A termination-independent role of Rat1 in cotranscriptional splicing

The yeast termination factor Rat1, and its human homolog Xrn2, have been implicated in multiple nuclear processes. Here we report a novel role of Rat1 in mRNA splicing. Rat1 mutants display increased levels of unspliced transcripts. Accumulation of unspliced transcripts was not due to a failure to degrade unspliced mRNA, disruption of termination or an increased elongation rate in Rat1 mutants. ChIP-Seq analysis revealed Rat1 crosslinking to the introns of a subset of yeast genes. Mass spectrometry and coimmunoprecipitation revealed interaction of Rat1 with the Clf1, Isy1, Yju2, Prp43, and Sub2 splicing factors. Furthermore, recruitment of the Prp2 splicing factor on the intron was compromised in the Rat1 mutant. Based on these findings we propose that Rat1 has a novel role in splicing of a subset of mRNA in budding yeast.