| 2003 |
hUpf3b contains a conserved C-terminal domain that mediates direct interaction with the EJC protein Y14; tethered function analysis showed the Y14/hUpf3b interaction is essential for NMD, while the hUpf3b–hUpf2 interaction is not strictly required for NMD activity when hUpf3b is tethered, though hUpf2 is still necessary for NMD induced by tethered Y14. |
Co-immunoprecipitation, tethered function (lambdaN/boxB) assay, RNAi knockdown and siRNA-rescue experiments |
Molecular cell |
High |
12718880
|
| 2006 |
Induction of NMD by hUpf3b requires interaction with EJC components Y14, Magoh, BTZ, and eIF4AIII via the C-terminal domain; stimulation of translation by hUpf3b is independent of this EJC interaction and is determined by other protein regions, indicating distinct downstream pathways for NMD versus translation stimulation. |
LambdaN/boxB tethered function assay, domain-swap and truncation analysis of hUpf3a vs hUpf3b |
RNA (New York, N.Y.) |
High |
16601204
|
| 2010 |
Crystal structure (3.4 Å) of a minimal UPF3b–EJC assembly (UPF3b C-terminal domain + MAGO + Y14 + eIF4AIII + Barentsz + RNA + AMP-PNP) showed that UPF3b binds with its C-terminal domain stretched over a composite surface formed by eIF4AIII, MAGO, and Y14; NMD-impairing mutations map to the core interacting surfaces, and differences between UPF3b and UPF3a map to peripheral interacting residues. |
X-ray crystallography at 3.4 Å resolution with functional validation by mutagenesis of interface residues |
Proceedings of the National Academy of Sciences of the United States of America |
High |
20479275
|
| 2016 |
UPF3A acts primarily as a potent NMD inhibitor that stabilizes hundreds of transcripts, while UPF3B is the critical NMD activator; UPF3A acquired repressor activity through impairment of a critical EJC-interaction domain present in UPF3B; mice conditionally lacking UPF3A exhibit hyper-NMD with defects in embryogenesis and gametogenesis. |
Loss-of-function mouse genetics (conditional knockout), in vitro NMD reporter assays, transcriptome profiling |
Cell |
High |
27040500
|
| 2017 |
Using a fully reconstituted in vitro translation system, UPF3B was found to (i) directly interact with eukaryotic release factors (eRFs), (ii) delay translation termination under conditions mimicking premature termination, and (iii) dissociate post-termination ribosomal complexes lacking nascent peptide; UPF1 and ribosomes were identified as new interaction partners of UPF3B. |
Fully reconstituted in vitro translation/termination assay, direct binding assays with release factors and ribosomes |
The EMBO journal |
High |
28899899
|
| 2022 |
Crystal structures of UPF2's MIF4GIII domain in complex with either UPF3B or UPF3A revealed intimate binding interfaces; UPF3B's disease-causing mutation Y160D displaces Y160 from a hydrophobic cleft in UPF2, reducing binding affinity ~40-fold; UPF3A (upregulated in UPF3B-Y160D patients) binds UPF2 with ~10-fold higher affinity than UPF3B via NOPS-L residues; the middle domain (RRM-L and NOPS-L) is essential for RNA/ribosome-binding, RNA-induced oligomerization, and UPF2 interaction. |
X-ray crystallography of UPF3B–UPF2 and UPF3A–UPF2 complexes, isothermal titration calorimetry (binding affinity measurements), mutagenesis of interface residues |
Nucleic acids research |
High |
35640974
|
| 2022 |
NMD remains partially active in human HCT116 cells lacking both UPF3 paralogs; the EJC-binding domain of UPF3 paralogs is dispensable for NMD activation; instead, the conserved 'mid' domain of UPF3 paralogs is consequential for NMD activity; UPF3A strongly activates NMD in cells lacking UPF3B, demonstrating functional redundancy. |
CRISPR/Cas9 knockout of UPF3A, UPF3B, or both; complementation with domain-deletion and EJC-binding-deficient mutants; NMD reporter assays and RNA-seq |
The EMBO journal |
High |
35451084 35451102
|
| 2022 |
Co-depletion of UPF3A and UPF3B markedly inhibits global NMD with transcriptome-wide upregulation of NMD substrates; EJC-binding-deficient or UPF2-binding-deficient UPF3B largely retains NMD activity when tested alone, but combinations of middle-domain deletions with these mutations show additive/synergistic NMD loss, indicating the middle domain is a critical functional unit. |
CRISPR/Cas9 knockout; NMD reporter assays; domain-deletion and point-mutant rescue experiments; transcriptome-wide RNA-seq |
The EMBO journal |
High |
35451084
|
| 2004 |
UPF3B-mediated mRNA degradation occurs exclusively in the cytoplasm; nuclear mRNA export is required for UPF3B-mediated NMD even though the UPF3B fusion protein used is a nucleocytoplasmic shuttling protein predominantly localized to the nucleus. |
Tethered UPF3B combined with retroviral Rev/RRE-based nuclear export regulation; subcellular localization by fluorescence microscopy |
RNA biology |
Medium |
17194930
|
| 2013 |
SATB2 directly binds the UPF3B promoter (shown by ChIP) and activates UPF3B transcription (shown by luciferase reporter assay); siRNA knockdown of SATB2 in HEK293 cells and Satb2-knockout mouse embryonic tissue both showed significantly decreased UPF3B expression, placing SATB2 as a transcriptional activator upstream of UPF3B. |
Chromatin immunoprecipitation (ChIP), luciferase reporter assay, siRNA knockdown in HEK293 cells, Satb2-knockout mouse embryonic tissue analysis |
Human genetics |
Medium |
23925499
|
| 2011 |
In UPF3B-null patient lymphoblastoid cells, UPF3A protein (but not mRNA) is stabilized in proportion inversely correlated with phenotype severity, demonstrating that UPF3B normally competes with UPF3A for UPF2 binding and that free UPF3A is unstable; UPF3A partially compensates for loss of UPF3B function. |
Western blot and qRT-PCR from patient-derived lymphoblastoid cell lines with UPF3B loss-of-function mutations; correlation analysis across multiple patients |
Molecular psychiatry |
Medium |
22182939
|
| 2009 |
UPF3B protein is expressed in neurons and localizes to dendritic spines in mouse primary hippocampal neurons as determined by immunofluorescence. |
Immunofluorescence/immunolocalization in mouse primary hippocampal neurons |
Molecular psychiatry |
Low |
19238151
|
| 2013 |
Loss of Upf3b-NMD in neural progenitor cells results in expansion of cell numbers at the expense of differentiation; in primary hippocampal neurons, loss of Upf3b-NMD causes subtle neurite growth defects; Upf3b subcellular localization is regulated during development. |
siRNA knockdown of Upf3b in neural progenitor cells and primary hippocampal neurons; cell proliferation and differentiation assays; immunocytochemistry for subcellular localization |
Human molecular genetics |
Medium |
23821644
|
| 2015 |
UPF3B missense mutations associated with neurodevelopmental disorders reduce NMD activity in tethered function assays; expression of missense mutant UPF3B disturbs neuronal differentiation and reduces neurite branching complexity; NMD is downregulated during neural stem cell differentiation with concurrent downregulation of UPF3B and UPF1. |
Tethered function NMD assay with mutant UPF3B constructs; GFP-tagged UPF3B localization in neural stem cells and neurons; neurite complexity assay; NMD inhibitor (Amlexanox) treatment |
Molecular brain |
Medium |
26012578
|
| 2017 |
Upf3b-null mice display deficits in fear-conditioned learning, profound impairment in prepulse inhibition, and deficient dendritic spine maturation in cortical pyramidal neurons in vivo; neural stem cells from Upf3b-null mice have impaired differentiation capacity. |
Upf3b-null mouse generation; behavioral testing (fear conditioning, Morris water maze, PPI); in vivo dendritic spine morphology; neural stem cell differentiation assay; RNA-seq of frontal cortex |
Molecular psychiatry |
High |
28948974
|
| 2024 |
UPF3B directly interacts with IRE1α (the ER stress sensor); this interaction inhibits IRE1α kinase activity, abolishes autophosphorylation, and reduces IRE1α clustering; the disease-causing mutation UPF3BY160D abolishes the UPF3B–IRE1α interaction; phosphorylation of UPF3B at Thr169 abolishes its interaction with UPF2. |
Co-immunoprecipitation, kinase activity assay, autophosphorylation assay, IRE1α clustering assay, site-directed mutagenesis (Y160D, T169 phosphomimetic) |
Cell death & disease |
Medium |
39138189
|
| 2024 |
UPF3B binds the 3'-UTR of CDH1 mRNA to promote its degradation (via the truncated splice variant UPF3B-S generated by HnRNPR-dependent exon 8 exclusion); UPF3B-S overexpression enhances dephosphorylation of LATS1 and nuclear accumulation of YAP1, activating Hippo signaling. |
RNA immunoprecipitation (RIP), in vitro and in vivo HCC models with UPF3B-S knockdown/overexpression, Basescope assay |
Journal of advanced research |
Low |
38402949
|
| 2024 |
UPF3B binds to PPP2R2C mRNA (a regulatory subunit of PP2A) and promotes its degradation, activating the PI3K/AKT/mTOR pathway; E2F6 transcription factor directly binds the UPF3B promoter and activates its transcription. |
Co-immunoprecipitation, RNA-binding/pulldown assays, mRNA stability assays, luciferase reporter assay for E2F6-UPF3B promoter, in vivo and in vitro HCC proliferation assays |
Cancer science |
Low |
38889220
|
| 2025 |
RBM8A interacts with UPF3B (shown by co-immunoprecipitation) to jointly regulate the stability of BBC3 (PUMA) mRNA, promoting its degradation in gastric cancer cells. |
Co-immunoprecipitation; RNA immunoprecipitation-seq; RNA pulldown; Actinomycin D mRNA stability assay |
International journal of molecular medicine |
Low |
40613240
|
| 2023 |
In cardiac sarcomeres, UPF3B (but not UPF1 or UPF2) localizes specifically to Z-discs, the presumed site of sarcomeric protein translation, suggesting a role for UPF3B-dependent NMD at the site of initial translation. |
Immunofluorescence localization in cardiac tissue from HCM patients and controls; RNA-seq gene set enrichment analysis |
Journal of molecular and cellular cardiology |
Low |
37797718
|