To better understand transcriptional regulation during human oogenesis and pre-implantation development, we defined stage-specific transcription, which revealed the cleavage stage as highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific, multi-copy retrogene, DUX4, encodes a transcription factor which activates hundreds of endogenous genes (e.g. ZSCAN4, ZFP352, KDM4E) and retroviral elements (MERVL/HERVL-family) that defines the cleavage-specific transcriptional programs in mouse and human. Remarkably, mouse Dux expression is both necessary and sufficient to convert mouse embryonic stem cells into two-cell embryo-like (‘2C-like’) cells, measured here by the reactivation of ‘2C’ genes and repeat elements, the loss of POU5F1 protein and chromocenters, and by the conversion of the chromatin landscape (assessed by ATAC-seq) to a state strongly resembling mouse two-cell embryos. Taken together, we propose mouse DUX and human DUX4 as major drivers of the cleavage/‘2C’ state.

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ertilization and early embryogenesis involve the transition from specialized unipotent gametes to totipotent embryos. After fertilization, mammalian embryos rely on maternally deposited RNA but subsequently initiate ZGA during which embryonic transcription begins 1 . Diverse mechanisms control the timing of ZGA, such as controlling RNA polymerase activity, the nuclear/ cytoplasmic ratio, or translation of critical ZGA transcription factors (TFs) in Caenorhabditis elegans, Drosophila melanogaster or Danio rerio, respectively 1 . Currently, we have an incomplete understanding of how the transcriptional machinery (RNA polymerases) and/or sequence-specific TFs dictate the timing of ZGA in mammals and contribute to developmental potential.Recent work identified the TF DUX (DUX4 in humans) as a key regulator of ZGA gene expression 2-5 . When ectopically expressed in cells, DUX and DUX4 activate many ZGA genes, including the earliest wave of ZGA genes in humans and mice 2,3 . However, the extent to which DUX is required for appropriate ZGA is unclear, as the reported effect of genetic loss of Dux ranges from minor molecular to major transcriptional defects and decreased development in mouse or human embryos 4-6 .To study ZGA using a cellular model, we and others have used 2C-embryo-like cells (2CLCs), which are an endogenously fluctuating subpopulation of mouse embryonic stem cells (mESCs) that recapitulate several key features of ZGA 7 . The 2CLCs activate transcripts characteristic of the 2C mouse embryo (including Dux,