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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.    Electronic supplementary material  Supplementary information accompanies this paper at 10.1186/s13059-020-02022-2.

RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function