Intron retention analysis using isogrowth profiling

We present an analysis of intron retention under stress from two different drugs and their combinations in yeast Saccharomyces cerevisiae. We previously established isogrowth profiling, a method to abstract the non-specific effects of growth rate inhibition from the specific effect of perturbation by a small molecule: two drugs are used at varied ratios, but at fixed overall growth inhibition. Here, cycloheximide and LiCl were used at seven different ratios along the 50% growth inhibition isobole and the total ribodepleted RNA was sequenced. This allowed us to gauge the changes in intron retention due to the used drugs, while ensuring that the effects are not caused by growth inhibition. We found a prominent increase in intron retention under LiCl treatment that preferentially affects introns contained in the transcripts of ribosomal proteins. Saccharomyces cerevisiae strain BY4741 was grown in 7 conditions of varying ratios of LiCl and cycloheximide, ensuring 50% growth inhibition, and in YPD containing no drug. Before sequencing, the extracted RNA was ribodepleted rather than polyA-enriched.