Multiple decay events target HAC1 mRNA during splicing to regulate the unfolded protein response

Abstract

In the unfolded protein response (UPR), stress in the endoplasmic reticulum (ER) activates a large transcriptional program to increase ER folding capacity. During the budding yeast UPR, Ire1 excises an intron from the HAC1 mRNA and the exon products of cleavage are ligated, and the translated protein induces hundreds of stress-response genes. Using cells with mutations in RNA repair and decay enzymes, we show that phosphorylation of two different HAC1 splicing intermediates is required for their degradation by the 50′→30′ exonuclease Xrn1 to enact opposing effects on the UPR. We also found that ligated but 20′-phosphorylated HAC1 mRNA is cleaved, yielding a decay intermediate with both 50′- and 20′-phosphates at its 50′-end that inhibit 50′→30′ decay and suggesting that Ire1 degrades incompletely processed HAC1. These decay events expand the scope of RNA-based regulation in the budding yeast UPR and have implications for the control of the metazoan UPR.