Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

Abstract

RNA folding plays a crucial role in RNA function. However, knowledge of the global structure of the transcriptome is limited to cellular systems at steady state, thus hindering the understanding of RNA structure dynamics during biological transitions and how it influences gene function. Here, we characterized mRNA structure dynamics during zebrafish development. We observed that on a global level, translation guides structure rather than structure guiding translation. We detected a decrease in structure in translated regions and identified the ribosome as a major remodeler of RNA structure in vivo. In contrast, we found that 3' untranslated regions (UTRs) form highly folded structures in vivo, which can affect gene expression by modulating microRNA activity. Furthermore, dynamic 3'-UTR structures contain RNA-decay elements, such as the regulatory elements in nanog and ccna1, two genes encoding key maternal factors orchestrating the maternal-to-zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs.

mRNA structural dynamics shape Argonaute-target interactions

“…Recent reports showed that ribosomes reduce the overall degree of structure in the coding sequence of the transcriptome (Adivarahan et al, 2018;Beaudoin et al, 2018;Mizrahi et al, 2018;Mustoe et al, 2018). In addition, several studies have shown that AGO target sites are less efficiently recognized if they are embedded within a strong structure (Ameres et al, 2007;Beaudoin et al, 2018). Here, we show that ribosome-dependent unfolding of mRNA structures stimulates AGO-target interactions, providing a direct, causal link between mRNA translation and AGO2-target binding.…”

“…Recent studies have also revealed that mRNAs can undergo structural rearrangements throughout an mRNA's life. For example, when zebrafish embryos undergo the maternal-to-zygotic transition (Beaudoin et al, 2018), or as mRNAs transition from the nucleus to the cytoplasm (Adivarahan et al, 2018;Sun et al, 2019), or upon translation of mRNAs by ribosomes (Beaudoin et al, 2018;Mizrahi et al, 2018;Mustoe et al, 2018). While these studies demonstrate that mRNAs can adopt distinct structural conformations, they provide limited insights into the dynamics of mRNA structure, especially on the short timescales at which AGO-target interactions likely occur.…”

Synonymous codon substitutions perturb co-translational protein foldingin vivoand impair cell fitness

“…In vitro, synonymous codons have been shown to alter elongation rate either by altering the rate of decoding (59) or by altering downstream mRNA stability, which can impede ribosome translocation (60). In vivo, there is some evidence that stable mRNA stem-loop structures can alter the elongation rate of the ribosome (61-63), although other studies have detected no difference (38,64,65), likely due to destabilization of mRNA structure by polysomes and/or the helicase activity of the ribosome. Although the overall predicted mRNA stability of the WT and Shuf1 genes are similar, a predicted stable 3' stem-loop structure in Shuf1 is not present in the WT coding sequence ( Fig.…”

RSVdb: A comprehensive database of transcriptome RNA structure

“…This method can effectively detect the structure of mRNA in vivo at the transcriptome level. In recent years, an increasing number of studies have used this method or improved techniques, such as structure-seq, CIRS-seq, and DMS-MaPseq, to detect mRNA structures (12)(13)(14)(15)(16)(17)(18). Currently, there are several databases collecting in vivo mRNA structure information: RMDB (https://rmdb.stanford.edu/browse/), FoldAtlas (http://www.foldatlas.com/), and Structure Surfer (http://tesla.pcbi.upenn.edu/structuresurfer/) (19)(20)(21).…”