P-bodies act as dynamic control hubs for RNA processing and storage

Processing bodies (PBs) are cytoplasmic granules that function in the cellular response to stress conditions by regulating mRNA metabolism. Initially, they were thought to represent sites of mRNA turnover, whereas more recent work points to a role in the storage of useful mRNAs. However, their exact intracellular role remains unclear. We used SH-linked alkylation for the metabolic sequencing of RNA (SH-linked alkylation for the metabolic sequencing of RNA) to study PB-localization and global mRNA fate during glucose depletion conditions that induce PB formation in yeast. This enabled us to differentiate newly synthesized and preexisting RNAs and to separately track mRNA synthesis and degradation. We show that preexisting mRNAs localize to PBs with differing kinetics with some transcripts localizing over the time course of glucose starvation and some transcripts localizing in a more dynamic manner. We identified a small number of transcripts that are enriched only transiently in PBs, consistent with the traditional view of PBs acting as sites for RNA decay. However, most transiently localized transcripts are not destabilized following glucose starvation, with PBs appearing to act as temporary storage sites for transcripts that later undergo alternative fates. For other transcripts, both their preexisting and newly made transcripts accumulate in PBs over the time course of glucose depletion, and we suggest that these transcripts are important for adaptation once the nutrient stress is relieved. Together, our data indicate a model where transcripts partition into different classes that behave differently following nutrient depletion with PBs acting as triage sites for mRNAs to direct their fate.