Uncovering Genes Regulating Differentiation Using Entropy, Inference and Modeling: A study on the mechanism of epiblast specification in the early mouse embryo

In the pre-implantation mammalian embryo, stochastic cell-to-cell expression heterogeneity is followed by signal reinforcement to initiate the specification of Inner Cell Mass cells into Epiblast cells. The expression of NANOG, the key transcription factor for the Epi fate, is necessary but not sufficient: coincident expression of other factors is required. By quantifying gene expression variability at the single-cell level using inter-cellular entropy, a specific subset of genes sharing the same variability signature as Nanog was identified. Gene regulatory network analysis revealed that the uncovered genes are functionally linked to Nanog through mutual activation, and that these interactions emerge precisely when differentiation is initiated. Combining these observations with mathematical modeling leads to the conclusion that the coordination between Nanog and its helper genes generates coordinated high-expression states which are likely to act as the molecular trigger for the ICM to Epi/PrE transition.