Deciphering the pluripotency continuum in rabbit preimplantation embryos by RNA sequencing, epigenetic and metabolomics analysis

International audienceDespite the growing interest in the rabbit model for developmental and stem cell biology, the characterization of early embryos at the molecular level is still poorly documented. In this study, we conducted a transcriptome analysis of rabbit pre-implantation embryos from E2.7 (morula stage) to E6.6 (early primitive streak stage) using using two complementary techniques: bulk RNA-sequencing (Illumina NextSeq) and single-cell RNAseq (10x Genomics). We confirmed our findings by immunodetection of known developmental markers and identified new ones. We also analysed epigenetic marks such as histone post-translational modifications, DNA hydroxyl/methylation and chromosome X inactivation, during the transition from naive to primed pluripotency. In parallel, we studied oxidative phosphorylation and glycolysis in the embryos by live confocal imaging. We thus generated a transcriptomic, epigenetic, and metabolic map of the pluripotency continuum in rabbit preimplantation embryos. We found that the transcriptome of rabbit epiblast cells shares common features with that of mouse and primates. We also identified novel markers of naive pluripotency that might be instrumental for deriving naive pluripotent stem cell lines