RNA structure landscape ofS. cerevisiaeintrons

Abstract

Pre-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.

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain

“…Ribosomal protein gene (RPG) introns as a class appear to be more resistant to Plad-B and Thail-A than introns in other genes (Figs 4 and 6). The RPG introns are also characteristically longer (~400 nt) and often contain secondary structure elements that influence splicing (Howe and Ares 1997;Rangan et al 2023;Spingola et al 1999;Charpentier and Rosbash 1996;Rogic et al 2008;Meyer et al 2011). Even within the more resistant RPG class, a range of sensitivities is evident (Figs 4,6).…”