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


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.


  1. 1

    Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006)

    CAS  Article  Google Scholar 

  2. 2

    Mikkelsen, T. S. et al. Dissecting direct reprogramming through integrative genomic analysis. Nature 454, 49–55 (2008)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930 (2009)

    ADS  CAS  Article  Google Scholar 

  4. 4

    Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935 (2009)

    ADS  CAS  Article  Google Scholar 

  5. 5

    Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466, 1129–1133 (2010)

    ADS  CAS  Article  Google Scholar 

  6. 6

    Figueroa, M. E. et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18, 553–567 (2010)

    CAS  Article  Google Scholar 

  7. 7

    Guo, J. U. et al. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423–434 (2011)

    CAS  Article  Google Scholar 

  8. 8

    Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839–843 (2011)

    ADS  Article  Google Scholar 

  9. 9

    Krishnakumar, R. & Kraus, W. L. The PARP side of the nucleus: molecular actions, physiological outcomes, and clinical targets. Mol. Cell 39, 8–24 (2010)

    CAS  Article  Google Scholar 

  10. 10

    Wacker, D. A. et al. The DNA binding and catalytic domains of poly(ADP-ribose) polymerase 1 cooperate in the regulation of chromatin structure and transcription. Mol. Cell. Biol. 27, 7475–7485 (2007)

    CAS  Article  Google Scholar 

  11. 11

    Langelier, M. F. et al. The Zn3 domain of human poly(ADP-ribose) polymerase-1 (PARP-1) functions in both DNA-dependent poly(ADP-ribose) synthesis activity and chromatin compaction. J. Biol. Chem. 285, 18877–18887 (2010)

    CAS  Article  Google Scholar 

  12. 12

    Hajkova, P. et al. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 329, 78–82 (2010)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Williams, K. et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 473, 343–348 (2011)

    ADS  CAS  Article  Google Scholar 

  14. 14

    Pastor, W. A. et al. Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 473, 394–397 (2011)

    ADS  CAS  Article  Google Scholar 

  15. 15

    Wu, H. et al. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes Dev. 25, 679–684 (2011)

    CAS  Article  Google Scholar 

  16. 16

    Ficz, G. et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473, 398–402 (2011)

    ADS  CAS  Article  Google Scholar 

  17. 17

    Wu, H. et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389–393 (2011)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Davis, T. & Vaisvila, R. High sensitivity 5-hydroxymethylcytosine detection in Balb/C brain tissue. J. Vis. Exp.. (48), e2661, http://dx.doi.org/10.3791/2661 (2011)

  19. 19

    Meissner, A. et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766–770 (2008)

    ADS  CAS  Article  Google Scholar 

  20. 20

    Bhutani, N., Burns, D. M. & Blau, H. M. DNA demethylation dynamics. Cell 146, 866–872 (2011)

    CAS  Article  Google Scholar 

  21. 21

    Yildirim, O. et al. Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells. Cell 147, 1498–1510 (2011)

    CAS  Article  Google Scholar 

  22. 22

    Bernstein, B. E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169–181 (2005)

    CAS  Article  Google Scholar 

  23. 23

    Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007)

    CAS  Article  Google Scholar 

  24. 24

    Bernstein, B. E. et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125, 315–326 (2006)

    CAS  Article  Google Scholar 

  25. 25

    Lee, T. I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006)

    CAS  Article  Google Scholar 

  26. 26

    Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007)

    ADS  CAS  Article  Google Scholar 

  27. 27

    Koh, K. P. et al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 8, 200–213 (2011)

    CAS  Article  Google Scholar 

  28. 28

    Wang, Z. Q. et al. Mice lacking ADPRT and poly(ADP-ribosyl)ation develop normally but are susceptible to skin disease. Genes Dev. 9, 509–520 (1995)

    CAS  Article  Google Scholar 

  29. 29

    Moran-Crusio, K. et al. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell 20, 11–24 (2011)

    CAS  Article  Google Scholar 

  30. 30

    Smith, Z. D., Nachman, I., Regev, A. & Meissner, A. Dynamic single-cell imaging of direct reprogramming reveals an early specifying event. Nature Biotechnol. 28, 521–526 (2010)

    CAS  Article  Google Scholar 

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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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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.

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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)

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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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