Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition.
Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition.
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DOI：
10.1261/rna.079168.122
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发表时间：
2023-05
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母体向合子转变（MZT）是动物中一个保守的胚胎过程，其中发育控制从母体基因组转移到合子基因组。这一转变的关键步骤是合子转录，破译 MZT 需要对新转录的基因进行分类。然而，由于目前的技术限制，这个起点对于研究许多物种来说仍然是一个挑战。在这里，我们提出了一种仅基于 RNA-seq 数据来表征转录组变化的替代方法。通过结合内含子作图读数和转录水平定量，我们表征了果蝇 MZT 期间的转录组动态。我们的方法提供了一个可访问的平台来研究转录组动力学，该平台可应用于非模型生物中的 MZT。除了对合子转录基因进行分类之外，我们的分析还表明，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体和合子转录亚型。这些合子亚型中的绝大多数有可能受到不同的监管控制，并且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 期间的额外一层调控，其中新的合子转录本可以产生额外的蛋白质组多样性。
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 Drosophila melanogaster 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.