Genome-wide screening reveals repression by nuclear exosome as a prerequisite for intron-mediated enhancement in Saccharomyces cerevisiae

Introns can enhance gene expression, a phenomenon called intron-mediated enhancement (IME). Previously proposed IME mechanisms do not sufficiently explain the variability in enhancement levels, suggesting that IME mechanism has not been fully understood. A comprehensive screening of genes involved in IME can provide valuable insights. Recently, using a luciferase coding sequence (yCLuc), we showed that IME functions by relieving repression rather than simply enhancing expression. The expression of yCLuc is repressed by the specific nucleotide sequence UCUU, and adding an intron relieves this repression in the yeast Saccharomyces cerevisiae. Herein, genome-wide screenings were conducted using S. cerevisiae knockout strain libraries to identify genes involved in IME. For screening, yCLuc was expressed with and without an intron in knockout strains. Consequently, CDC73, a regulator of RNA polymerase II (RNAPII), was identified as essential for enhancement. Additionally, 23 genes specifically involved in the repression were identified. These 23 genes are related to nuclear exosomes, RNA modification, RNAPII regulation, the nuclear pore complex, ribosomes, and chromatin modification. Among these, genes associated with nuclear exosomes, which degrade various RNAs in the nucleus, showed the largest impact on expression. The RNA sequence UCUU has been reported as a target for RNA degradation by nuclear exosomes. These findings suggested that UCUU-containing coding sequences are primarily repressed via RNA degradation by the nuclear exosome through UCUU recognition, with this repression being relieved by the presence of an intron.