Identification of a regulated pathway for nuclear pre-mRNA turnover

We have identified a nuclear pathway that rapidly degrades unspliced pre-mRNAs in yeast. This involves 3′→5′ degradation by the exosome complex and 5′→3′ degradation by the exonuclease Rat1p. 3′→5′ degradation is normally the major pathway and is regulated in response to carbon source. Inhibition of pre-mRNA degradation resulted in increased levels of pre-mRNAs and spliced mRNAs. When splicing was inhibited by mutation of a splicing factor, inhibition of turnover resulted in 20- to 50-fold accumulation of pre-mRNAs, accompanied by increased mRNA production. Splicing of a reporter construct with a 3′ splice site mutation was also increased on inhibition of turnover, showing competition between degradation and splicing. We propose that nuclear pre-mRNA turnover represents a novel step in the regulation of gene expression.