Transposable elements have rewired the core regulatory network of human embryonic stem cells (original) (raw)

• Letter
• Published: 06 June 2010
• Na-Yu Chia3,4,
• Justin Jeyakani1,
• Catalina Hwang1,5,
• Xinyi Lu3,6,
• Yun-Shen Chan3,7,
• Huck-Hui Ng3,4,6,7,8 &
• …
• Guillaume Bourque1

Nature Genetics volume 42, pages 631–634 (2010)Cite this article

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Abstract

Detection of new genomic control elements is critical in understanding transcriptional regulatory networks in their entirety. We studied the genome-wide binding locations of three key regulatory proteins (POU5F1, also known as OCT4; NANOG; and CTCF) in human and mouse embryonic stem cells. In contrast to CTCF, we found that the binding profiles of OCT4 and NANOG are markedly different, with only ∼5% of the regions being homologously occupied. We show that transposable elements contributed up to 25% of the bound sites in humans and mice and have wired new genes into the core regulatory network of embryonic stem cells. These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells.

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• 13 June 2010

In the version of this article initially published online, the phrase “the genes encoding” was erroneously inserted into the second sentence of the abstract and the protein name of POU5F1 was incorrect. The error has been corrected for the print, PDF and HTML versions of this article.

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Acknowledgements

This work was supported by the Agency for Science, Technology and Research (A*STAR) of Singapore.

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Authors and Affiliations

1. Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore
   Galih Kunarso, Justin Jeyakani, Catalina Hwang & Guillaume Bourque
2. Duke–National University of Singapore Graduate Medical School, Singapore, Singapore
   Galih Kunarso
3. Gene Regulation Laboratory, Genome Institute of Singapore, Singapore, Singapore
   Na-Yu Chia, Xinyi Lu, Yun-Shen Chan & Huck-Hui Ng
4. School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
   Na-Yu Chia & Huck-Hui Ng
5. Princeton University, Princeton, New Jersey, USA
   Catalina Hwang
6. Department of Biological Sciences, National University of Singapore, Singapore, Singapore
   Xinyi Lu & Huck-Hui Ng
7. Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
   Yun-Shen Chan & Huck-Hui Ng
8. Department of Biochemistry, National University of Singapore, Singapore, Singapore
   Huck-Hui Ng

Authors

1. Galih Kunarso
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2. Na-Yu Chia
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3. Justin Jeyakani
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4. Catalina Hwang
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5. Xinyi Lu
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6. Yun-Shen Chan
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7. Huck-Hui Ng
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8. Guillaume Bourque
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Contributions

H.-H.N. and G.B. designed the experiments. N.-Y.C., X.L. and Y.-S.C. performed the experiments. G.K. performed the data analysis with contributions from J.J. and C.H. G.B. wrote the manuscript with contributions from H.-H.N. and G.K.

Corresponding author

Correspondence toGuillaume Bourque.

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The authors declare no competing financial interests.

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Kunarso, G., Chia, NY., Jeyakani, J. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells.Nat Genet 42, 631–634 (2010). https://doi.org/10.1038/ng.600

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• Received: 30 November 2009
• Accepted: 20 April 2010
• Published: 06 June 2010
• Issue Date: July 2010
• DOI: https://doi.org/10.1038/ng.600

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