Pin4 Links Post-transcriptional and Transcriptional Responses to Energy Depletion in Yeast
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Abstract
Adaptation to environmental change is essential in all organisms, with RNA-binding proteins (RBPs) playing critical roles in rapid cellular responses. We analyzed the largely uncharacterized yeast RBP Pin4, and its involvement in adaptation to glucose depletion. UV crosslinking (reCRAC) revealed that in glucose conditions Pin4 binds mRNA 3’ UTRs with preference for a specific motif in mRNAs involved in glycolysis, amino acid, and mitochondrial metabolism. Following glucose withdrawal, Pin4-RNA binding was greatly reduced, with residual binding favoring transcripts associated with protein translation. Cells lacking Pin4 were greatly impaired in recovery from nutrient starvation and hypersensitive to oxidative stress, consistent with the mRNA targets. RNAseq and reporter assays indicated that loss of Pin4 correlated with some increases in target mRNA abundance. In wildtype yeast, glucose depletion induces diauxic shift, with massive changes in transcription patterns. Unexpectedly, this response was almost entirely abolished in cells lacking Pin4, its C-terminal prion-like domain, the RNA-recognition motif (RRM) or with an RRM point mutation. Pin4 is implicated in sensing energy depletion, which also occurs during the approach to stationary phase. We postulate that Pin4 helps coordinate post-transcriptional and transcriptional responses to energy stress, via riboregulation.
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However, comparison of Pin4 mRNA binding andchanges in abundance in pin4 cells revealed generally increased abundance forpreferential Pin4 targets
Can your analysis detect potential changes in alternative splicing that may result from Pin4 binding?
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These high-confidence targets showed good reproducibility acrossreplicates in both conditions
How predictive are these motifs for Pin4 binding? Are these motifs enriched on mRNAs bound by Pin4, or are they present but not bound throughout the genome?
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correspond to the mRNAs showing Pin4 association across the CDS (e.g.RPS12)
Is there any correlation between the number of motifs in a particular 3'UTR and the likelihood of being bound by Pin4?
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