Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation

Abstract

Self‐renewal of embryonic stem cells (ESCs) cultured in LIF/fetal calf serum (FCS) is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here, we purify ESCs with distinct TF expression levels from LIF/FCS cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in Nanoglow cells. Independent Esrrb reporter lines demonstrate that Esrrbnegative ESCs cannot effectively self‐renew. Upon Esrrb loss, pre‐implantation pluripotency gene expression collapses. ChIP‐Seq identifies different regulatory element classes that bind both OCT4 and NANOG in Esrrbpositive cells. Class I elements lose NANOG and OCT4 binding in Esrrbnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, Class II elements retain OCT4 but not NANOG binding in ESRRB‐negative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.

Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors

“…The net consequence would then be that single‐cell expression analysis shows that in all stages a subset of cells is more resilient to differentiation cues. Similar observations of associations between transcriptional heterogeneity and differences in differentiation or reprogramming have previously been documented for several single factors, including Esrrb and Nanog , with particular focus on the pluripotent state …”

“…Similar observations of associations between transcriptional heterogeneity and differences in differentiation or reprogramming have previously been documented for several single factors, including Esrrb and Nanog, with particular focus on the pluripotent state. [78][79][80][81] A more complex narrative applies to N4 with its three subpopulations ( Figure 6A, right, and Figure S7D). Besides the aforementioned delayed subpopulation (ie, 14 cells here in blue), there were two more subpopulations (which can be described by six groups of gene expression dynamics): (a) a more neural-orientated group of 22 cells marked by higher average levels of NP-cell associated genes such as Zfp521, Pax6, Cxcr4, Zeb2, Zic3, and Sox9, and (b) the largest group of 39 cells that showed slightly lower levels of neural mRNAs and higher levels of specific combinations of genes, such as Stat3, Srf, Snai1, Tagln, Skil, Pou3f1, and Cdh1.…”

G2M splits mouse embryonic stem cells into naïve and formative pluripotency states

“…Esrrb has been shown to be critical for the sustained activity of the naïve pluripotency regulatory network and in enhanced reprogramming to the naïve state [41]. Moreover, drop in Esrrb concentration below certain levels has been shown to trigger exit from naïve pluripotency [42]. Our finding that G2M cells exist either as Esrrb-H or Esrrb-L populations therefore strongly suggest G2M to be the phase when the decision to maintain or exit the naïve state is made.…”

Cell cycle-balanced expression of pluripotency regulators via cyclin-dependent kinase 1

“…The reduction in expression of some pluripotency TFs including Esrrb marks mESC commitment to differentiation (Festuccia et al, 2018). Moreover, variable Esrrb levels separate distinct pluripotency states in G2M (Jääger et al, 2019).…”