Single-cell analysis of non-human primate preimplantation development in comparison to humans and mice

Genetic programs underlying preimplantation development and early lineage segregation are highly conserved across mammals. It has been suggested that non-human primates would be better model organisms for human embryogenesis, but a limited number of studies have investigated the monkey preimplantation development. In this study, we collect single-cells from cynomolgus monkey preimplantation embryos for transcriptome profiling and compare with single-cell RNA-seq data derived from human and mouse embryos. By weighted gene-coexpression network analysis (WGCNA), we found that cynomolgus gene networks have greater conservation with human embryos including a greater number of conserved hub genes than that of mouse embryos. Consistently, we found that early ICM/TE lineage-segregating genes in monkeys exhibit greater similarity with human when compared to mouse, so are the genes in signaling pathways such as LRP1 and TCF7 involving in WNT pathway. Lastly, we tested the role of one conserved pre-EGA hub gene, SIN3A, using a morpholino knock-down of maternal RNA transcripts in monkey embryos followed by single-cell RNA-seq. We found that SIN3A knock-down disrupts the gene silencing program during the embryonic genome activation transition and results in developmental delay of cynomolgus embryos. Taken together, our study provided new insight into evolutionarily conserved and divergent transcriptome dynamics during mammalian pre-implantation development.