RT Journal Article SR Electronic T1 Single-cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development JF bioRxiv FD Cold Spring Harbor Laboratory SP 385815 DO 10.1101/385815 A1 Thorsten Boroviak A1 Giuliano G Stirparo A1 Sabine Dietmann A1 Irene H Herraez A1 Hisham Mohammed A1 Wolf Reik A1 Austin Smith A1 Erika Sasaki A1 Jennifer Nichols A1 Paul Bertone YR 2018 UL http://biorxiv.org/content/early/2018/08/07/385815.abstract AB The mouse embryo is the canonical model for mammalian preimplantation development. Recent advances in single-cell profiling allow detailed analysis of embryogenesis in other eutherian species, including human, to distinguish conserved from divergent regulatory programs and signalling pathways in the rodent paradigm. Here, we identify and compare transcriptional features of human, marmoset and mouse embryos by single-cell RNA-seq. Zygotic genome activation correlates with the presence of Polycomb Repressive Complexes in all three species, while ribosome biogenesis emerges as a predominant attribute in primate embryos, supporting prolonged translation of maternally deposited RNAs. We find that transposable element expression signatures are species-, stage- and lineage-specific. The pluripotency network in the primate epiblast lacks certain regulators operative in mouse, but encompasses WNT components and genes associated with trophoblast specification. Sequential activation of GATA6, SOX17 and GATA4 markers of primitive endoderm identity is conserved in primates. Unexpectedly, OTX2 is also associated with primitive endoderm specification in human and nonhuman primate blastocysts. Our cross-species analysis demarcates both conserved and primate-specific features of preimplantation development and underscores the molecular adaptability of early mammalian embryogenesis.