GSE105762
In vitro capture and characterization of embryonic rosette-stage pluripotency between naive and primed states (I, bulk RNA-Seq data)
Naive pluripotent cells in the implanting mouse blastocyst generate a rosette structure before undergoing lumenogenesis to form the egg cylinder. Simultaneously, they acquire primed pluripotency, the ability to differentiate into the primary germ layers. The existence of discrete intermediate pluripotent states during this transition has not been demonstrated. We identify here a distinct rosette pluripotent state, defined by co-expression of naive factors with transcription factor OTX2. Downregulation of WNT signals in the blastocyst drives transition into rosette pluripotency by inducing OTX2. The rosette then activates MEK signals that induce lumenogenesis and drive progression to primed pluripotency. Consequently, combined WNT and MEK inhibition supports rosette-like stem cells (RSCs), a self-renewing naive-primed intermediate. RSCs gain a unique epigenome that includes erasure of constitutive heterochromatin and bivalent marking of primed pluripotency genes. Notwithstanding this primed chromatin landscape, WNT induces reversion to naive pluripotency. The rosette is therefore a reversible pluripotent intermediate where control over pluripotency progression and morphogenesis pivots from WNT to MEK signals. Overall design: Using Illumina HiSeq, mRNA profiles were generated from mouse embryonic stem cells cultured in various conditions or differentiated to the primed pluripotent state.  As biological replicates, R1 and CGR8 embryonic stem cell lines were used. The cells were cultured in serumfree N2B27 medium supplemented with the cytokine LIF, and either the GSK3-inhibitor CHIR99021 and the MEK-inhibitor PD325901 (L2i), or a combination of PD325901 and the Wnt inhibitor IWP2 (LIM). Furthermore, mRNA profiles were also generated from cells differentiated towards the primed pluripotent state for 35 hrs and for 4 days by culture in the presence of LIF, FGF2, Activin A, and IWP2 (LFAI). Finally, mRNA profiles were generated from time courses of R1 embryonic stem cells switched from LIF+2i to LIF supplemented with either FGF2, Activin A and IWP2 (LFAI), or with IWP2 and PD325901 (LIM). The time courses lasted for 4 days, and mRNA profiles were generated from every day. No replicates were generated for the time courses.