Single-Cell Analysis Reveals that Expression of Nanog Is Biallelic and Equally Variable as that of Other Pluripotency Factors in Mouse ESCs

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 in ESCs 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.National Science Foundation (U.S.) (Graduate Research Fellowship)Whitehead Institute for Biomedical Research (Jerome and Florence Brill Graduate Student Fellowship)Croucher Foundation (Research Fellowship)Virginia and Daniel K. Ludwig Graduate FellowshipNational Institutes of Health (U.S.) ((NIH) Kirschstein National Research Service Award (1 F32 GM099153-01A1))National Institutes of Health (U.S.) (NIH grant HD 045022)National Institutes of Health (U.S.) (NIH grant R37CA084198