Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation

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 perform a genome-wide characterisation of this process and explore the contribution of the nuclear mRNA surveillance (RRP6) to this process. Using S. cerevisiae as a model organism, we investigate changes in mRNA abundance, mRNA stability and chromatin organization. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory. 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) and rrp6delta strains. For mRNA abundance we measured mRNA abundance during exponential growth in YPD (t0, naïve) and 30 min, 1 hour and 3 hours after change to galactose (t30, t60 and t180). Then we transferred cells to YPD for 3 hours (t0’, primed) and measured galactose reinduction at 15 min, 30 min and 1 hour (t15’, t30’ and t60’). We perform 3 independent biological replicates. For ChIP-Seq we compare naïve and primed cells. We Perform MNase treatment to map nucleosomes and investigate Input material (MNase treated) and after IP for H3, H3K4me2 and H3K4me2. We perform 3 independent biological replicates. For RNA stability (nascent mRNA synthesis), we perform RNA metabolic labeling (SLAM-Seq) for naïve and primed cells. We investigate both prior to change to galactose (t0) and after 30 minutes in galactose (t30). We perform 2 independent biological replicates.