Cellular responses to environmental stress are frequently mediated by RNA-binding proteins (RBPs). Here, we examined global RBP dynamics in Saccharomyces cerevisiae in response to glucose starvation and heat shock. Each stress induced rapid remodeling of the RNA-protein interactome, without corresponding changes in RBP abundance. Consistent with general translation shutdown, ribosomal proteins contacting the mRNA showed decreased RNA-association. Among translation components, RNA-association was most reduced for initiation factors involved in 40S scanning (eIF4A, eIF4B, and Ded1), indicating a common mechanism of translational repression. In unstressed cells, eIF4A, eIF4B, and Ded1 primarily targeted the 5′-ends of mRNAs. Following glucose withdrawal, 5’-binding was abolished within 30sec, explaining the rapid translation shutdown, but mRNAs remained stable. Heat shock induced progressive loss of 5’ RNA-binding by initiation factors over ~16min. Translation shutoff provoked selective 5′-degradation of mRNAs encoding translation-related factors, mediated by Xrn1. These results reveal mechanisms underlying translational control of gene expression during stress.
There are 56 CRAC datasets, and 18 RNAseq datasets. The CRAC datasets were generated using one of three different affinity-tagged proteins: eIF4A, eIF4B, and Ded1. Cells without any tagged proteins ('untagged') were tested as a negative control. For each tagged protein, we tested four different conditions: 1) a 'control' for cells grown at 30° in SC -TRP medium with 2% glucose; 2) a 'mock' shift, in which cells were harvested by filtration, and transferred to identical medium (2% glucose at 30°C); 3) 'GE', in which the cells were collected by filtration and transferred to medium lacking glucose but containing 2% each of glycerol and ethanol; and 4) '42C', in which cells were transferred to medium containing glucose but prewarmed to 42°C. These shifts were performed for either 30 seconds or 16 minutes. Each CRAC library is associated with a unique number (07-99) to differentiate different replicates. For some analyses (e.g. bedgraph files), different replicates were combined to provide improved coverage across individual transcripts. The relevant replicates are included in the file name. The RNAseq files (A-S) were designed to mimic the conditions used for CRAC and the different conditions and timepoints used are indicated in the file names.