Here we present the development and implementation of a genome-wide reverse 
genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples 
high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and 
quantitative PCR to allow for a robust determination of the level of nearly any 
cellular RNA in the background of ~5,500 different mutants. As an initial test 
of this approach, we sought to identify the full complement of factors that 
impact pre-mRNA splicing. Increasing lines of evidence suggest a relationship 
between pre-mRNA splicing and other cellular pathways including chromatin 
remodeling, transcription, and 3' end processing, yet in many cases the specific 
proteins responsible for functionally connecting these pathways remain unclear. 
Moreover, it is unclear whether all pathways that are coupled to splicing have 
been identified. As expected, our approach sensitively detects pre-mRNA 
accumulation in the vast majority of strains containing mutations in known 
splicing factors. Remarkably, however, several additional candidates were found 
to cause increases in pre-mRNA levels similar to that seen for canonical 
splicing mutants, none of which had previously been implicated in the splicing 
pathway. Instead, several of these factors have been previously implicated to 
play roles in chromatin remodeling, 3' end processing, and other novel 
categories. Further analysis of these factors using splicing-sensitive 
microarrays confirms that deletion of Bdf1, a factor that links transcription 
initiation and chromatin remodeling, leads to a global splicing defect, 
providing evidence for a novel connection between pre-mRNA splicing and this 
component of the SWR1 complex. By contrast, mutations in 3' end processing 
factors such as Cft2 and Yth1 also result in pre-mRNA splicing defects, although 
only for a subset of transcripts, suggesting that spliceosome assembly in S. 
cerevisiae may more closely resemble mammalian models of exon-definition. More 
broadly, our work demonstrates the capacity of this approach to identify novel 
regulators of various cellular RNAs.