In order to better understand human preimplantation development we applied massively parallel RNA sequencing on 337 single cells from oocytes up to 8-cell embryo blastomeres. Surprisingly, already before zygote pronuclear fusion we observed drastic changes in the transcriptome compared to the unfertilized egg: 1,804 gene transcripts and 32 repeat elements become more abundant, among these the double-homeobox gene DUX4. Several genes previously identified as DUX4 targets, such as CCNA1, KHDC1L and ZSCAN4, as well as several members of the RFPLs, TRIMS and PRAMEFs1 were accumulated in 4-cell stage blastomeres, suggesting DUX4 as an early regulator. In the 8-cell stage, we observed two distinct cell types — a transcript-poor cell type, and a transcript-rich cell type with many Alu repeats and accumulated markers for pluripotency and stemness, telomere elongation and growth. In summary, this unprecedented detailed view of the first three days of human embryonic development reveals more complex changes in the transcriptome than what was previously known.

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