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Nature Genetics
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The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells

Nature Geneticsvolume 38, pages431–440 (2006)Cite this article

Abstract

Oct4 and Nanog are transcription factors required to maintain the pluripotency and self-renewal of embryonic stem (ES) cells. Using the chromatin immunoprecipitation paired-end ditags method, we mapped the binding sites of these factors in the mouse ES cell genome. We identified 1,083 and 3,006 high-confidence binding sites for Oct4 and Nanog, respectively. Comparative location analyses indicated that Oct4 and Nanog overlap substantially in their targets, and they are bound to genes in different configurations. Usingde novo motif discovery algorithms, we defined thecis-acting elements mediating their respective binding to genomic sites. By integrating RNA interference–mediated depletion of Oct4 and Nanog with microarray expression profiling, we demonstrated that these factors can activate or suppress transcription. We further showed that common core downstream targets are important to keep ES cells from differentiating. The emerging picture is one in which Oct4 and Nanog control a cascade of pathways that are intricately connected to govern pluripotency, self-renewal, genome surveillance and cell fate determination.

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Figure 1: Schematic diagram of genome-wide mapping of Oct4 and Nanog binding sites using ChIP-PET.
Figure 2: Distribution of Oct4 and Nanog binding sites.
Figure 3: Oct4 and Nanog binding site configurations at genomic locations.
Figure 4:De novo prediction of motifs that mediate specific transcription factor–DNA interaction.
Figure 5: Genome-wide association of Oct4 and Nanog binding sites with differentiation profiles of mouse ES cells.
Figure 6: Genome-wide association of Oct4 and Nanog binding sites with expression profiles of mouse ES cells depleted of Oct4 or Nanog.
Figure 7: Regulation of pluripotency by downstream targets of Oct4 and Nanog.
Figure 8: Conserved and diverged Oct4 and Nanog circuitries of mouse and human ES cells.

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References

  1. Smith, A.G. Embryo-derived stem cells: of mice and men.Annu. Rev. Cell Dev. Biol.17, 435–462 (2001).

    Article CAS  Google Scholar 

  2. Pera, M.F., Reubinoff, B. & Trounson, A. Human embryonic stem cells.J. Cell Sci.113, 5–10 (2000).

    CAS PubMed  Google Scholar 

  3. Donovan, P.J. & Gearhart, J. The end of the beginning for pluripotent stem cells.Nature414, 92–97 (2001).

    Article CAS  Google Scholar 

  4. Loebel, D.A., Watson, C.M., De Young, R.A. & Tam, P.P. Lineage choice and differentiation in mouse embryos and embryonic stem cells.Dev. Biol.264, 1–14 (2003).

    Article CAS  Google Scholar 

  5. Scholer, H.R., Ruppert, S., Suzuki, N., Chowdhury, K. & Gruss, P. New type of POU domain in germ line-specific protein Oct-4.Nature344, 435–439 (1990).

    Article CAS  Google Scholar 

  6. Nichols, J. et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4.Cell95, 379–391 (1998).

    Article CAS  Google Scholar 

  7. Niwa, H., Miyazaki, J. & Smith, A.G. Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells.Nat. Genet.24, 372–376 (2000).

    Article CAS  Google Scholar 

  8. Avilion, A.A. et al. Multipotent cell lineages in early mouse development depend on SOX2 function.Genes Dev.17, 126–140 (2003).

    Article CAS  Google Scholar 

  9. Chambers, I. et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells.Cell113, 643–655 (2003).

    Article CAS  Google Scholar 

  10. Mitsui, K. et al. The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells.Cell113, 631–642 (2003).

    Article CAS  Google Scholar 

  11. Pesce, M. & Scholer, H.R.Oct-4: gatekeeper in the beginnings of mammalian development.Stem Cells19, 271–278 (2001).

    Article CAS  Google Scholar 

  12. Chambers, I. & Smith, A. Self-renewal of teratocarcinoma and embryonic stem cells.Oncogene23, 7150–7160 (2004).

    Article CAS  Google Scholar 

  13. Ng, P. et al. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.Nat. Methods2, 105–111 (2005).

    Article CAS  Google Scholar 

  14. Wei, C.L. et al. A global map of p53 transcription-factor binding sites in the human genome.Cell124, 207–219 (2006).

    Article CAS  Google Scholar 

  15. Chew, J.L. et al. Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells.Mol. Cell. Biol.25, 6031–6046 (2005).

    Article CAS  Google Scholar 

  16. Mi, H. et al. The PANTHER database of protein families, subfamilies, functions and pathways.Nucleic Acids Res.33, D284–D288 (2005).

    Article CAS  Google Scholar 

  17. Yeom, Y.I. et al. Germline regulatory element of Oct-4 specific for the totipotent cycle of embryonal cells.Development122, 881–894 (1996).

    CAS PubMed  Google Scholar 

  18. Pavesi, G., Mauri, G. & Pesole, G. An algorithm for finding signals of unknown length in unaligned DNA sequences.Bioinformatics17 (Suppl.), 207–214 (2001).

    Article  Google Scholar 

  19. Down, T.A. & Hubbard, T.J. NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence.Nucleic Acids Res.33, 1445–1453 (2005).

    Article CAS  Google Scholar 

  20. Boyer, L.A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells.Cell122, 947–956 (2005).

    Article CAS  Google Scholar 

  21. Cartwright, P. et al. LIF/STAT3 controls ES cell self-renewal and pluripotency by a Myc-dependent mechanism.Development132, 885–896 (2005).

    Article CAS  Google Scholar 

  22. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.Cell116, 499–509 (2004).

    Article CAS  Google Scholar 

  23. Kim, T.H. et al. A high-resolution map of active promoters in the human genome.Nature436, 876–880 (2005).

    Article CAS  Google Scholar 

  24. Pollack, J.R. & Iyer, V.R. Characterizing the physical genome.Nat. Genet.32, 515–521 (2002).

    Article CAS  Google Scholar 

  25. Buck, M.J. & Lieb, J.D. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments.Genomics83, 349–360 (2004).

    Article CAS  Google Scholar 

  26. Impey, S. et al. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.Cell119, 1041–1054 (2004).

    CAS PubMed  Google Scholar 

  27. Kim, J., Bhinge, A.A., Morgan, X.C. & Iyer, V.R. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.Nat. Methods2, 47–53 (2005).

    Article CAS  Google Scholar 

  28. Rodda, D.J. et al. Transcriptional regulation of nanog by OCT4 and SOX2.J. Biol. Chem.280, 24731–24737 (2005).

    Article CAS  Google Scholar 

  29. Kuroda, T. et al. Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression.Mol. Cell. Biol.25, 2475–2485 (2005).

    Article CAS  Google Scholar 

  30. Okumura-Nakanishi, S., Saito, M., Niwa, H. & Ishikawa, F. Oct-3/4 and Sox2 regulate Oct-3/4 gene in embryonic stem cells.J. Biol. Chem.280, 5307–5317 (2005).

    Article CAS  Google Scholar 

  31. Ambrosetti, D.C., Scholer, H.R., Dailey, L. & Basilico, C. Modulation of the activity of multiple transcriptional activation domains by the DNA binding domains mediates the synergistic action of Sox2 and Oct-3 on the fibroblast growth factor-4 enhancer.J. Biol. Chem.275, 23387–23397 (2000).

    Article CAS  Google Scholar 

  32. Tokuzawa, Y. et al. Fbx15 is a novel target of Oct3/4 but is dispensable for embryonic stem cell self-renewal and mouse development.Mol. Cell. Biol.23, 2699–2708 (2003).

    Article CAS  Google Scholar 

  33. Nishimoto, M., Fukushima, A., Okuda, A. & Muramatsu, M. The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2.Mol. Cell. Biol.19, 5453–5465 (1999).

    Article CAS  Google Scholar 

  34. Kornberg, T.B. Understanding the homeodomain.J. Biol. Chem.268, 26813–26816 (1993).

    CAS PubMed  Google Scholar 

  35. Affolter, M., Schier, A. & Gehring, W.J. Homeodomain proteins and the regulation of gene expression.Curr. Opin. Cell Biol.2, 485–495 (1990).

    Article CAS  Google Scholar 

  36. Brandenberger, R. et al. MPSS profiling of human embryonic stem cells.BMC Dev. Biol.4, 10 (2004).

    Article  Google Scholar 

  37. Wei, C.L. et al. Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state.Stem Cells23, 166–185 (2005).

    Article CAS  Google Scholar 

  38. Martone, R. et al. Distribution of NF-kappaB-binding sites across human chromosome 22.Proc. Natl. Acad. Sci. USA100, 12247–12252 (2003).

    Article CAS  Google Scholar 

  39. Hanna, L.A., Foreman, R.K., Tarasenko, I.A., Kessler, D.S. & Labosky, P.A. Requirement for Foxd3 in maintaining pluripotent cells of the early mouse embryo.Genes Dev.16, 2650–2661 (2002).

    Article CAS  Google Scholar 

  40. Guo, Y. et al. The embryonic stem cell transcription factors Oct-4 and FoxD3 interact to regulate endodermal-specific promoter expression.Proc. Natl. Acad. Sci. USA99, 3663–3667 (2002).

    Article CAS  Google Scholar 

  41. Dodge, J.E., Kang, Y.K., Beppu, H., Lei, H. & Li, E. Histone H3–K9 methyltransferase ESET is essential for early development.Mol. Cell. Biol.24, 2478–2486 (2004).

    Article CAS  Google Scholar 

  42. Luo, J. et al. Placental abnormalities in mouse embryos lacking the orphan nuclear receptor ERR-beta.Nature388, 778–782 (1997).

    Article CAS  Google Scholar 

  43. Mitsunaga, K. et al. Loss of PGC-specific expression of the orphan nuclear receptor ERR-beta results in reduction of germ cell number in mouse embryos.Mech. Dev.121, 237–246 (2004).

    Article CAS  Google Scholar 

  44. Adams, I.R. & McLaren, A. Identification and characterisation of mRif1: a mouse telomere-associated protein highly expressed in germ cells and embryo-derived pluripotent stem cells.Dev. Dyn.229, 733–744 (2004).

    Article CAS  Google Scholar 

  45. Xu, L. & Blackburn, E.H. Human Rif1 protein binds aberrant telomeres and aligns along anaphase midzone microtubules.J. Cell Biol.167, 819–830 (2004).

    Article CAS  Google Scholar 

  46. Silverman, J., Takai, H., Buonomo, S.B., Eisenhaber, F. & de Lange, T. Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint.Genes Dev.18, 2108–2119 (2004).

    Article CAS  Google Scholar 

Download references

Acknowledgements

We are grateful to the Biomedical Research Council (BMRC) and Agency for Science, Technology and Research (A*STAR) for funding. Y.-H.L is supported by the A*STAR graduate scholarship. J.-L.C is supported by the Singapore Millennium Foundation graduate scholarship. W.Z. and X.C. are supported by the National University of Singapore graduate scholarship. B.L. is partially supported by grants from the US National Institutes of Health (DK47636 and AI54973). We thank E. Cheung, T. Lufkin, N. Clarke, C.-A. Lim, P. Melamed and J. Buhlman for critical comments on the manuscript. We are grateful to E. Ng, A. Ang and Y.-C. Chong for assistance in annotating the binding sites.

Author information

Author notes

  1. Yuin-Han Loh, Qiang Wu and Joon-Lin Chew: These authors contributed equally to this work.

Authors and Affiliations

  1. Gene Regulation Laboratory, Genome Institute of Singapore, 138672, Singapore

    Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Weiwei Zhang, Xi Chen & Huck-Hui Ng

  2. Department of Biological Sciences, National University of Singapore, 117543, Singapore

    Yuin-Han Loh, Joon-Lin Chew, Weiwei Zhang, Xi Chen, Paul Robson & Huck-Hui Ng

  3. Information & Mathematical Sciences Group, Genome Institute of Singapore, 138672, Singapore

    Vinsensius B Vega, Guillaume Bourque, Joshy George, Bernard Leong, Ken W Sung, Charlie W H Lee, Kuo-Ping Chiu, Leonard Lipovich & Vladimir A Kuznetsov

  4. Cloning and Sequencing Group, Genome Institute of Singapore, 138672, Singapore

    Jun Liu, Xiao-Dong Zhao, Chia-Lin Wei & Yijun Ruan

  5. Stem Cell & Developmental Biology, Genome Institute of Singapore, 138672, Singapore

    Kee-Yew Wong, Paul Robson, Lawrence W Stanton & Bing Lim

  6. Harvard Institutes of Medicine, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Bing Lim

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Supplementary information

Supplementary Figure 1

Validation of Oct4 ChIP-PET data by real-time PCR. (PDF 26 kb)

Supplementary Figure 2

Profiles of Oct4 binding as shown by by ChIP-PET. (PDF 38 kb)

Supplementary Figure 3

Validation of Nanog ChIP-PET data by real-time PCR. (PDF 27 kb)

Supplementary Figure 4

Validation of ChIP-PET data with epitope-tagged Nanog. (PDF 27 kb)

Supplementary Figure 5

Validation of Nanog binding profiles atPou5f1,Sox2 andNanog upstream regulatory regions. (PDF 57 kb)

Supplementary Figure 6

Co-occupancies of Oct4 and Sox2 on target sites. (PDF 38 kb)

Supplementary Figure 7

Binding of Nanog to DNA containing CATT motifs. (PDF 37 kb)

Supplementary Figure 8

Rescue experiments demonstrate the specificity of thePou5f1 RNAi results. (PDF 69 kb)

Supplementary Figure 9

Specificity ofNanog siRNA. (PDF 107 kb)

Supplementary Figure 10

Locations of ChIP-PET clusters relative to genes that are differentially expressed afterPou5f1 orNanog RNAi knockdown. (PDF 23 kb)

Supplementary Figure 11

Characterization of Nanog-overexpressing ES cell line. (PDF 100 kb)

Supplementary Figure 12

ES cells expressing scrambledEsrrb orRif1 siRNA sequences retained non-differentiated cell morphology. (PDF 63 kb)

Supplementary Table 1

Coordinates of loci for validation of Oct4 binding. (XLS 41 kb)

Supplementary Table 2

Coordinates of Oct4 and Nanog binding loci and their associated genes. (XLS 2890 kb)

Supplementary Table 3

Common genes that are bound by both Oct4 and Nanog. (XLS 180 kb)

Supplementary Table 4

Differentiation profiles of ES cells (data set for Fig. 5). (XLS 9944 kb)

Supplementary Table 5

Differentially expressed genes afterPou5f1 orNanog RNAi (data sets for Figs. 6a,b). (XLS 2096 kb)

Supplementary Table 6

List of differentially expressed genes bound by Oct4 or Nanog (data set for Fig. 6c). (XLS 266 kb)

Supplementary Table 7

Mouse and human targets: location comparison. (XLS 255 kb)

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Loh, YH., Wu, Q., Chew, JL.et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells.Nat Genet38, 431–440 (2006). https://doi.org/10.1038/ng1760

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