Background Vertebrate early embryogenesis is initially directed by a set of maternal RNAs and proteins, yet the mechanisms controlling this program remain largely unknown. Recent transcriptome-wide studies on RNA structure have revealed its pervasive and crucial roles in RNA processing and functions, but whether and how RNA structure regulates the fate of the maternal transcriptome have yet to be determined. Results Here we establish the global map of four nucleotide-based mRNA structures by icSHAPE during zebrafish early embryogenesis. Strikingly, we observe that RNA structurally variable regions are enriched in the 3′ UTR and contain cis -regulatory elements important for maternal-to-zygotic transition (MZT). We find that the RNA-binding protein Elavl1a stabilizes maternal mRNAs by binding to the cis -elements. Conversely, RNA structure formation suppresses Elavl1a’s binding leading to the decay of its maternal targets. Conclusions Our study finds that RNA structurally variable regions are enriched in mRNA 3′ UTRs and contain cis -regulatory elements during zebrafish early embryogenesis. We reveal that Elavl1a regulates maternal RNA stability in an RNA structure-dependent fashion. Overall, our findings reveal a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.

中文翻译：

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RNA结构动力学通过控制转录组的命运和功能来调节早期胚胎发生

背景脊椎动物早期胚胎发生最初是由一组母体 RNA 和蛋白质指导的，但控制该程序的机制在很大程度上仍然未知。最近对 RNA 结构的全转录组研究揭示了其在 RNA 加工和功能中的普遍和关键作用，但 RNA 结构是否以及如何调节母体转录组的命运还有待确定。结果在这里，我们在斑马鱼早期胚胎发生过程中通过 icSHAPE 建立了四种基于核苷酸的 mRNA 结构的全局图谱。引人注目的是，我们观察到 RNA 结构可变区在 3' UTR 中富集，并含有对母体到合子转变 (MZT) 重要的顺式调节元件。我们发现 RNA 结合蛋白 Elavl1a 通过与顺式元件结合来稳定母体 mRNA。反过来，RNA 结构的形成抑制了 Elavl1a 的结合，导致其母体目标的衰变。结论 我们的研究发现，在斑马鱼早期胚胎发生过程中，RNA 结构可变区富含 mRNA 3' UTR 并含有顺式调节元件。我们揭示 Elavl1a 以依赖于 RNA 结构的方式调节母体 RNA 的稳定性。总体而言，我们的研究结果揭示了基于 RNA 结构的调控在脊椎动物早期胚胎发生中的广泛而基本的作用。