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Induction of unfolded protein response involves activation of transcription factor Hac1p that is encoded by  HAC1  pre-mRNA harboring an intron and a bipartite element (BE), which is subjected to nuclear mRNA decay by the nuclear exosome/Cbc1p-Tif4631p-dependent Exosome Targeting (CTEXT) complex. Using a combination of genetic and biochemical approaches, we demonstrate that a Rab-GTPase Ypt1p controls unfolded protein response signaling dynamics. This regulation relies on the nuclear localization of a small fraction of the cellular Ypt1p pool in the absence of endoplasmic reticulum (ER)-stress causing a strong association of the nuclear Ypt1p with pre- HAC1  mRNA that eventually promotes sequential recruitments of NNS, CTEXT, and the nuclear exosome onto this pre-mRNA. Recruitment of these decay factors onto pre- HAC1  mRNA is accompanied by its rapid nuclear decay that produces a precursor RNA pool lacking functional BE thereby causing its inefficient targeting to Ire1p foci leading to their diminished splicing and translation. ER stress triggers rapid relocalization of the nuclear pool of Ypt1p to the cytoplasm leading to its dissociation from pre- HAC1  mRNA thereby causing decreased recruitment of these decay factors to precursor  HAC1  RNA leading to its diminished degradation. Reduced decay results in an increased abundance of pre- HAC1  mRNA with intact functional BE leading to its enhanced recruitment to Ire1p foci.

The Sequential Recruitments of Rab-GTPase Ypt1p and the NNS Complex onto pre- HAC1 mRNA Promote Its Nuclear Degradation in Baker’s Yeast