scholarly journals Genetic screens identify connections between ribosome recycling and nonsense mediated decay

2021 ◽  
Author(s):  
Karole N D'Orazio ◽  
Laura N. Lessen ◽  
Anthony J. Veltri ◽  
Zachary Neiman ◽  
Miguel E. Pacheco ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Premature Termination ◽  
Stop Codon ◽  
Premature Termination Codon ◽  
Termination Codon ◽  
Genetic Screens ◽  
Regulatory Pathway ◽  
Nonsense Mediated Decay ◽  
Stop Codons ◽  
Reported Data

The decay of messenger RNA with a premature termination codon (PTC) by nonsense mediated decay (NMD) is an important regulatory pathway for eukaryotes and an essential pathway in mammals. NMD is typically triggered by the ribosome terminating at a stop codon that is aberrantly distant from the poly-A tail. Here, we use a fluorescence screen to identify factors involved in NMD in S. cerevisiae . In addition to the known NMD factors, including the entire UPF family (UPF1, UPF2 and UPF3), as well as NMD4 and EBS1 , we identify factors known to function in post-termination recycling and characterize their contribution to NMD. We then use a series of modified reporter constructs that block both elongating and scanning ribosomes downstream of stop codons and demonstrate that a deficiency in recycling of 80S ribosomes or 40S subunits stabilizes NMD substrates. These observations in S. cerevisiae expand on recently reported data in mammals indicating that the 60S recycling factor ABCE1 is important for NMD (1,2) by showing that increased activities of both elongating and scanning ribosomes (80S or 40S) in the 3’UTR correlate with a loss of NMD.

scholarly journals Aberrant splicing of the E-cadherin transcript is a novel mechanism of gene silencing in chronic lymphocytic leukemia cells

Blood ◽  
2009 ◽  
Vol 114 (19) ◽  
pp. 4179-4185 ◽  
Author(s):  
Sanjai Sharma ◽  
Alan Lichtenstein
Keyword(s):  
B Cells ◽  
Chronic Lymphocytic Leukemia ◽  
Premature Termination ◽  
Ectopic Expression ◽  
Premature Termination Codon ◽  
Lymphocytic Leukemia ◽  
Termination Codon ◽  
Nonsense Mediated Decay ◽  
Aberrant Transcript ◽  
E Cadherin

Abstract Premature termination codon (PTC) mutations are due to insertion or deletion of nucleotides causing a frameshift and premature termination codon in RNA. These transcripts are degraded by the nonsense-mediated decay pathway and have a very short half-life. We used a microarray technique to screen for genes that up-regulate their RNA signal upon nonsense-mediated decay pathway blockade in chronic lymphocytic leukemia (CLL) specimens and identified an E-cadherin transcript with PTC. Sequencing revealed an aberrant E-cadherin transcript lacking exon 11, resulting in a frameshift and PTC. The aberrant E-cadherin transcript was also identified in normal B cells, but occurred at a much lower level compared with CLL cells. In CLL specimens, E-cadherin expression was depressed more than 50% in 62% cases (relative to normal B cells). By real-time polymerase chain reaction analysis, the relative amounts of wild-type transcript inversely correlated with amounts of aberrant transcript (P = .018). Ectopic expression of E-cadherin in CLL specimens containing high amounts of aberrant transcript resulted in down-regulation of the wnt–β-catenin pathway reporter, a pathway known to be up-regulated in CLL. Our data point to a novel mechanism of E-cadherin gene inactivation, with CLL cells displaying a higher proportion of aberrant nonfunctional transcripts and resulting up-regulation of the wnt–β-catenin pathway.

scholarly journals A murine Zic3 transcript with a premature termination codon evades nonsense-mediated decay during axis formation

2013 ◽  
Vol 6 (3) ◽  
pp. 755-767 ◽  
Author(s):  
J. N. Ahmed ◽  
R. G. Ali ◽  
N. Warr ◽  
H. M. Wilson ◽  
H. M. Bellchambers ◽  
...  
Keyword(s):  
Premature Termination ◽  
Premature Termination Codon ◽  
Termination Codon ◽  
Axis Formation ◽  
Nonsense Mediated Decay

scholarly journals Selective destabilization of polypeptides synthesized from NMD-targeted transcripts

2021 ◽  
Author(s):  
Vincent Chu ◽  
Qing Feng ◽  
Yang Lim ◽  
Sichen Shao
Keyword(s):  
Mammalian Cells ◽  
Premature Termination ◽  
Proteasome Inhibition ◽  
Premature Termination Codon ◽  
Dominant Negative ◽  
Termination Codon ◽  
Negative Effects ◽  
Nonsense Mediated Decay ◽  
Mrna Surveillance ◽  
Reporter Systems

The translation of mRNAs that contain a premature termination codon (PTC) generates truncated proteins that may have toxic dominant negative effects. Nonsense-mediated decay (NMD) is an mRNA surveillance pathway that degrades PTC-containing mRNAs to limit the production of truncated proteins. NMD activation requires a ribosome terminating translation at a PTC, but what happens to the polypeptides synthesized during the translation cycle needed to activate NMD is incompletely understood. Here, by establishing reporter systems that encode the same polypeptide sequence before a normal or premature termination codon, we show that termination of protein synthesis at a PTC is sufficient to selectively destabilize polypeptides in mammalian cells. Proteasome inhibition specifically rescues the levels of nascent polypeptides produced from PTC-containing mRNAs within an hour, but also disrupts mRNA homeostasis within a few hours. PTC-terminated polypeptide destabilization is also alleviated by depleting the central NMD factor UPF1 or SMG1, the kinase that phosphorylates UPF1 to activate NMD, but not by inhibiting SMG1 kinase activity. Our results suggest that polypeptide degradation is linked to PTC recognition in mammalian cells and clarify a framework to investigate these mechanisms.

scholarly journals Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2

2020 ◽  
Author(s):  
Haowei Jiang ◽  
Stephen Martin Pederson ◽  
Morgan Newman ◽  
Yang Dong ◽  
Michael Lardelli
Keyword(s):  
Transcriptome Analysis ◽  
Premature Termination ◽  
Fluorescent Protein ◽  
Premature Termination Codon ◽  
Significant Loss ◽  
Targeted Mutagenesis ◽  
Termination Codon ◽  
Nonsense Mediated Decay ◽  
Reading Frame ◽  
Translation Start

AbstractPRESENILIN 2 (PSEN2) is one of the genes mutated in early onset familial Alzheimer’s disease (EOfAD). PSEN2 shares significant amino acid sequence identity with another EOfAD-related gene PRESENILIN 1 (PSEN1), and partial functional redundancy is seen between these two genes. However, the complete range of functions of PSEN1 and PSEN2 is not yet understood. In this study, we performed targeted mutagenesis of the zebrafish psen2 gene to generate a premature termination codon close downstream of the translation start with the intention of creating a null mutation. Homozygotes for this mutation, psen2S4Ter, are viable and fertile, and adults do not show any gross pigmentation defects, arguing against significant loss of γ-secretase activity. Also, assessment of the numbers of Dorsal Longitudinal Ascending (DoLA) interneurons that are responsive to psen2 but not psen1 activity during embryogenesis did not reveal decreased psen2 function. Transcripts containing the S4Ter mutation show no evidence of destabilization by nonsense-mediated decay. Forced expression in zebrafish embryos of fusions of psen2S4Ter 5’ mRNA sequences with sequence encoding enhanced green fluorescent protein (EGFP) indicated that the psen2S4Ter mutation permits utilization of cryptic, novel downstream translation start codons. These likely initiate translation of N-terminally truncated Psen2 proteins that obey the “reading frame preservation rule” of PRESENILIN EOfAD mutations. Transcriptome analysis of entire brains from a 6-month-old family of wild type, heterozygous and homozygous psen2S4Ter female siblings revealed profoundly dominant effects on gene expression likely indicating changes in ribosomal, mitochondrial, and anion transport functions.

scholarly journals The Ig heavy chain protein but not its message controls early B cell development

2020 ◽  
Vol 117 (49) ◽  
pp. 31343-31352
Author(s):  
Muhammad Assad Aslam ◽  
Mir Farshid Alemdehy ◽  
Bingtao Hao ◽  
Peter H. L. Krijger ◽  
Colin E. J. Pritchard ◽  
...  
Keyword(s):  
B Cells ◽  
Heavy Chain ◽  
Messenger Rna ◽  
Stop Codon ◽  
Receptor Gene ◽  
Premature Termination Codon ◽  
Cell Receptor ◽  
Allelic Exclusion ◽  
Nonsense Mediated Decay ◽  
Precursor B Cells

Development of progenitor B cells (ProB cells) into precursor B cells (PreB cells) is dictated by immunoglobulin heavy chain checkpoint (IgHCC), where the IgHC encoded by a productively rearrangedIghallele assembles into a PreB cell receptor complex (PreBCR) to generate signals to initiate this transition and suppressing antigen receptor gene recombination, ensuring that only one productiveIghallele is expressed, a phenomenon known asIghallelic exclusion. In contrast to a productively rearrangedIghallele, theIghmessenger RNA (mRNA) (IgHR) from a nonproductively rearrangedIghallele is degraded by nonsense-mediated decay (NMD). This fact prohibited firm conclusions regarding the contribution of stableIgHRto the molecular and developmental changes associated with the IgHCC. This point was addressed by generating theIghTer5H∆TMmouse model fromIghTer5Hmice having a premature termination codon at position +5 in leader exon ofIghTer5Hallele. This prohibited NMD, and the lack of a transmembrane region (∆TM) prevented the formation of any signaling-competent PreBCR complexes that may arise as a result of read-through translation across premature Ter5 stop codon. A highly sensitive sandwich Western blot revealed read-through translation ofIghTer5Hmessage, indicating that previous conclusions regarding a role ofIgHRin establishing allelic exclusion requires further exploration. As determined by RNA sequencing (RNA-Seq), this low amount of IgHC sufficed to initiate PreB cell markers normally associated with PreBCR signaling. In contrast, theIghTer5H∆TMknock-in allele, which generated stableIgHRbut no detectable IgHC, failed to induce PreB development. Our data indicate that the IgHCC is controlled at the level of IgHC and notIgHRexpression.

scholarly journals Premature Termination Codon in 5′ Region of Desmoplakin and Plakoglobin Genes May Escape Nonsense-Mediated Decay through the Reinitiation of Translation

2022 ◽  
Vol 23 (2) ◽  
pp. 656
Author(s):  
Marta Vallverdú-Prats ◽  
Ramon Brugada ◽  
Mireia Alcalde
Keyword(s):  
Null Allele ◽  
Premature Termination ◽  
Premature Termination Codon ◽  
Termination Codon ◽  
Related Gene ◽  
Arrhythmogenic Cardiomyopathy ◽  
Genomic Context ◽  
Truncated Protein ◽  
Nonsense Mediated Decay ◽  
In Silico Predictions

Arrhythmogenic cardiomyopathy is a heritable heart disease associated with desmosomal mutations, especially premature termination codon (PTC) variants. It is known that PTC triggers the nonsense-mediated decay (NMD) mechanism. It is also accepted that PTC in the last exon escapes NMD; however, the mechanisms involving NMD escaping in 5′-PTC, such as reinitiation of translation, are less known. The main objective of the present study is to evaluate the likelihood that desmosomal genes carrying 5′-PTC will trigger reinitiation. HL1 cell lines were edited by CRISPR/Cas9 to generate isogenic clones carrying 5′-PTC for each of the five desmosomal genes. The genomic context of the ATG in-frame in the 5′ region of desmosomal genes was evaluated by in silico predictions. The expression levels of the edited genes were assessed by Western blot and real-time PCR. Our results indicate that the 5′-PTC in PKP2, DSG2 and DSC2 acts as a null allele with no expression, whereas in the DSP and JUP gene, N-truncated protein is expressed. In concordance with this, the genomic context of the 5′-region of DSP and JUP presents an ATG in-frame with an optimal context for the reinitiation of translation. Thus, 5′-PTC triggers NMD in the PKP2, DSG2* and DSC2 genes, whereas it may escape NMD through the reinitiation of the translation in DSP and JUP genes, with no major effects on ACM-related gene expression.

scholarly journals Prediction of Premature Termination Codon Suppressing Compounds for Treatment of Duchenne Muscular Dystrophy Using Machine Learning

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3886
Author(s):  
Kate Wang ◽  
Eden L. Romm ◽  
Valentina L. Kouznetsova ◽  
Igor F. Tsigelny
Keyword(s):  
Machine Learning ◽  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Premature Termination ◽  
Stop Codon ◽  
Pharmacophore Model ◽  
Dystrophin Gene ◽  
Protein Translation ◽  
Premature Termination Codon ◽  
Termination Codon

A significant percentage of Duchenne muscular dystrophy (DMD) cases are caused by premature termination codon (PTC) mutations in the dystrophin gene, leading to the production of a truncated, non-functional dystrophin polypeptide. PTC-suppressing compounds (PTCSC) have been developed in order to restore protein translation by allowing the incorporation of an amino acid in place of a stop codon. However, limitations exist in terms of efficacy and toxicity. To identify new compounds that have PTC-suppressing ability, we selected and clustered existing PTCSC, allowing for the construction of a common pharmacophore model. Machine learning (ML) and deep learning (DL) models were developed for prediction of new PTCSC based on known compounds. We conducted a search of the NCI compounds database using the pharmacophore-based model and a search of the DrugBank database using pharmacophore-based, ML and DL models. Sixteen drug compounds were selected as a consensus of pharmacophore-based, ML, and DL searches. Our results suggest notable correspondence of the pharmacophore-based, ML, and DL models in prediction of new PTC-suppressing compounds.

scholarly journals Nonsense mutation-dependent reinitiation of translation in mammalian cells

2019 ◽  
Vol 47 (12) ◽  
pp. 6330-6338 ◽  
Author(s):  
Sarit Cohen ◽  
Lior Kramarski ◽  
Shahar Levi ◽  
Noa Deshe ◽  
Oshrit Ben David ◽  
...  
Keyword(s):  
Nonsense Mutation ◽  
Mammalian Cells ◽  
Premature Termination ◽  
Premature Termination Codon ◽  
Initiation Site ◽  
Open Reading Frames ◽  
Termination Codon ◽  
Nonsense Mutations ◽  
Nonsense Mediated Decay ◽  
P53 Isoforms

AbstractIn-frame stop codons mark the termination of translation. However, post-termination ribosomes can reinitiate translation at downstream AUG codons. In mammals, reinitiation is most efficient when the termination codon is positioned close to the 5′-proximal initiation site and around 78 bases upstream of the reinitiation site. The phenomenon was studied mainly in the context of open reading frames (ORFs) found within the 5′-untranslated region, or polycicstronic viral mRNA. We hypothesized that reinitiation of translation following nonsense mutations within the main ORF of p53 can promote the expression of N-truncated p53 isoforms such as Δ40, Δ133 and Δ160p53. Here, we report that expression of all known N-truncated p53 isoforms by reinitiation is mechanistically feasible, including expression of the previously unidentified variant Δ66p53. Moreover, we found that significant reinitiation of translation can be promoted by nonsense mutations located even 126 codons downstream of the 5′-proximal initiation site, and observed when the reinitiation site is positioned between 6 and 243 bases downstream of the nonsense mutation. We also demonstrate that reinitiation can stabilise p53 mRNA transcripts with a premature termination codon, by allowing such transcripts to evade the nonsense mediated decay pathway. Our data suggest that the expression of N-truncated proteins from alleles carrying a premature termination codon is more prevalent than previously thought.

scholarly journals Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides

2019 ◽  
Author(s):  
Jamie R Wangen ◽  
Rachel Green
Keyword(s):  
Mammalian Cells ◽  
Stop Codon ◽  
Translation Termination ◽  
Premature Termination Codon ◽  
Ribosome Profiling ◽  
Termination Codon ◽  
Stop Codons ◽  
Genome Wide ◽  
A Genome

AbstractStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418 treatment globally alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1).

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