scholarly journals Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis

2020 ◽  
Vol 32 (9) ◽  
pp. 2725-2741 ◽  
Author(s):  
Vivek K. Raxwal ◽  
Craig G. Simpson ◽  
Jiradet Gloggnitzer ◽  
Juan Carlos Entinze ◽  
Wenbin Guo ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Rna Decay ◽  
Decay Factor ◽  
Nonsense Mediated Rna Decay

scholarly journals Inhibition of Nonsense-Mediated RNA Decay by the Tumor Microenvironment Promotes Tumorigenesis

2011 ◽  
Vol 31 (17) ◽  
pp. 3670-3680 ◽  
Author(s):  
D. Wang ◽  
J. Zavadil ◽  
L. Martin ◽  
F. Parisi ◽  
E. Friedman ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Rna Decay ◽  
Nonsense Mediated Rna Decay

scholarly journals RNA Decay Factor UPF1 Promotes Protein Decay: A Hidden Talent

BioEssays ◽  
2017 ◽  
Vol 40 (1) ◽  
pp. 1700170 ◽  
Author(s):  
Terra-Dawn M. Plank ◽  
Miles F. Wilkinson
Keyword(s):  
Rna Decay ◽  
Decay Factor

scholarly journals The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay

Cell ◽  
2016 ◽  
Vol 165 (2) ◽  
pp. 382-395 ◽  
Author(s):  
Eleen Y. Shum ◽  
Samantha H. Jones ◽  
Ada Shao ◽  
Jennifer Dumdie ◽  
Matthew D. Krause ◽  
...  
Keyword(s):  
Rna Decay ◽  
Nonsense Mediated Rna Decay

scholarly journals Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
pp. 154 ◽  
Author(s):  
Sho Maekawa ◽  
Naoto Imamachi ◽  
Takuma Irie ◽  
Hidenori Tani ◽  
Kyoko Matsumoto ◽  
...  
Keyword(s):  
Rna Stability ◽  
Rna Decay ◽  
Decay Factor

scholarly journals Nonsense mediated RNA decay factor UPF1 is critical for post-transcriptional and translational gene regulation in Arabidopsis

2020 ◽  
Author(s):  
Vivek K. Raxwal ◽  
Craig G. Simpson ◽  
Jiradet Gloggnitzer ◽  
Juan Carlos Entinze ◽  
Wenbin Guo ◽  
...  
Keyword(s):  
Ribosome Biogenesis ◽  
Control Mechanism ◽  
Transcriptome Assembly ◽  
Regulation Of Gene Expression ◽  
Translational Repression ◽  
Rna Decay ◽  
Genome Wide ◽  
Mrna Variants ◽  
Nonsense Mediated Rna Decay ◽  
Rapid Activation

AbstractNonsense mediated RNA decay (NMD) is an evolutionary conserved RNA control mechanism that has also been implicated in the broader regulation of gene expression. Nevertheless, a role for NMD in genome regulation has not been fully assessed, partially because NMD inactivation is lethal in many organisms. Here, we performed in depth comparative analysis of Arabidopsis mutants lacking key proteins involved in different steps of NMD. We observed that UPF3, UPF1, and SMG7 have different impacts on NMD and the Arabidopsis transcriptome, with UPF1 having the biggest effect. Transcriptome assembly using stringent pipeline in UPF1-null plants revealed genome wide changes in alternative splicing, including switches in mRNA variants, suggesting a role for UPF1 in splicing. We further found that UPF1 inactivation leads to translational repression, manifested by a global shift in mRNAs from polysomes to monosomes and a downregulation of genes involved in translation and ribosome biogenesis. Despite this global change, NMD targets and low-expressed mRNAs with short half-lives were enriched in polysomes, indicating that UPF1 specifically suppresses the translation of aberrant RNAs. Particularly striking was an increase in the translation of TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptors. The regulation of TNLs via UPF1/NMD-mediated mRNA stability and translational de-repression offers a dynamic mechanism for the rapid activation of TNLs in response to pathogen attack.

scholarly journals UPF1-Mediated RNA Decay—Danse Macabre in a Cloud

Biomolecules ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 999 ◽  
Author(s):  
Daria Lavysh ◽  
Gabriele Neu-Yilik
Keyword(s):  
High Variability ◽  
Effector Proteins ◽  
Degradation Efficiency ◽  
Rna Decay ◽  
User Needs ◽  
Effector Protein ◽  
Higher Eukaryotes ◽  
Flexible Infrastructure ◽  
Nonsense Mediated Rna Decay ◽  
Central Effector

Nonsense-mediated RNA decay (NMD) is the prototype example of a whole family of RNA decay pathways that unfold around a common central effector protein called UPF1. While NMD in yeast appears to be a linear pathway, NMD in higher eukaryotes is a multifaceted phenomenon with high variability with respect to substrate RNAs, degradation efficiency, effector proteins and decay-triggering RNA features. Despite increasing knowledge of the mechanistic details, it seems ever more difficult to define NMD and to clearly distinguish it from a growing list of other UPF1-mediated RNA decay pathways (UMDs). With a focus on mammalian NMD, we here critically examine the prevailing NMD models and the gaps and inconsistencies in these models. By exploring the minimal requirements for NMD and other UMDs, we try to elucidate whether they are separate and definable pathways, or rather variations of the same phenomenon. Finally, we suggest that the operating principle of the UPF1-mediated decay family could be considered similar to that of a computing cloud providing a flexible infrastructure with rapid elasticity and dynamic access according to specific user needs.

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