RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.
RNA. 2023 May;29(5):596-608. doi: 10.1261/rna.079168.122. Epub 2023 Feb 10.
The maternal-to-zygotic transition (MZT) is a conserved embryonic process in animals where developmental control shifts from the maternal to zygotic genome. A key step in this transition is zygotic transcription, and deciphering the MZT requires classifying newly transcribed genes. However, due to current technological limitations, this starting point remains a challenge for studying many species. Here, we present an alternative approach that characterizes transcriptome changes based solely on RNA-seq data. By combining intron-mapping reads and transcript-level quantification, we characterized transcriptome dynamics during the MZT. Our approach provides an accessible platform to investigate transcriptome dynamics that can be applied to the MZT in nonmodel organisms. In addition to classifying zygotically transcribed genes, our analysis revealed that over 300 genes express different maternal and zygotic transcript isoforms due to alternative splicing, polyadenylation, and promoter usage. The vast majority of these zygotic isoforms have the potential to be subject to different regulatory control, and over two-thirds encode different proteins. Thus, our analysis reveals an additional layer of regulation during the MZT, where new zygotic transcripts can generate additional proteome diversity.
母源至合子过渡（MZT）是动物中保守的胚胎过程，其中发育控制从母源基因组转移到合子基因组。这个过渡的一个关键步骤是合子转录，而破译 MZT 需要对新转录的基因进行分类。然而，由于当前技术的限制，这一起点仍然是研究许多物种的挑战。在这里，我们提出了一种替代方法，该方法仅基于 RNA-seq 数据来描述转录组的变化。通过结合内含子映射读取和转录水平的定量，我们描述了 MZT 期间的转录组动态。我们的方法为研究非模式生物中的 MZT 提供了一个易于访问的平台来研究转录组动态。除了对合子转录基因进行分类外，我们的分析还揭示了由于选择性剪接、多聚腺苷酸化和启动子使用，超过 300 个基因表达不同的母源和合子转录本异构体。这些合子异构体的绝大多数都有可能受到不同的调控控制，超过三分之二编码不同的蛋白质。因此，我们的分析揭示了 MZT 期间的另一个调控层，新的合子转录本可以产生额外的蛋白质组多样性。
