Analysing environmentally induced genome-wide frameshift in S. cerevisiae using SLAM-Seq

In this study, we examine the impact of poor nutrient conditions on -1 ribosome frameshifting and its effect on mRNA degradation. To measure the RNA degradation, we utilized SLAM-seq (Herzog, et.al, 2017, PMID: 28945705) in S.cerevisiae in wildtype and NMD mutant (upf1Δ). Our goal with SLAM-seq is to quantify the fraction of the transcriptome that is directly degraded as a result of environmentally induced ribosome frameshifts through an NMD-dependent mechanism. To perform pulse and chase experiment, RNA molecules were labelled with 4tU for 1h during cell grown at mid exponential phase. Cells were washed and resuspend in prewarmed medium (YPD with MES buffer or CSM with MES buffer) without 4tU and time points were collected at 0, 15 and 30 mins.