The RNA fold interactome of evolutionary conserved yeast RNA structures in S. cerevisiae

Based on previous DMS-Seq data that provides in vivo structural conformation of RNA, we here applied a streamlined RNA pull-down approach to study 186 evolutionary conserved RNA folds in S. cerevisiae. These folds bound 162 different proteins, with the majority known or inferred to be RNA-binding proteins. In contrast to global RNA interactome capture methods; we were able to associate individual messenger RNAs harboring conserved RNA folds with their set of bound regulating proteins. Our data suggests a more widespread function of tRNA synthetases as mRNA regulators. Using an in vivo RNA reporter screen, we show that specific mRNA-RBP pairs regulate protein expression, which connects structural RNA features recognized by the RNA-binding protein to functionality.