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ProteomicsDeciphering the role of the SMG1:SMG8:SMG9 complex during the first authentication step in NMD
Nonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA turnover pathway, which degrades transcripts containing premature termination codons. The execution of NMD requires the phosphorylation of N- and C-terminal tails of the key NMD factor UPF1, which thereby serve as binding platforms f...
ORGANISM(S): Homo sapiens (Human) 
2026-02-13 | PXD051058 | Pride
Smg8 Smg9 Smg1i Nmd Nonsense-mediated mrna decay Upf1 Smg1 
TranscriptomicsmRNA-Seq from control cells and two clones of Flp-In-T-REx-293 cells modified via CRISPR-Cas9 to knockout SMG7 in combination to knockdowns of control, SMG5, and SMG6
Mature mRNAs undergo quality control during translation that may lead to RNA degradation by triggering the nonsense mediated decay (NMD) pathway. Aberrant translation due to features such as the presence of a premature stop codon downstream on an exon-exon junction or an intron in the 3'UTR activate...
ORGANISM(S): Homo sapiens 
2021-05-07 | E-MTAB-9330 | biostudies-arrayexpress
ProteomicsDeciphering the cellular roles and dissecting functional regions of UPF3A and UPF3B in human NMD
The paralogous proteins UPF3A and UPF3B are involved in recognizing defective mRNAs that are degraded by nonsense-mediated mRNA decay (NMD). While UPF3B has been demonstrated to support NMD, UPF3A was reported to act either an NMD activator or an NMD inhibitor. Here, we present a comprehensive funct...
ORGANISM(S): Homo sapiens (Human) 
2022-05-04 | PXD027120 | Pride
Mrna turnover Upf3 Nonsense-mediated mrna decay Gene paralogs 
ProteomicsProximity labelling of FLAG-TurboID-tagged UPF3B wild type and interaction-deficient mutant proteins followed by proteomics analysis
UPF3A and UPF3B are paralogous genes in human cells that are involved in the nonsense-mediated decay (NMD) pathway. NMD is a cellular quality control mechanism that monitors mRNAs during translation. Aberrant translation due to features such as the presence of a premature stop codon downstream on an...
ORGANISM(S): Homo sapiens (Human) 
2022-05-04 | PXD029898 | Pride
Mrna turnover Upf3 Nonsense-mediated mrna decay Gene paralogs 
ProteomicsThe exon junction complex component CASC3 is a major effector of nonsense-mediated mRNA decay in human cells
In metazoans, the exon junction complex (EJC) is a central component of spliced messenger ribonucleoprotein particles (mRNPs). CASC3 has been reported to be a core component of the EJC and to be crucial for assembly, the splicing regulating function of the EJC and nonsense-mediated mRNA decay (NMD)....
ORGANISM(S): Homo sapiens (Human) 
2021-02-25 | PXD015754 | Pride
Exon junction complex Splicing Nonsense-mediated mrna decay 
ProteomicsThe exon junction complex component CASC3 is a major effector of nonsense-mediated mRNA decay in human cells
In metazoans, the exon junction complex (EJC) is a central component of spliced messenger ribonucleoprotein particles (mRNPs). CASC3 has been reported to be a core component of the EJC and to be crucial for assembly, the splicing regulating function of the EJC and nonsense-mediated mRNA decay (NMD)....
ORGANISM(S): Homo sapiens (Human) 
2021-09-09 | PXD019161 | Pride
Nmd Non-sense mediated mrna decay Exon junction complex (ejc) 
TranscriptomicsRNA-Seq of UPF1 recovery in human colorectal adenocarcinoma cell line HCT116 previously depleted via the auxin-inducible degron (AID) system
UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation...
ORGANISM(S): Homo sapiens 
2025-09-01 | E-MTAB-13789 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system
UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation...
ORGANISM(S): Homo sapiens 
2025-09-01 | E-MTAB-13788 | biostudies-arrayexpress
ProteomicsProximity labelling of FLAG-TurboID-tagged UPF3B wild type and interaction-deficient mutant proteins followed by proteomics analysis
UPF3A and UPF3B are paralogous genes in human cells that are involved in the nonsense-mediated decay (NMD) pathway. NMD is a cellular quality control mechanism that monitors mRNAs during translation. Aberrant translation due to features such as the presence of a premature stop codon downstream on an...
ORGANISM(S): Homo sapiens (Human) 
2022-05-04 | PXD032337 | Pride
Mrna turnover Upf3 Nonsense-mediated mrna decay Gene paralogs 
ProteomicsInsights into transcriptome surveillance and alternative splicing regulation by the EJC-associated splicing factor RNPS1
Alternative splicing of pre-mRNAs increases the potential for regulation and complexity of gene expression. The exon junction complex (EJC) and its associated splicing factor RNPS1 were recently shown to suppress mis-splicing resulting from the usage of cryptic and reconstituted 5’ and 3’ splice sit...
ORGANISM(S): Homo sapiens (Human) 
2022-05-31 | PXD027251 | Pride
Exon junction complex Rnps1 Mrna splicing 
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