mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis

RNA folding plays a crucial role in RNA function. However, our knowledge of the global structure of the transcriptome is limited to steady-state conditions, hindering our understanding of how RNA structure dynamics influences gene function. Here, we have characterized mRNA structure dynamics during the maternal-to-zygotic transition in zebrafish. We observe that on a global level, translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions, and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast, we find that 3’-UTRs form highly folded structures in vivo, which can affect gene expression by modulating miRNA activity. Furthermore, we find that dynamic 3’-UTR structures are enriched in RNA decay elements, including regulatory elements in nanog, and cyclin A1, key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.