RNA structure landscape of S. cerevisiae introns

Abstract

AbstractPre-mRNA secondary structure is hypothesized to play widespread roles in regulating splicing of eukaryotic introns, but direct detection of such structure in vivo has been challenging. Here, we characterize S. cerevisiae pre-mRNA secondary structures through transcriptome-wide dimethyl sulfate (DMS) probing experiments, enriching for low-abundance pre-mRNA through splicing inhibition. These data enable evaluation of structures predicted in phylogenetic and mutational studies. The data further reveal the widespread formation of zipper stems between the 5’ splice site and branch point, ‘downstream stems’ between the branch point and the 3’ splice site, and previously uncharacterized long stems that distinguish pre-mRNA from spliced mRNA. Structure ensemble prediction for introns across the Saccharomyces genus suggests that these structural patterns appear in all these yeast species. Together, these findings represent the first transcriptome-wide mapping of intron RNA structures and suggest new ideas and model systems for understanding how pre-mRNA folding promotes splicing efficiency and regulation of gene expression.