Nascent transcript sequencing visualizes mouse preimplantation embryonic genome activation

Embryonic genome activation (EGA), a pivotal transcriptional event during preimplantation development, is accompanied by post-transcriptional regulation of maternal mRNAs. Disentangling the transcriptional output of the newly activated embryonic genome from concomitant post-transcriptional processing is important for decoding EGA dynamics.Here, using optimized low-input SLAM-seq (thiol(SH)-linked alkylation for the metabolic sequencing) in mouse embryos, we delineates the temporal hierarchy of EGA nascent transcription during mouse preimplantation embryogenesis and uncovers a mechanistic link between EGA and the first lineage specification, providing new insights into the regulatory architecture of early mammalian development. Overall design: For the SLAM-seq profiling of mouse preimplantation embryos from nine stages, we adopted the criteria of 2 mM 4SU, 6-hour interval labeling and 10 embryos per sample for profiling; For the ATAC-seq, we selected the embryos from seven stages across the preimplantation development; For the function validation of KLF17, we collected contrl (ctrl), KO, mKO, pKO embryos at the M2C stage to perform SLAM-seq.

胚胎基因组激活（Embryonic genome activation, EGA）是着床前发育过程中的关键转录事件，伴随母源mRNA的转录后调控。将新激活的胚胎基因组的转录产物与伴随的转录后加工过程加以区分，对于解析EGA的动态变化具有重要意义。本研究通过在小鼠胚胎中使用优化的低起始量SLAM-seq（巯基（SH）偶联烷基化代谢测序，thiol(SH)-linked alkylation for the metabolic sequencing），阐明了小鼠着床前胚胎发生过程中EGA新生转录的时间层级关系，并揭示了EGA与首个细胞谱系特化之间的机制关联，为早期哺乳动物发育的调控网络提供了新见解。整体实验设计：针对9个发育时期的小鼠着床前胚胎的SLAM-seq测序分析，本研究采用的实验参数为：2 mM 4SU标记、6小时间隔标记时长、每份样本使用10枚胚胎；对于转座酶可及性染色质测序（ATAC-seq）实验，我们选取了着床前发育过程中7个时期的胚胎；为验证KLF17的功能，我们收集了M2C时期的对照组（ctrl）、基因敲除（KO）、定点敲除（mKO）以及启动子敲除（pKO）胚胎，用于SLAM-seq实验。