mRNA structure dynamics identifies the embryonic RNA regulome

Jean-Denis Beaudoin, Eva Maria Novoa, Charles E. Vejnar, Valeria Yartseva, Carter Takacs, Manolis Kellis, Antonio J Giraldez
2018 · doi:10.1101/274290
preprint OA: closed
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Abstract

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 zebrafish development. We observe that on a global level, translation guides structure rather than structure guiding translation. We detect a decrease in structure in translated regions, and we 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 encode 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.

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