Mammalian UPF3A and UPF3B can activate nonsense‐mediated mRNA decay independently of their exon junction complex binding
Zhongxia Yi, René M. Arvola, Sean Myers, Corinne Dilsavor, Rabab Abu Alhasan, Bayley N Carter, Robert D. Patton, Ralf Bundschuh, Guramrit Singh
Abstract
Nonsense‐mediated mRNA decay (NMD) is governed by the three conserved factors—UPF1, UPF2, and UPF3. While all three are required for NMD in yeast, UPF3B is dispensable for NMD in mammals, and its paralog UPF3A is suggested to only weakly activate or even repress NMD due to its weaker binding to the exon junction complex (EJC). Here, we characterize the UPF3A/B‐dependence of NMD in human cell lines deleted of one or both UPF3 paralogs. We show that in human colorectal cancer HCT116 cells, NMD can operate in a UPF3B‐dependent and ‐independent manner. While UPF3A is almost dispensable for NMD in wild‐type cells, it strongly activates NMD in cells lacking UPF3B. Notably, NMD remains partially active in cells lacking both UPF3 paralogs. Complementation studies in these cells show that EJC‐binding domain of UPF3 paralogs is dispensable for NMD. Instead, the conserved “mid” domain of UPF3 paralogs is consequential for their NMD activity. Altogether, our results demonstrate that the mammalian UPF3 proteins play a more active role in NMD than simply bridging the EJC and the UPF complex. Mammalian cells are known to express two paralogs of the nonsense‐mediated mRNA decay (NMD) factor UPF3, yet their individual roles in NMD are still debated. Here the two forms are found to activate NMD without binding to the exon junction complex (EJC). Deletion of the NMD‐factor UPF3A and/or UPF3B in human cell lines reveals UPF3B‐dependent and ‐independent NMD.