Whole-transcriptome splicing profiling of embryonic day (E)7.5 mouse primary germ layers [RNA-seq]

Alternative splicing (AS) and alternative promoter (AP) usage expand the repertories of mammalian transcriptome profiles and thus diversify gene functions. However, our knowledge about the extent and functions of AS and AP usage in mouse early embryogenesis remains elusive. Here, by performing whole-transcriptome splicing profiling with high-throughput next generation sequencing, we report that AS extensively occurs in embryonic day (E) 7.5 mouse primary germ layers, and may be involved in multiple developmental processes. In addition, numerous RNA splicing factors are differentially expressed and alternatively spliced across the three germ layers, implying the potential importance of AS machinery in shaping early embryogenesis. Notably, AP usage is remarkably frequent at this stage, accounting for more than one quarter (430/1648) of the total significantly different AS events. Genes generating the 430 AP events participate in numerous biological processes, and include important regulators essential for mouse early embryogenesis, suggesting that AP usage is widely used and might be relevant to mouse germ layer specification. Our data underline the potential significance of AP usage in mouse gastrulation, providing a rich data source and opening another dimension for understanding the regulatory mechanisms of mammalian early development. Overall design: The alternative splicing patterns were captured and compared between the three germ layers from E7.5 mouse可变剪接（Alternative splicing，AS）与可变启动子（alternative promoter，AP）的使用可拓展哺乳动物转录组谱的种类多样性，进而使基因功能趋于多样化。然而，目前学界对于小鼠早期胚胎发生过程中AS与AP使用的范围及功能仍不甚明晰。本研究通过高通量下一代测序开展全转录组剪接谱分析，结果显示，AS在胚胎发育第7.5天（E7.5）的小鼠初级胚层中广泛存在，并可能参与多项发育进程。 此外，大量RNA剪接因子在三个初级胚层间存在差异表达与可变剪接现象，暗示AS调控机制在塑造早期胚胎发生过程中具有潜在重要作用。值得注意的是，该阶段AP的使用频率极高，占所有显著差异可变剪接事件的四分之一以上（430/1648）。产生这430种AP相关事件的基因参与了众多生物学过程，其中包含小鼠早期胚胎发生所必需的重要调控因子，这表明AP的使用是一种广泛存在的调控方式，且可能与小鼠胚层特化密切相关。 我们的研究结果凸显了AP使用在小鼠原肠胚形成过程中的潜在重要意义，同时提供了丰富的数据集资源，并为解析哺乳动物早期发育的调控机制开辟了新的研究维度。 总体实验设计：本研究捕获并比较了E7.5小鼠三个初级胚层的可变剪接模式。