The homeodomain transcription factor Nanog is a central part of the core pluripotency transcriptional network and plays a critical role in embryonic stem cell (ESC) self-renewal. Several reports have suggested that Nanog expression is allelically regulated and that transient downregulation of Nanog in a subset of pluripotent cells predisposes them toward differentiation. Using single-cell gene expression analyses combined with different reporters for the two alleles of Nanog, we show that Nanog is biallelically expressed in ESCs independently of culture condition. We also show that the overall variation in endogenous Nanog expression inESCs is very similar to that of several other pluripotency markers. Our analysis suggests that reporter-based studies of gene expression in pluripotent cells can be significantly influenced by the gene-targeting strategy and genetic background employed. 2013
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We thank A. Smith for sharing TNGA cells; B. Carey, M. Dawlaty, F. Soldner, and A. Salama for helpful discussions; T. Theunissen for help with sorting; and A. van Oudenaarden and S. Klemm for insightful discussions and Stella probe. D.A.F. is a Vertex scholar and was supported by a National Science Foundation Graduate Research Fellowship and a Jerome and Florence Brill Graduate Student Fellowship. A.W.C. was supported by a Croucher and Ludwig Research Fellowship. Y.B. was supported by a National Institutes of Health (NIH) Kirschstein National Research Service Award (1 F32 GM099153-01A1). This work was supported by NIH grants HD 045022 and R37CA084198 to R.J. R.J. is a cofounder of Fate Therapeutics and an advisor to Stemgent.