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ProteomicsRapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome
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 (Human) 
2025-09-03 | PXD061797 | Pride
Mrna degradation Nmd Gene expression Nonsense-mediated mrna decay Upf1 Translation 
ProteomicsNonsense-mediated mRNA decay relies on "two-factor authentication" by SMG5-SMG7
Eukaryotic gene expression is constantly regulated and controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches....
ORGANISM(S): Homo sapiens (Human) 
2021-05-08 | PXD024747 | Pride
Smg6 Mrna degradation Gene expression Smg5-smg7 Nonsense-mediated mrna decay Upf1 
TranscriptomicsRNA-Seq of control and RNPS1 knockdown with or without RNPS1-RRM domain rescue in HeLa Tet-Off cells
RNPS1 is a splicing regulatory protein and a component of the ASAP/PSAP complex, which is associated with the exon junction complex and modulates alternative splicing. It was previously postulated that the isolated RRM domain of RNPS1 in complex with ASAP/PSAP is able to regulate certain alternative...
ORGANISM(S): Homo sapiens 
2022-06-22 | E-MTAB-10768 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of control and RNPS1 knockdown with or without RNPS1 wildtype or RNPS1-RRM domain rescue in Flp-In T-REx 293 cells
RNPS1 is a splicing regulatory protein and a component of the ASAP/PSAP complex, which is associated with the exon junction complex and modulates alternative splicing. It was previously postulated that the isolated RRM domain of RNPS1 in complex with ASAP/PSAP is able to regulate certain alternative...
ORGANISM(S): Homo sapiens 
2022-05-06 | E-MTAB-10770 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of WT Flp-In T-REx 293, UPF3A knockout and UPF3A overexpression cell lines in part with additional siRNA-mediated control or UPF3B knockdowns
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 
2022-08-31 | E-MTAB-10718 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of WT Flp-In T-REx 293, UPF3B knockout and UPF3A-UPF3B double knockout cell lines with additional siRNA-mediated control or UPF3B knockdowns
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 
2022-04-25 | E-MTAB-10716 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of control and EJC factor (EIF4A3, RBM8A, MAGOH) knockdowns in part with EIF4A3 rescue in HeLa Tet-Off cells
The exon junction complex is involved in gene expression regulation on multiple co- and post-transcriptional levels. We aimed to investigate in HeLa Tet-Off cells which gene expression alterations can be observed upon knockdown of core EJC factors (EIF4A3, RBM8A and MAGOH) or upon EIF4A3 knockdown a...
ORGANISM(S): Homo sapiens 
2022-05-06 | E-MTAB-10771 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of WT Flp-In T-REx 293 and UPF3B knockout cell lines with additional siRNA-mediated control or UPF3A knockdowns
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 
2022-04-25 | E-MTAB-10711 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of SARS-CoV-2 Nucleocapsid protein expression in human embryonic kidney cell line HEK293
The RNA genome of the SARS-CoV-2 virus encodes for four structural proteins, 16 non-structural proteins and nine putative accessory factors. A high throughput analysis of interactions between human and SARS-CoV-2 proteins identified multiple interactions of the structural Nucleocapsid (N) protein wi...
ORGANISM(S): Homo sapiens 
2024-09-16 | E-MTAB-14342 | 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
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