Genome-wide characterization of the routes to pluripotency

Samer M.I. Hussein, Mira C. Puri, Peter D. Tonge, Marco Benevento, Andrew J. Corso, Jennifer L. Clancy, Rowland Mosbergen, Mira Li, Dong Sung Lee, Nicole Cloonan, David L.A. Wood, Javier Munoz, Robert Middleton, Othmar Korn, Hardip R. Patel, Carl A. White, Jong Yeon Shin, Maely E. Gauthier, Kim Anh Lê Cao, Jong Il KimJessica C. Mar, Nika Shakiba, William Ritchie, John E.J. Rasko, Sean M. Grimmond, Peter W. Zandstra, Christine A. Wells, Thomas Preiss, Jeong Sun Seo, Albert J.R. Heck, Ian M. Rogers, Andras Nagy

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123 Citations (Scopus)


Somatic cell reprogramming to a pluripotent state continues to challenge many of our assumptions about cellular specification, and despite major efforts, we lack a complete molecular characterization of the reprograming process. To address this gap in knowledge, we generated extensive transcriptomic, epigenomic and proteomic data sets describing the reprogramming routes leading from mouse embryonic fibroblasts to induced pluripotency. Through integrative analysis, we reveal that cells transition through distinct gene expression and epigenetic signatures and bifurcate towards reprogramming transgene-dependent and-independent stable pluripotent states. Early transcriptional events, driven by high levels of reprogramming transcription factor expression, are associated with widespread loss of histone H3 lysine 27 (H3K27me3) trimethylation, representing a general opening of the chromatin state. Maintenance of high transgene levels leads to re-acquisition of H3K27me3 and a stable pluripotent state that is alternative to the embryonic stem cell (ESC)-like fate. Lowering transgene levels at an intermediate phase, however, guides the process to the acquisition of ESC-like chromatin and DNA methylation signature. Our data provide a comprehensive molecular description of the reprogramming routes and is accessible through the Project Grandiose portal at

Original languageEnglish
Pages (from-to)198-206
Number of pages9
Issue number7530
Publication statusPublished - 11 Dec 2014
Externally publishedYes


  • induced pluripotent stem cells

Cite this

Hussein, S. M. I., Puri, M. C., Tonge, P. D., Benevento, M., Corso, A. J., Clancy, J. L., Mosbergen, R., Li, M., Lee, D. S., Cloonan, N., Wood, D. L. A., Munoz, J., Middleton, R., Korn, O., Patel, H. R., White, C. A., Shin, J. Y., Gauthier, M. E., Cao, K. A. L., ... Nagy, A. (2014). Genome-wide characterization of the routes to pluripotency. Nature, 516(7530), 198-206.