Single-cell analysis reveals that expression of nanog is biallelic and equally variable as that of other pluripotency factors in mouse ESCs

Cell Stem Cell. 2013 Jul 3;13(1):23-9. doi: 10.1016/j.stem.2013.04.019.


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.

MeSH terms

  • Animals
  • Biomarkers / analysis*
  • Cells, Cultured
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism*
  • Flow Cytometry
  • Green Fluorescent Proteins / metabolism*
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / metabolism*
  • In Situ Hybridization, Fluorescence
  • Luminescent Proteins / metabolism*
  • Mice
  • Mice, Inbred C57BL
  • Nanog Homeobox Protein
  • Pluripotent Stem Cells / cytology
  • Pluripotent Stem Cells / metabolism*
  • RNA, Messenger / genetics


  • Biomarkers
  • Homeodomain Proteins
  • Luminescent Proteins
  • Nanog Homeobox Protein
  • Nanog protein, mouse
  • RNA, Messenger
  • red fluorescent protein
  • Green Fluorescent Proteins