RNA Structural Dynamics Regulates Early Embryogenesis Through Controlling Transcriptome Fate and Function

Abstract

Early embryogenesis in vertebrates is initially directed by 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. Here we established the first global map of four nucleotide-based mRNA structures during zebrafish early embryogenesis. Strikingly, we observed RNA structurally variable regions are enriched in the 3’ UTR, and contain cis-regulatory elements important for maternal-to-zygotic transition (MZT). We found that the RNA binding protein Elavl1a stabilized maternal mRNAs by binding to the cis-elements. Conversely, RNA structure formation suppressed Elavl1a’s binding leading to the decay of its maternal targets. Overall, our findings revealed a broad and fundamental role of RNA structure-based regulation in vertebrate early embryogenesis.