Esrrb is a cell cycle dependent associated factor balancing pluripotency and XEN differentiation

Cell cycle and differentiation decisions are linked; however, the underlying principles that drive these decisions are unclear. Here, we combined cell-cycle reporter system and scRNA-seq profiling to study the transcriptomes of embryonic stem cells (ESCs) in the context of cell cycle states and differentiation. By applying retinoic acid, to G1 and G2/M ESCs, we show that while both populations can differentiate towards Epiblast Stem Cells (EpiSCs), only G2/M ESCs could differentiate into extraembryonic endoderm cells.

We identified Esrrb, a pluripotency factor that is upregulated during G2/M, as a driver of XEN differentiation. Furthermore, enhancer chromatin states based on WT and ESRRB-KO ESCs show association of ESRRB with XEN poised enhancers. G1 Cells overexpressing Esrrb allow ESCs to produce XENs, while ESRRB-KO ESCs lost their potential to differentiate into XEN. Overall, this study reveals a vital link between Esrrb and cell-cycle states during the exit from pluripotency.