scholarly journals Small uORFs favor translation re-initiation but do not protect mRNAs from nonsense-mediated decay

2022 ◽  
Author(s):  
Paul J. Russell ◽  
Jacob A. Slivka ◽  
Elaina P. Boyle ◽  
Arthur H.M. Burghes ◽  
Michael G. Kearse
Keyword(s):  
Mrna Stability ◽  
Translational Control ◽  
Upstream Open Reading Frame ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Initiation Factors ◽  
Nonsense Mediated Mrna Decay ◽  
Mrna Half Life ◽  
Reporter Mrna ◽  
Coding Capacity

It is estimated that nearly 50% of mammalian transcripts contain at least one upstream open reading frame (uORF), which are typically one to two orders of magnitude smaller than the downstream main ORF. Most uORFs are thought to be inhibitory as they sequester the scanning ribosome, but in some cases allow for translation re-initiation. However, termination in the 5ʹ UTR at the end of uORFs resembles pre-mature termination that is normally sensed by the nonsense-mediated mRNA decay (NMD) pathway. Translation re-initiation has been proposed as a method for mRNAs to prevent NMD. Here we test how uORF length influences translation re-initiation and mRNA stability. Using custom 5ʹ UTRs and uORF sequences, we show that re-initiation can occur on heterologous mRNA sequences, favors small uORFs, and is supported when initiation occurs with more initiation factors. After determining reporter mRNA half-lives and mining available mRNA half-life datasets for cumulative uORF length, we conclude that translation re-initiation after uORFs is not a robust method for mRNAs to evade NMD. Together, these data support a model where uORFs have evolved to balance coding capacity, translational control, and mRNA stability.

scholarly journals A UV-Induced Mutation in Neurospora That Affects Translational Regulation in Response to Arginine

Genetics ◽  
1996 ◽  
Vol 142 (1) ◽  
pp. 117-127 ◽  
Author(s):  
Michael Freitag ◽  
Nelima Dighde ◽  
Matthew S Sachs
Keyword(s):  
Translational Control ◽  
Translational Regulation ◽  
Fusion Gene ◽  
Mrna Translation ◽  
Small Subunit ◽  
Upstream Open Reading Frame ◽  
Control Mechanisms ◽  
Carbamoyl Phosphate ◽  
Altered Expression ◽  
Reading Frame

The Neurospora crmsu arg-2 gene encodes the small subunit of arginine-specific carbamoyl phosphate synthetase. The levels of arg-2 mRNA and mRNA translation are negatively regulated by arginine. An upstream open reading frame (uORF) in the transcript’s 5′ region has been implicated in arginine-specific control. An arg-2-hph fusion gene encoding hygromycin phosphotransferase conferred arginine-regulated resistance to hygromycin when introduced into N. crassa. We used an arg-2-hph strain to select for UV-induced mutants that grew in the presence of hygromycin and arginine, and we isolated 46 mutants that had either of two phenotypes. One phenotype indicated altered expression of both arg-2-hph and urg-2 genes; the other, altered expression of urg-2-hph but not arg-2. One of the latter mutations, which was genetically closely linked to arg-2-hph, was recovered from the 5′ region of the arg-2-hph gene using PCR. Sequence analyses and transformation experiments revealed a mutation at uORF codon 12 (Asp to Asn) that abrogated negative regulation. Examination of the distribution of ribosomes on arg-2-hph transcripts showed that loss of regulation had a translational component, indicating the uORF sequence was important for Arg-specific translational control. Comparisons with other uORFS suggest common elements in translational control mechanisms.

scholarly journals Translational Control by an Upstream Open Reading Frame in the HER-2/neuTranscript

1999 ◽  
Vol 274 (34) ◽  
pp. 24335-24341 ◽  
Author(s):  
Stephanie J. Child ◽  
Melanie K. Miller ◽  
Adam P. Geballe
Keyword(s):  
Translational Control ◽  
Open Reading Frame ◽  
Upstream Open Reading Frame ◽  
Reading Frame ◽  
Her 2

scholarly journals A role for DIS3L2 over human nonsense-mediated mRNA decay targets

2019 ◽  
Author(s):  
Paulo J. da Costa ◽  
Juliane Menezes ◽  
Margarida Saramago ◽  
Juan F. García-Moreno ◽  
Hugo A. Santos ◽  
...  
Keyword(s):  
Translation Termination ◽  
Full Length ◽  
Nonsense Mediated Decay ◽  
Endonucleolytic Cleavage ◽  
Nonsense Mediated Mrna Decay ◽  
Translation Termination Codon ◽  
Life Analysis ◽  
Mrna Half Life ◽  
Premature Translation Termination Codon

ABSTRACTThe nonsense-mediated decay (NMD) pathway selectively degrades mRNAs carrying a premature translation-termination codon but also regulates the abundance of a large number of physiological mRNAs that encode full-length proteins. In human cells, NMD-targeted mRNAs are degraded by endonucleolytic cleavage and exonucleolytic degradation from both 5’ and 3’ ends. This is done by a process not yet completely understood that recruits decapping and 5’-to-3’ exonuclease activities, as well as deadenylating and 3’-to-5’ exonuclease exosome activities. In yeast, DIS3/Rrp44 protein is the catalytic subunit of the exosome, but in humans, there are three known paralogues of this enzyme: DIS3, DIS3L1, and DIS3L2. DIS3L1 and DIS3L2 exoribonucleases localize in the same compartment where NMD occurs, but little is known about their role in this process. In order to unveil the role of DIS3L2 in NMD, here we show that some NMD-targets accumulate in DIS3L2-depleted cells. mRNA half-life analysis further supports that these NMD-targets are in fact DIS3L2 substrates. Besides, we observed that DIS3L2 acts over full-length transcripts, through a process that also involves UPF1. Moreover, DIS3L2-mediated decay is dependent on the activity of the terminal uridylyl transferases Zcchc6/11 (TUT7/4). Together, our findings establish a role for DIS3L2 and uridylation in NMD.

scholarly journals Quality control of transcription start site selection by nonsense-mediated-mRNA decay

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Christophe Malabat ◽  
Frank Feuerbach ◽  
Laurence Ma ◽  
Cosmin Saveanu ◽  
Alain Jacquier
Keyword(s):  
Quality Control ◽  
Rna Polymerase Ii ◽  
Mrna Decay ◽  
Rna Degradation ◽  
Upstream Open Reading Frame ◽  
Start Codon ◽  
Messenger Rnas ◽  
Transcription Start ◽  
Reading Frame ◽  
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 deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. Moreover, we found that the low specificity of RNA polymerase II TSSs selection generates, for 47% of the expressed genes, NMD-sensitive transcript isoforms carrying uORFs or starting downstream of the ATG START codon. Despite the low abundance of this last category of isoforms, their presence seems to constrain genomic sequences, as suggested by the significant bias against in-frame ATGs specifically found at the beginning of the corresponding genes and reflected by a depletion of methionines in the N-terminus of the encoded proteins.

scholarly journals Transgenic zebrafish model to study translational control mediated by upstream open reading frame of human chop gene

2011 ◽  
Vol 39 (20) ◽  
pp. e139-e139 ◽  
Author(s):  
Hung-Chieh Lee ◽  
Yi-Jiun Chen ◽  
Yu-Wei Liu ◽  
Kai-Yen Lin ◽  
Shaio-Wen Chen ◽  
...  
Keyword(s):  
Translational Control ◽  
Open Reading Frame ◽  
Upstream Open Reading Frame ◽  
Transgenic Zebrafish ◽  
Zebrafish Model ◽  
Reading Frame

scholarly journals Sucrose-induced translational repression of plant bZIP-type transcription factors

2005 ◽  
Vol 33 (1) ◽  
pp. 272-275 ◽  
Author(s):  
A. Wiese ◽  
N. Elzinga ◽  
B. Wobbes ◽  
S. Smeekens
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Translational Control ◽  
Leucine Zipper ◽  
Upstream Open Reading Frame ◽  
Bzip Transcription Factor ◽  
Reading Frame ◽  
Signalling Molecules ◽  
Transcription Factor Genes ◽  
Plant Genes

Sugars as signalling molecules exert control on the transcription of many plant genes. Sugar signals also alter mRNA and protein stability. Increased sucrose concentrations specifically repress translation of the S-class basic region leucine zipper (bZIP) type transcription factor AtbZIP11/ATB2. This sucrose-induced repression of translation (SIRT) depends on translation of a highly conserved upstream open reading frame (uORF) in the 5′ UTR of the gene. This conserved uORF is exclusively encoded in 5′ UTRs of several plant S-class bZIP transcription factors. Arabidopsis homologues of ATB2/AtbZIP11, which harbour the conserved uORF, also show SIRT. Therefore, SIRT emerges as a general sucrose translational control mechanism of a group of transcription factors. SIRT might be part of a sucrose-specific signalling pathway, controlling expression of plant bZIP transcription factor genes.

scholarly journals Translational control of C/EBPα and C/EBPβ isoform expression

2000 ◽  
Vol 14 (15) ◽  
pp. 1920-1932 ◽  
Author(s):  
Cor F. Calkhoven ◽  
Christine Müller ◽  
Achim Leutz
Keyword(s):  
Cell Fate ◽  
Translation Initiation ◽  
Translational Control ◽  
Ectopic Expression ◽  
Cell Types ◽  
Upstream Open Reading Frame ◽  
Reading Frame ◽  
Initiation Of Translation ◽  
Isoform Expression ◽  
Differentiation And Proliferation

Transcription factors derived from CCAAT/enhancer binding protein (C/EBP)α and C/EBPβ genes control differentiation and proliferation in a number of cell types. Various C/EBP isoforms arise from unique C/EBPβ and C/EBPα mRNAs by differential initiation of translation. These isoforms retain different parts of the amino terminus and therefore display different functions in gene regulation and proliferation control. We show that PKR and mTOR signaling pathways control the ratio of C/EBP isoform expression through the eukaryotic translation initiation factors eIF-2α and eIF-4E, respectively. An evolutionary conserved upstream open reading frame in C/EBPα and C/EBPβ mRNAs is a prerequisite for regulated initiation from the different translation initiation sites and integrates translation factor activity. Deregulated translational control leading to aberrant C/EBPα and C/EBPβ isoform expression or ectopic expression of truncated isoforms disrupts terminal differentiation and induces a transformed phenotype in 3T3-L1 cells. Our results demonstrate that the translational controlled ratio of C/EBPα and C/EBPβ isoform expression determines cell fate.

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