The landscape of accessible chromatin in bovine oocytes and early embryos

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 <i>in vivo</i> and <i>in vitro</i> derived blastocysts, which provides insights to the potential mechanisms leading to low quality of embryos produced <i>in vitro</i>. Together, this comprehensive analysis revealed critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.

染色质重塑调控植入前发育过程中的基因表达。然而，牛植入前发育阶段的染色质动态变化图谱尚未得到解析。本研究采用改进型高通量测序转座酶可及性染色质分析（ATAC-seq），构建了牛卵母细胞与早期胚胎的全基因组开放染色质图谱，揭示了牛早期胚胎发育过程中开放染色质的独特特征。我们发现，卵母细胞及2-细胞/4-细胞胚胎的染色质可及性较低，在主要胚胎基因组激活（EGA）阶段，胚胎染色质可及性显著升高，并在伸长期第14天胚胎达到峰值。开放染色质的全基因组特征显示，转录起始位点（TSS）与转录终止位点（TES）处的ATAC-seq信号均较强。此外，远端ATAC-seq峰以类型特异性和阶段特异性的方式富集于重复元件中。我们进一步从远端ATAC-seq峰中解析出一系列富集模式存在显著差异的转录因子（TF）基序。通过整合分析牛早期胚胎的染色质可及性、转录组与DNA甲基化组数据，我们发现启动子可及性与基因表达呈正相关，这一关联在主要胚胎基因组激活阶段尤为显著，且启动子可及性与DNA甲基化水平及CpG密度密切相关。最后，我们鉴定出体内（in vivo）与体外（in vitro）来源囊胚之间存在差异的关键染色质特征与转录因子，为解析体外生产胚胎质量低下的潜在机制提供了新的见解。综上，本综合分析揭示了牛植入前胚胎发育过程中染色质图谱与表观重编程的关键特征。