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RNA structure landscape of S. cerevisiae introns

ABSTRACT: Pre-mRNA secondary structures are hypothesized to play widespread roles in regulating RNA processing pathways, but these structures have been difficult to visualize in vivo. Here, we characterize S. cerevisiae pre-mRNA structures through transcriptome-wide dimethyl sulfate (DMS) probing, enriching for low-abundance pre-mRNA through splicing inhibition. These data enable evaluation of structures from phylogenetic and mutational studies as well as identification of new structures across 161 introns. We find 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. Multi-dimensional chemical mapping reveals that intron structures can form in vitro without the presence of binding partners, and structure ensemble prediction suggests that these structures appear in introns across the Saccharomyces genus. We develop the functional assay VARS-seq to characterize variants of RNA structure in high-throughput and we apply the method on 135 sets of stems across 7 introns, finding that some structured elements can increase spliced mRNA levels despite being distal from canonical splice sites. Unexpectedly, other structures including zipper stems can increase retained intron levels. This transcriptome-wide inference of intron RNA structures suggests new ideas and model systems for understanding how pre-mRNA folding influences gene expression.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE209857 | GEO | 2022/07/28

REPOSITORIES: GEO

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