Monaghan, L.; Srinath, C. F.; Mann, A. R.; Grimes, G. R.; Longman, D.; Caceres, J. F.

The nonsense-mediated decay pathway (NMD) is an RNA quality control mechanism that regulates the stability of target RNAs. We previously identified the ER-localized SEC13 protein as a novel NMD factor in C. elegans and in HeLa cells; raising the possibility that it could be involved in regulating the stability of mRNAs translated at the ER. SEC13 is a component of several cellular complexes, including the COPII vesicle coat, the nuclear pore complex (NPC) and the nutrient sensing GATOR2 complex. Here, we show that SEC13 interacts with core NMD factors and using a newly developed dual-color fluorescent NMD sensor in U2OS cells, we assessed SEC13 NMD activity, at a single-cell level. Transcriptomic profiling revealed that unlike the previously described ER-NMD factor, NBAS, SEC13 co-regulates the stability of substrates translated both in the cytoplasm and at the ER. We also show that SEC13 function in NMD is largely independent of its function in other cellular complexes. Altogether, these results show that SEC13 is a bona fide NMD factor in mammalian cells. Finally, we utilized an ER stress-activated indicator (ERAI) in U2OS cells to demonstrate that SEC13, together with canonical NMD factors, has a role in the regulation of the unfolded protein response (UPR) at the ER. Thus, the moonlighting functions of SEC13 include a role in NMD pathway and the regulation of ER stress.