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 single-cell RNA sequencing (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 toward 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 extraembryonic endoderm stem cell (XEN) differentiation. Furthermore, enhancer chromatin states based on wild-type (WT) and ESRRB knockout (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. •The ESC G2/M cell-cycle stage promotes XEN differentiation•ESRRB accumulation during G2/M is an inducer of XEN•ESRRB associates with ESC XEN poised enhancers•Loss of ESRRB impairs XEN differentiation potential In this article, Ram and colleagues show that Esrrb, a pluripotency factor that is upregulated during G2/M, is 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 ESCs overexpressing Esrrb allow XEN differentiation, while ESRRB-KO ESCs lost their potential to differentiate into XEN.