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TranscriptomicsQuality control of transcription start site selection by Nonsense-Mediated-mRNA Decay
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficie...
ORGANISM(S): Saccharomyces cerevisiae BY4741 
2015-04-24 | E-GEOD-64139 | 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 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 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
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) 
TranscriptomicsGlobal analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay
Nonsense-mediated mRNA decay (NMD) is a conserved RNA surveillance pathway that is an important modulator of disease pathology and is required for embryonic development. Despite significant research effort, the rules that govern NMD remain incompletely understood. Here we used a combined¬ approach,...
ORGANISM(S): Mus musculus 
2013-06-12 | E-GEOD-41785 | biostudies-arrayexpress
TranscriptomicsTarget discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity (RIP-Seq)
RNA quality control pathways serve to get rid of faulty RNAs and therefore must be able to discriminate these RNAs from those that are normal. Here we present evidence that the ATPase cycle of SF1 Helicase Upf1 is required for mRNA discrimination during Nonsense-Mediated Decay (NMD). Mutations affec...
ORGANISM(S): Homo sapiens 
2015-07-06 | E-GEOD-69585 | biostudies-arrayexpress
TranscriptomicsTarget discrimination in nonsense-mediated mRNA decay requires Upf1 ATPase activity (CLIP-Seq)
RNA quality control pathways serve to get rid of faulty RNAs and therefore must be able to discriminate these RNAs from those that are normal. Here we present evidence that the ATPase cycle of SF1 Helicase Upf1 is required for mRNA discrimination during Nonsense-Mediated Decay (NMD). Mutations affec...
ORGANISM(S): Homo sapiens 
2015-07-06 | E-GEOD-69584 | biostudies-arrayexpress
TranscriptomicsTDRD6 instructs correct assembly of mRNPs in the chromatoid body to potentiate UPF1 dependent mRNA decay.
RNA sequencing of heterozygote or Tudor domain contian protein 6 (TDRD6) knockout round spermatid cells. Chromatoid bodies (CBs) are germ cell-specific organelles of largely unknown function. CBs harbor various RNA species, RNA-associated proteins and proteins of the tudor domain family such as TDRD...
ORGANISM(S): Mus musculus 
2015-12-08 | E-GEOD-63948 | biostudies-arrayexpress
TranscriptomicsA single SR-like protein, Npl3, promotes pre-mRNA splicing in budding yeast
Mammalian SR proteins are a family of reversibly phosphorylated RNA binding proteins primarily studied for their roles in alternative splicing. While budding yeast lack alternative splicing, they do have three SR-like proteins: Npl3, Gbp2, and Hrb1. However, these have been primarily studied for the...
ORGANISM(S): Saccharomyces cerevisiae 
2008-12-30 | E-GEOD-11491 | biostudies-arrayexpress
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