scholarly journals Analysis of HCM in an understudied population reveals a new mechanism of pathogenicity

2020 ◽  
Author(s):  
Mona Allouba ◽  
Yasmine Aguib ◽  
Roddy Walsh ◽  
Alaa Afify ◽  
Pantazis I. Theotokis ◽  
...  
Keyword(s):  
Large Scale ◽  
Large Family ◽  
Premature Termination Codon ◽  
Myocardial Tissue ◽  
Inherited Disease ◽  
Lod Score ◽  
Nonsense Mediated Decay ◽  
Exon Junction ◽  
Surgical Myectomy ◽  
Encoding Genes

Hypertrophic Cardiomyopathy (HCM) is an inherited disease characterized by genetic and phenotypic heterogeneity. MYH7 represents one of the main sarcomere-encoding genes associated with HCM. Missense variants in this gene cause HCM through gain-of-function actions, whereby variants produce an abnormal activated protein which incorporates into the sarcomere as a ‘poison peptide’. Here we report a frameshift variant in MYH7, c.5769delG, that is associated with HCM in an Egyptian cohort (3.3%) compared with ethnically-matched controls. This variant is absent from previously published large-scale Caucasian HCM cohorts. We further demonstrate strong evidence of co-segregation of c.5769delG with HCM in a large family (LOD score: 3.01). The predicted sequence of the variant MYH7 transcript shows that the frameshift results in a premature termination codon (PTC) downstream of the last exon-exon junction of the gene that is expected to escape nonsense-mediated decay (NMD). RNA sequencing of myocardial tissue obtained from a patient with the variant during surgical myectomy confirmed the expression of the variant MYH7 transcript. Our analysis reveals a new mechanism of pathogenicity in the understudied Egyptian population whereby distal PTC in MYH7 may lead to the expression of an abnormal protein.

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 Identification of antiviral roles for the exon–junction complex and nonsense-mediated decay in flaviviral infection

2019 ◽  
Vol 4 (6) ◽  
pp. 985-995 ◽  
Author(s):  
Minghua Li ◽  
Jeffrey R. Johnson ◽  
Billy Truong ◽  
Grace Kim ◽  
Nathan Weinbren ◽  
...  
Keyword(s):  
Exon Junction Complex ◽  
Nonsense Mediated Decay ◽  
Exon Junction

Abstract 64: An Integrated Model for Titin Truncation Mutation Interpretation

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
Jun Zou ◽  
Diana Tran ◽  
Angelo Pelonero ◽  
Rahul C Deo
Keyword(s):  
Large Scale ◽  
Characteristic Curve ◽  
Severe Disease ◽  
Predictive Performance ◽  
Transcript Level ◽  
Data Interpretation ◽  
Integrated Model ◽  
Integrative Model ◽  
Nonsense Mediated Decay ◽  
Cardiac Phenotype

Background: We recently discovered a conserved internal promoter in the Titin gene, which explains why truncating mutations in the C-terminal two thirds of the zebrafish ttna protein result in more severe disease, recapitulating a puzzling observation in human dilated cardiomyopathy (DCM) patients. Here we focus on the contribution of alternative splicing to the DCM phenotype, both in zebrafish Titin truncation mutants and in the context of an integrative model for Titin mutation interpretation. Methods and Results: Using CRISPR/Cas9, we disrupted an alternatively spliced exon in the I-band of Titin , normally present in zebrafish heart but absent in skeletal muscle. The resulting mutants had, on average, a milder cardiac phenotype than those with mutations in constitutive exons but also showed striking inter-sibling variability in disease expression, ranging from intact cardiac blood flow to severe early demise. The mutant exon demonstrated nonsense-altered splicing and disease severity paralleled selective deficiency in Titin transcript level, implying that variability in mutated exon inclusion coupled with nonsense-mediated decay (NMD) modulated phenotype. We next amassed Titin mutation information from 1785 human DCM cases and >68,000 controls to model mutation distribution and found three variance components 1) splicing; 2) internal isoform disruption; and 3) targeting of the C-terminal 2000 amino acids. An integrated model demonstrated strong predictive performance with an area under the receiver operating characteristic curve of 0.79 and correctly identified the highest risk individuals. Conclusions: We conclude that genetically targeted models and large-scale human data can be complementary in overcoming the challenges of genetic data interpretation.

scholarly journals Comparison of oral microbiome profiles in stimulated and unstimulated saliva, tongue, and mouth-rinsed water

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ryutaro Jo ◽  
Yuichiro Nishimoto ◽  
Kouta Umezawa ◽  
Kazuma Yama ◽  
Yuto Aita ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Large Scale ◽  
Epidemiological Studies ◽  
Oral Microbiome ◽  
Tongue Coating ◽  
Microbial Composition ◽  
Microbiome Analysis ◽  
Unstimulated Saliva ◽  
Encoding Genes ◽  
Generation Sequencing

Abstract Epidemiological studies using saliva have revealed relationships between the oral microbiome and many oral and systemic diseases. However, when collecting from a large number of participants such as a large-scale cohort study, the time it takes to collect saliva can be a problem. Mouth-rinsed water, which is water that has been used to rinse the oral cavity, can be used as an alternative method for collecting saliva for oral microbiome analysis because it can be collected in a shorter time than saliva. The purpose of this study was to verify whether mouth-rinsed water is a suitable saliva substitute for analyzing the oral microbiome. We collected samples of mouth-rinsed water, stimulated saliva, unstimulated saliva, and tongue coating from 10 systemic healthy participants, and compared the microbial diversity and composition of the samples using next-generation sequencing of 16S rRNA-encoding genes. The results showed that the microbial diversity of mouth-rinsed water was similar to that of unstimulated and stimulated saliva, and significantly higher than that of tongue-coating samples. The microbial composition at the species level of mouth-rinsed water also showed a very high correlation with the composition of unstimulated and stimulated saliva. These results suggest that the mouth-rinsed water is a suitable collection method instead of saliva for oral microbiome analysis.

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

eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay

2004 ◽  
Vol 11 (4) ◽  
pp. 346-351 ◽  
Author(s):  
Toshiharu Shibuya ◽  
Thomas Ø Tange ◽  
Nahum Sonenberg ◽  
Melissa J Moore
Keyword(s):  
Exon Junction Complex ◽  
Nonsense Mediated Decay ◽  
Exon Junction

mRNA stability and control of cell proliferation

2011 ◽  
Vol 39 (5) ◽  
pp. 1461-1465 ◽  
Author(s):  
Cristina Mazzoni ◽  
Claudio Falcone
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Mrna Stability ◽  
Transcriptional Control ◽  
Mrna Translation ◽  
Premature Termination Codon ◽  
Termination Codon ◽  
Transcriptional Initiation ◽  
Control Of Gene Expression ◽  
Nonsense Mediated Decay

Most of the studies on cell proliferation examine the control of gene expression by specific transcription factors that act on transcriptional initiation. In the last few years, it became evident that mRNA stability/turnover provides an important mechanism for post-transcriptional control of gene expression. In eukaryotes, mRNAs are mainly degraded after deadenylation by decapping and exosome pathways. Mechanisms of mRNA surveillance comprise deadenylation-independent pathways such as NMD (nonsense-mediated decay), when mRNAs harbour a PTC (premature termination codon), NSD (non-stop decay, when mRNAs lack a termination codon, and NGD (no-go decay), when mRNA translation elongation stalls. Many proteins involved in these processes are conserved from bacteria to yeast and humans. Recent papers showed the involvement of proteins deputed to decapping in controlling cell proliferation, virus replication and cell death. In this paper, we will review the newest findings in this field.

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.

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