Figure 7. Two phases in reprogramming.

The reprogramming process can be split into two phases: an early stochastic phase (A and B) of gene activation followed by a later more deterministic phase (C) of gene activation that begins with the activation of the Sox2 locus. After a fibroblast is induced with OSKM, the cell can proceed into either one of two stochastic phases. In A, stochastic gene activation can lead to the activation of the Sox2 locus. In B, stochastic gene activation can lead to the activation of “predictive markers” like Utf1, Esrrb, Dppa2, Lin28, which then mark cells that have a higher probability of activating the Sox2 locus. Activation of the Sox2 locus can be via two potential paths: (1) direct activation of the Sox2 locus or (2) sequential gene activation that leads to the activation of the Sox2 locus. In this model, probabilistic events decrease and hierarchal events increase as the cell progresses from fibroblast to iPSC. Solid red arrows and black arrows denote hypothetical interactions and interactions supported by our data, respectively. The white gap shown between the stochastic (A and B) and deterministic (C) panels represents the transition from induced fibroblast to iPSC illustrated between the orange dotted cluster and red cluster in Figure 2A.