Abstract
As pluripotent human embryonic stem cells progress along the developmental trajectory towards one differentiated fate, they lose competence to adopt other fates. Here, we show that the loss of competence for alternative fates occurs at a specific point along the developmental trajectory and that this point can be moved using genetic perturbations. We first show that competence to adopt mesendoderm-derived fates in response to BMP4 and Activin A signal exposure is lost during ectoderm-directed differentiation. By monitoring each cell’s progression along its developmental trajectory, we can prospectively predict that cell’s mesendoderm competence. We then exploit this predictive ability using RNA-seq and ATAC-seq to identify and validate candidate transcription factors that can modulate mesendoderm competence. These factors exert their effects by controlling the cell’s progression along the developmental trajectory, by tuning its competence to form mesendoderm at any given point along that trajectory, or by altering both of these aspects. In the classical picture of a Waddington landscape, these effects correspond to changing the cell’s location on the landscape and altering the location of the barrier between fates, respectively. The ability of the underlying gene regulatory network to modulate these two aspects of the developmental landscape could allow separate control of the dynamics of differentiation and tissue size proportions.