Pathology and Cell Biology and Neurology, Taub Institute for Aging, Columbia University, New York, 10032, New York, USA

    Claudia A. Doege, Keiichi Inoue, Toru Yamashita, David B. Rhee, Skylar Travis, Ryousuke Fujita, Govind Bhagat, William B. Vanti & Asa Abeliovich

  2. Bioinformatics Division, Biomedical Informatics Shared Resources, Columbia University, New York, 10032, New York, USA

    Paolo Guarnieri

  3. Herbert Irving Comprehensive Cancer Center, Columbia University, New York, 10032, New York, USA

    Paolo Guarnieri & Govind Bhagat

  4. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10016, New York, USA

    Alan Shih & Ross L. Levine

  5. Department of Pharmacological Sciences, Stony Brook University, Stony Brook, 11794, New York, USA

    Sara Nik & Emily I. Chen

  6. Stony Brook University Proteomics Center, School Of Medicine, Stony Brook, 11794, New York, USA

    Emily I. Chen

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Contributions

C.A.D. and A.A. designed the experiments and analysed data. C.A.D., D.B.R., S.T., R.F. and W.B.V. conducted molecular and cellular experiments. T.Y., G.B. and K.I. performed and analysed murine in vivo studies. R.L.L. and A.S. supplied essential reagents. P.G. performed bioinformatics analyses. S.N. and E.I.C. conducted proteomics. C.A.D. and A.A. wrote the manuscript.

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Correspondence to Asa Abeliovich.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5, Supplementary Methods, a legend for Supplementary Table 1 (see separate excel file), Supplementary Tables 2-9 and Supplementary References. (PDF 1471 kb)

Supplementary Table 1

This file contains the mass spectrometry raw data – see legend in Supplementary Information file. (XLS 246 kb)

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Doege, C., Inoue, K., Yamashita, T. et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 488, 652–655 (2012). https://doi.org/10.1038/nature11333

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