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bioRxiv · 10.1101/2025.11.18.689056

FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

Palo, A.·Mohapatra, T.·Singh, A.·T, S.·Mohanty, S.·Swain, R. K.·Dixit, M.
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Abstract

FRG1 acts as a molecular double-edged sword: while its overexpression is linked to facioscapulohumeral muscular dystrophy (FSHD), its under expression activates tumorigenic signalling pathways--highlighting the importance of tightly regulated FRG1 levels. Although prior studies have hinted at FRG1s involvement in RNA biogenesis, its core molecular functions have remained largely elusive. Our previous work identified FRG1 as a transcriptional regulator of genes in the nonsense-mediated decay (NMD) pathway; however, the underlying mechanisms were not fully delineated. In this study, using a range of cellular models with altered FRG1 expression, we demonstrate that reduced FRG1 levels enhance NMD activity. We reveal that FRG1 is a structural component of both the spliceosome and the exon junction complex (EJC), and that it directly modulates NMD by interacting with UPF1--regulating its ubiquitination and degradation. Furthermore, we show that DUX4 inversely regulates the NMD machinery through FRG1, establishing a critical molecular axis. Despite its structural association with the EJC and spliceosome, the absence of FRG1 does not compromise the integrity of these complexes. Polysome profiling showed that FRG1 co-sediments with eIF4A3, a core EJC component, across translating ribosomal fractions. This interaction was further supported by proximity ligation assays confirming the close spatial proximity of FRG1 and eIF4A3. Importantly, we validated the impact of FRG1 perturbation on NMD efficiency and UPF1 levels in vivo using a transgenic FRG1 knockout zebrafish model. Together, these findings establish a direct, DUX4-independent role for FRG1 in regulating the NMD pathway and uncover a previously unrecognized function for FRG1 in post-transcriptional gene regulation. Our work provides mechanistic insight into FRG1s molecular roles and lays the groundwork for therapeutic strategies targeting diseases associated with its dysregulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/689056v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1ef00e1org.highwire.dtl.DTLVardef@22cd63org.highwire.dtl.DTLVardef@da4080org.highwire.dtl.DTLVardef@c0d283_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

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Palo, A., Mohapatra, T., Singh, A., T, S., Mohanty, S., Swain, R. K., Dixit, M.. 2025-11-18. FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels. https://doi.org/10.1101/2025.11.18.689056

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