Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Chromatin-modifying enzymes as modulators of reprogramming

This article has been updated


Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling1. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming2,3, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Screening for inhibitors and enhancers of reprogramming.
Figure 2: DOT1L inhibition enhances reprogramming efficiency and substitutes for KLF4 and Myc.
Figure 3: NANOG and LIN28 are required for enhancement of reprogramming by DOT1L inhibition.
Figure 4: Genome-wide analysis of H3K79me2 marks during reprogramming.

Accession codes

Primary accessions

Gene Expression Omnibus

Data deposits

The microarray and ChIP-seq data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) and are accessible through GEO Series accession numbers GSE29253 and GSE35791.

Change history

  • 29 March 2012

    Author name for B.O.M. was corrected.


  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. Hawkins, R. D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479–491 (2010)

    CAS  Article  Google Scholar 

  3. 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 

  4. Park, I.-H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 451, 141–146 (2008)

    ADS  CAS  Article  Google Scholar 

  5. Margueron, R. & Reinberg, D. The Polycomb complex PRC2 and its mark in life. Nature 469, 343–349 (2011)

    ADS  CAS  Article  Google Scholar 

  6. Pereira, C. F. et al. ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency. Cell Stem Cell 6, 547–556 (2010)

    CAS  Article  Google Scholar 

  7. Shi, Y. et al. Transcriptional repression by YY1, a human GLI-Krüippel-related protein, and relief of repression by adenovirus E1A protein. Cell 67, 377–388 (1991)

    CAS  Article  Google Scholar 

  8. Schotta, G., Ebert, A. & Reuter, G. S. U. (VAR)3–9 is a conserved key function in heterochromatic gene silencing. Genetica 117, 149–158 (2003)

    CAS  Article  Google Scholar 

  9. Jones, B. et al. The histone H3K79 methyltransferase Dot1L is essential for mammalian development and heterochromatin structure. PLoS Genet. 4, e1000190 (2008)

    Article  Google Scholar 

  10. Okada, Y. et al. hDOT1L links histone methylation to leukemogenesis. Cell 121, 167–178 (2005)

    CAS  Article  Google Scholar 

  11. Daigle, S. R. et al. Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor. Cancer Cell 20, 53–65 (2011)

    CAS  Article  Google Scholar 

  12. Bernt, K. M. et al. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell 20, 66–78 (2011)

    CAS  Article  Google Scholar 

  13. Carey, B. W. et al. Single-gene transgenic mouse strains for reprogramming adult somatic cells. Nature Methods 7, 56–59 (2010)

    CAS  Article  Google Scholar 

  14. Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005)

    CAS  Article  Google Scholar 

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

    ADS  CAS  Article  Google Scholar 

  16. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 318, 1917–1920 (2007)

    ADS  CAS  Article  Google Scholar 

  17. Charafe-Jauffret, E. et al. Gene expression profiling of breast cell lines identifies potential new basal markers. Oncogene 25, 2273–2284 (2006)

    CAS  Article  Google Scholar 

  18. Onder, T. T. et al. Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways. Cancer Res. 68, 3645–3654 (2008)

    CAS  Article  Google Scholar 

  19. Taube, J. H. et al. Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes. Proc. Natl Acad. Sci. USA 107, 15449–15454 (2010)

    ADS  CAS  Article  Google Scholar 

  20. Samavarchi-Tehrani, P. et al. Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell 7, 64–77 (2010)

    CAS  Article  Google Scholar 

  21. Stulemeijer, I. J. e. t. a. l. Dot1 binding induces chromatin rearrangements by histone methylation-dependent and -independent mechanisms. Epigenetics chromatin 4, 2 (2011)

    CAS  Article  Google Scholar 

  22. Olson, A. et al. RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs. Nucleic Acids Res. 34, D153–D157 (2006)

    CAS  Article  Google Scholar 

  23. Schlabach, M. R. et al. Cancer proliferation gene discovery through functional genomics. Science 319, 620–624 (2008)

    CAS  Article  Google Scholar 

  24. Zaehres, H. et al. High-efficiency RNA interference in human embryonic stem cells. Stem Cells 23, 299–305 (2005)

    CAS  Article  Google Scholar 

  25. Park, I.-H. et al. Generation of human-induced pluripotent stem cells. Nature Protocols 3, 1180–1186 (2008)

    CAS  Article  Google Scholar 

  26. Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797–801 (2009)

    ADS  CAS  Article  Google Scholar 

  27. Chan, E. M. et al. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nature Biotechnol. 27, 1033–1037 (2009)

    CAS  Article  Google Scholar 

  28. Loewer, S. et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genet. 42, 1113–1117 (2010)

    CAS  Article  Google Scholar 

  29. Langmead, B. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009)

    Article  Google Scholar 

  30. Subramanian, A. et al. GSEA-P: a desktop application for Gene Set Enrichment Analysis. Bioinformatics 23, 3251–3253 (2007)

    CAS  Article  Google Scholar 

Download references


We thank G. Hu and S. J. Elledge for providing the MSCV-PM vector, K. Ng and M. W. Lensch for teratoma injections and assessment and S. Loewer for discussions. We also thank E. Olhava and Epizyme Inc. for synthesizing and providing the DOT1L inhibitor, EPZ004777. G.Q.D. is an investigator of the Howard Hughes Medical Institute. Research was funded by grants from the US National Institutes of Health (NIH) to S.A.A. (CA140575) and G.Q.D., and the CHB Stem Cell Program.

Author information

Authors and Affiliations



T.T.O. performed project planning, experimental work, data interpretation and preparation of the manuscript. N.K., A.C, N.Z., J.U. and B.O.M. performed experimental work. P.C. and A.U.S. participated in data analysis. K.M.B. and S.A.A. provided critical materials and participated in the preparation of the manuscript. P.B.G. and E.S.L., participated in data acquisition, data interpretation and preparation of the manuscript. G.Q.D. supervised research and participated in project planning, data interpretation and preparation of the manuscript.

Corresponding author

Correspondence to George Q. Daley.

Ethics declarations

Competing interests

S.A.A. is a consultant for Epizyme Inc. G.Q.D. is a member of the scientific advisory boards and holds stock in or receives consulting fees from the following companies: Johnson & Johnson, Verastem, Epizyme, iPierian, Solasia KK and MPM Capital, LLP.

Supplementary information

Supplementary Figures

This file contains Supplementary Figures 1-22. (PDF 1698 kb)

Supplementary Table 1

This table contains a list of all the shRNA sequences used. (XLS 21 kb)

Supplementary Table 2

This table contains a list of qRT-PCR primers used. (XLS 11 kb)

Supplementary Table 3

This table contains genes upregulated and downregulated upon Dot1L inhibition during reprogramming based on gene expression profiling. (XLS 56 kb)

Supplementary Table 4

This table contains the enrichment scores for H3K79me2 and H3K27me3 Chip-seq and lists of genes significantly enriched in the indicated cell populations. (XLS 6867 kb)

Supplementary Table 5

This table shows gene sets significantly enriched in the gene set overlap analysis. (XLS 635 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Onder, T., Kara, N., Cherry, A. et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 483, 598–602 (2012).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing