Rapid, transcript-specific changes in splicing in response to environmental stress

While the core splicing machinery is highly conserved between budding yeast and mammals, the absence of alternative splicing in Saccharomyces cerevisiae raises the fundamental question of why introns have been retained in ~5% of the 6,000 genes. Because Ribosomal Protein-encoding Genes (RPGs) are highly over-represented in the set of intron-containing genes, we tested the hypothesis that splicing of these transcripts would be regulated under conditions where translation is impaired. Using a microarraybased strategy, we find that within minutes after the induction of amino acid starvation the splicing of the majority of RPGs is specifically inhibited. In response to an unrelated stress, exposure to toxic levels of ethanol, splicing of a different group of transcripts is inhibited, while the splicing of a third set is actually improved. We propose that regulation of splicing, like transcription, can afford rapid and specific changes in gene expression in response to the environment. Keywords: stress, environmental stress, time course, splicing, splicing-specific microarray Splicing-specific microarrays were used to assay changes to splicing induced in Saccharomyces cerevisiae in response to amino-acid starvation (50mM 3-AT), Ethanol toxicity (10% EtOH) and the deletion of several non-essential factors involved in mRNA decay. The data includes time courses of shifts into each environmental stress as well as dye-flipped technical replicates of each time point.