A transcriptional clock of the human pluripotency transition

Developmental timing differs strikingly between mammals. All embryonic and some placental lineages emerge from the pluripotent epiblast in a temporally defined sequence, lasting about two weeks in the human embryo, but only two days in mice. Moreover, the order of lineage segregation and gene expression differ between the species. We used human pluripotent stem cells to recapitulate this window of epiblast development in vitro. Simultaneous profiling of gene expression and chromatin accessibility in single cells revealed a robust, autonomous switch between cell states during this process. We reconstructed the integrative gene regulatory network (GRN) of transcription factors (TFs) and signalling molecules. Notably, this revealed a transcriptional cascade including temporally close positive and distant inhibitory connections. We suggest that this cascade acts as a transcriptional clock and governs the directionality, timing and intrinsic decisions during epiblast development. From individual gene interactions, we derived a mechanistic mathematical model of the transcriptional clock of pluripotency that closely reproduced gene expression dynamics and identified key regulatory connections. Moreover, our model revealed a bistable switch governing the transition, thus translating the GRN inference into an interpretable mechanism. Strikingly, the GRN model derived for humans predicted the acceleration of developmental timing in mice when initialised with mouse-specific expression patterns, yet still leading to a human-like expression state. Therefore, TF levels explain developmental timing, whereas the architecture of the network defines its trajectory. Together, our work provides novel conceptual insights into the intrinsic mechanisms of developmental transitions in the human embryo.