Poster abstracts
Poster number 3 submitted by Rene Arvola
Investigating the interactome and functions of UPF3 paralogs in Nonsense Mediated mRNA Decay
Rene Arvola (Department of Molecular Genetics, The Center for RNA Biology, The Ohio State University), Kristin Nedza (Department of Molecular Genetics, The Center for RNA Biology, The Ohio State University), Guramrit Singh (Department of Molecular Genetics, The Center for RNA Biology, The Ohio State University)
Abstract:
Nonsense Mediated mRNA Decay (NMD) degrades both aberrant transcripts containing Premature Termination Codons (PTCs) and “normal” transcripts with other specific features. Regulation by NMD is pervasive and estimated to impact around 10% of the transcriptome. UPF3 is a central NMD factor that engages with the mRNA bound Exon Junction Complex (EJC) and the rest of the NMD machinery to aid in PTC recognition. In mammals, there are two paralogs of UPF3, UPF3A and UPF3B, that have been documented to have both redundant and possibly distinct roles. In mice, Upf3a knockout is embryonic lethal [1], whereas Upf3b knockouts are viable, but exhibit neurodevelopmental defects [2]. Moreover, mutations in UPF3B are linked to various forms of intellectual disability in humans (summarized in [3]). We and others previously found that UPF3A can compensate for UPF3B in NMD, but is a weaker activator; this difference in activity is conferred by a poorly characterized “mid” domain [4]. Moreover, overexpression of UPF3A, but not UPF3B stabilizes an NMD reporter mRNA. To understand the different propensities of UPF3 paralogs to stimulate NMD, we performed immunoprecipitation from a human colorectal carcinoma cell line (HCT116) followed by mass spectrometry to identify their associated factors. In addition to the known EJC and NMD components, we identified transcriptional regulators and nucleocytoplasmic shuttling factors to be among some of the most enriched factors in UPF3A and UPF3B immunoprecipitation. Ongoing work includes investigating whether these factors underlie any differences between UPF3A and UPF3B function and whether UPF3B mutations found in patients alter these interactions. Furthermore, we will investigate how perturbations in UPF3 nucleocytoplasmic shuttling impact NMD function. Taken together, this work will deepen our understanding of how mRNA decay is modulated and how these processes become dysregulated in development and disease.
References:
[1] Shum EY, et al. The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay. Cell. 2016 Apr 7;165(2):382-95.
[2] Huang L, et al. A Upf3b-mutant mouse model with behavioral and neurogenesis defects. Mol Psychiatry. 2018 Aug;23(8):1773-1786.
[3] Deka B, Chandra P, Singh KK. Functional roles of human Up-frameshift suppressor 3 (UPF3) proteins: From nonsense-mediated mRNA decay to neurodevelopmental disorders. Biochimie. 2021 Jan;180:10-22
[4] Yi Z, et al. Mammalian UPF3A and UPF3B can activate nonsense-mediated mRNA decay independently of their exon junction complex binding. EMBO J. 2022 May 16;41(10):e109202.
Keywords: mRNA decay, Nonsense Mediated Decay, Exon Junction Complex