Measurement of mRNA stability during transcriptional memory in mutants for RNA degradation

Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, we investigate the contribution of cytoplasmic RNA decay to this process, we investigate global changes in mRNA turnover in ski2? (component of the cytoplasmic 3'-5'exosome) and xrn1? (cytoplasmic 5'-3'exonuclease) strains in S. cerevisiae. Overall design: We use S. cerevisiae as a model organism and investigate the gene expression changes associated to the change from rich media with glucose as carbon source (YPD) to rich media with galactose as carbon source (YPGal). We investigate naïve and primed cells in both wild type (BY4741), ski2? and xrn1? strains. For the wild-type strain we perform a pulse chase strategy (labeling for 1h prior to change to YPGal and measuring at t0,10 and 30 min). While for mutant strains we assume steady state for RNA turnover and measure in YPD (for naïve and primed cells). We perform 3 independent biological replicates.