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Chromatin reorganization governs the regulation of gene expression during preimplantation development. However, the landscape of chromatin dynamics in this period has not been explored in bovine. In this study, we constructed a genome-wide map of accessible chromatin in bovine oocytes and early embryos using an improved assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) which revealed unique features of the accessible chromatin during bovine early embryo development. We found that chromatin accessibility is low in oocytes and 2-/4-cell embryos, followed by a significant increase in embryos during major embryonic genome activation (EGA), and peaked in elongating day 14 embryos. Genome-wide characteristics of open chromatin showed that ATAC-seq signals in both transcription start sites (TSS) and transcription end sites (TES) were strong. Additionally, the distal ATAC-seq peaks were enriched in repeat elements in a type-specific and stage-specific manner. We further unveiled a series of transcription factor (TF) motifs with distinct variation of enrichment from distal ATAC-seq peaks. By integrated analysis of chromatin accessibility with transcriptomes and DNA methylomes in bovine early embryos, we showed that promoter accessibility was positively correlated with gene expression, especially during major EGA, and was strongly correlated to DNA methylation and CpG density. Finally, we identified the critical chromatin signatures and TFs that differ between in vivo and in vitro derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced in vitro. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.

The frequency of PCR positive detection of exogenous DNA was determined in bovine embryos over a 21 day period of culture after microinjection. After in vitro maturation and in vitro fertilization, embryos were microinjected with one of two genomic DNA constructs. Approximately 5% of the injected embryos were prepared for PCR analysis immediately after injection (d 0). After culture for 7 d on Buffalo Rat liver (BRL) cells, embryos were assessed for stage of development. Embryos developing to the morula or blastocyst stage were randomly assigned to two groups; PCR analysis (d 7) or extended culture. Extended culture embryos were cultured for an additional 7 d. Embryos maintaining a blastocoel at d 14 were considered alive, and were assigned randomly to either further culture or PCR analysis. Of zygotes examined after d 7 of culture, 26% (189/733) of control and 12% (294/2482) of injected embryos had developed to the morula or blastocyst stage (control vs. injected; P