Characterization of Two Novel Intronic Variants Affecting Splicing in FBN1-Related Disorders

FBN1 encodes fibrillin 1, a key structural component of the extracellular matrix, and its variants are associated with a wide range of hereditary connective tissues disorders, such as Marfan syndrome (MFS) and mitral valve–aorta–skeleton–skin (MASS) syndrome. Interpretations of the genomic data and possible genotype–phenotype correlations in FBN1 are complicated by the high rate of intronic variants of unknown significance. Here, we report two unrelated individuals with the FBN1 deep intronic variants c.6872-24T>A and c.7571-12T>A, clinically associated with MFS and MASS syndrome, respectively. The individual carrying the c.6872-24T>A variant is positive for aortic disease. Both individuals lacked ectopia lentis. In silico analysis and subsequent mRNA study by RT-PCR demonstrated the effect of the identified variant on the splicing process in both cases. The c.6872-24T>A and c.7571-12T>A variants generate the retention of intronic nucleotides and lead to the introduction of a premature stop codon. This study enlarges the mutation spectrum of FBN1 and points out the importance of intronic sequence analysis and the need for integrative functional studies in FBN1 diagnostics.

Download Full-text

Identification of the genomic mutation in Epha4rb-2J/rb-2J mice

Genome ◽

10.1139/gen-2015-0142 ◽

2016 ◽

Vol 59 (7) ◽

pp. 439-448 ◽

Cited By ~ 2

Author(s):

Siti W. Mohd-Zin ◽

Nor-Linda Abdullah ◽

Aminah Abdullah ◽

Nicholas D.E. Greene ◽

Pike-See Cheah ◽

...

Keyword(s):

Protein Interactions ◽

Tyrosine Kinases ◽

Stop Codon ◽

Cell Signalling ◽

Experimental Studies ◽

Premature Stop Codon ◽

Mouse Mutant ◽

Functional Studies ◽

Base Pair Deletion ◽

Numerous Cell

The EphA4 receptor tyrosine kinase is involved in numerous cell-signalling activities during embryonic development. EphA4 has the ability to bind to both types of ephrin ligands, the ephrinAs and ephrinBs. The C57BL/6J-Epha4rb-2J/GrsrJ strain, denoted Epha4rb-2J/rb-2J, is a spontaneous mouse mutant that arose at The Jackson Laboratory. These mutants exhibited a synchronous hind limb locomotion defect or “hopping gait” phenotype, which is also characteristic of EphA4 null mice. Genetic complementation experiments suggested that Epha4rb-2J corresponds to an allele of EphA4, but details of the genomic defect in this mouse mutant are currently unavailable. We found a single base-pair deletion in exon 9 resulting in a frame shift mutation that subsequently resulted in a premature stop codon. Analysis of the predicted structure of the truncated protein suggests that both the kinase and sterile α motif (SAM) domains are absent. Definitive determination of genotype is needed for experimental studies of mice carrying the Epha4rb-2J allele, and we have also developed a method to ease detection of the mutation through RFLP. Eph-ephrin family members are reportedly expressed as numerous isoforms. Hence, delineation of the specific mutation in EphA4 in this strain is important for further functional studies, such as protein–protein interactions, immunostaining and gene compensatory studies, investigating the mechanism underlying the effects of altered function of Eph family of receptor tyrosine kinases on phenotype.

Download Full-text

Genetic variability of spelt factor gene in Triticum and Aegilops species

BMC Plant Biology ◽

10.1186/s12870-020-02536-8 ◽

2020 ◽

Vol 20 (S1) ◽

Author(s):

Valeriya Vavilova ◽

Irina Konopatskaia ◽

Alexandr Blinov ◽

Elena Ya. Kondratenko ◽

Yuliya V. Kruchinina ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Chinese Spring ◽

Stop Codon ◽

Aegilops Tauschii ◽

Premature Stop Codon ◽

Gene Sequences ◽

D Genome ◽

Factor Gene ◽

Spike Shape ◽

Wide Range

Abstract Background Threshability, rachis fragility and spike shape are critical traits for the domestication and evolution of wheat, determining the crop yield and efficiency of the harvest. Spelt factor gene Q controls a wide range of domestication-related traits in polyploid wheats, including those mentioned above. The main goal of the present study was to characterise the Q gene for uninvestigated accessions of wheats, including four endemics, and Aegilops accessions, and to analyze the species evolution based on differences in Q gene sequences. Results We have studied the spike morphology for 15 accessions of wheat species, including four endemics, namely Triticum macha, T. tibetanum, T. aestivum ssp. petropavlovskyi and T. spelta ssp. yunnanense, and 24 Aegilops accessions, which are donors of B and D genomes for polyploid wheat. The Q-5A, q-5D and q-5S genes were investigated, and a novel allele of the Q-5A gene was found in accessions of T. tibetanum (KU510 and KU515). This allele was similar to the Q allele of T. aestivum cv. Chinese Spring but had an insertion 161 bp in length within exon 5. This insertion led to a frameshift and premature stop codon formation. Thus, the T. tibetanum have spelt spikes, which is probably determined by the gene Tg, rather than Q. We determined the variability within the q-5D genes among hexaploid wheat and their D genome donor Aegilops tauschii. Moreover, we studied the accessions C21–5129, KU-2074, and K-1100 of Ae. tauschii ssp. strangulata, which could be involved in the origin of hexaploid wheats. Conclusions The variability and phylogenetic relationships of the Q gene sequences studied allowed us to clarify the relationships between species of the genus Triticum and to predict the donor of the D genome among the Ae. tauschii accessions. Ae. tauschii ssp. strangulata accessions C21–5129, KU-2074 and K-1100 are the most interesting among the analysed accessions, since their partial sequence of q-5D is identical to the q-5D of T. aestivum cv. Chinese Spring. This result indicates that the donor is Ae. tauschii ssp. strangulata but not Ae. tauschii ssp. tauschii. Our analysis allowed us to clarify the phylogenetic relationships in the genus Triticum.

Download Full-text

Molecular structure of soybean E-genes and their functional mutations

Visnyk of Lviv University Biological series ◽

10.30970/vlubs.2020.82.01 ◽

2020 ◽

pp. 3-13

Author(s):

O. Okhrymovych ◽

◽

S. Chebotar ◽

G. Chebotar ◽

D. Zharikova ◽

...

Keyword(s):

Molecular Structure ◽

Stop Codon ◽

Premature Stop Codon ◽

Genetic Network ◽

Structural Features ◽

Loss Of Function ◽

Nucleotide Substitutions ◽

Early Maturity ◽

E Gene ◽

Wide Range

In this review, we discuss features of the molecular structure of known E-loci (early maturity) and their involvement in signaling to plant flowering, depending on the sensitivity of soybean genotypes to the photoperiod. These loci contribute to the adaptation of plants to a wide range of natural conditions due to mutations in genes and QTL that control flowering time. At the molecular level, E-genes are significantly different in structural features, origin and function. The lenghth of the identified genes range from one exon to 525 bp encoding the transcription factor (E1), up to 14 exons and about 20 kb for the GmGIa gene (E2). Among the functional mutations that in most cases lead to partial or complete loss of function, there are single-nucleotide substitutions or deletions, insertions of transposon-like sequences that can lead to amino acid substitutions in the protein, shift of the reading frame, appearance of the premature stop-codon. E-gene products are receptors of signals coming from the environment and they participate in signaling pathways that control the photoperiod. The overall impact and interactions between E-genes have not been fully studied yet, the molecular structure was investigated only for E1-E4, for which a genetic network of interactions was proposed, while at the same time five loci (E6-E9 and E11) were only mapped on soybean chromosomes, and the existence of a separate E5 locus has not yet been established. In eight of the 11 E-loci, the dominant allele causes late flowering. Also there is a pleiotropic effect of E-gene alleles on yield, plant height, stress resistance, and response to low temperatures. Knowledge of the allelic state of only some of the 11 genes is not sufficient. A comprehensive understanding of the functioning of the photoperiodic genetic response network is needed. E-genes are genetic determinants that can be used during selection and creation of new varieties with programmed rates of development.

Download Full-text

Potential Ad Hoc Markers of Persistence and Virulence in Canadian Listeria monocytogenes Food and Clinical Isolates

Journal of Food Protection ◽

10.4315/0362-028x.jfp-19-028 ◽

2019 ◽

Vol 82 (11) ◽

pp. 1909-1921 ◽

Cited By ~ 2

Author(s):

JACQUELINE UPHAM ◽

STEPHEN CHEN ◽

ELIZABETH BOUTILIER ◽

LISA HODGES ◽

MIKAELA EISEBRAUN ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Ad Hoc ◽

Stop Codon ◽

Premature Stop Codon ◽

In Silico Analysis ◽

Clinical Isolates ◽

Intestinal Epithelial ◽

Virulence Protein ◽

Islet 1 ◽

Experimental Findings

ABSTRACT The Listeria monocytogenes gene inlA, encoding a surface virulence protein, was examined for the presence of premature stop codon (PMSC) mutations in 82 isolates obtained by the Canadian Food Inspection Agency (CFIA) from foods and food contact surfaces. These mutations were coanalyzed for the presence of stress survival islet 1 (SSI-1) and for the abilities of the isolates to invade Caco-2 intestinal epithelial cells and form biofilms on polystyrene. PMSC mutations were present in one-third of the isolates (predominantly those of serogroup 1/2a), and their presence was correlated with a noninvasive phenotype. The presence of SSI-1 and the ability to form biofilms were also linked to the 1/2a serogroup. Serogroup 4b isolates lacked inlA PMSC mutations and were invasive, but neither formed biofilms nor carried SSI-1. To expand upon these experimental findings, an in silico analysis was performed on L. monocytogenes genomes from Canadian databases of 278 food isolates and 607 clinical isolates. The prevalence of inlA PMSC mutations in genomes of food isolates was significantly higher (P < 0.0001) than that in clinical isolates. Also, a three-codon deletion in inlA associated with a hyperinvasive phenotype was more prevalent in genomes from clinical isolates (primarily of clonal complex 6, serogroup 4b) than in those from food isolates (P < 0.001). In contrast, SSI-1 was significantly overrepresented (P < 0.001) in genomes from food isolates. We propose the hypothesis that SSI-1 and inlA play a role in the evolution of Canadian L. monocytogenes strains into either a virulent (represented by serogroup 4b clinical isolates) or an environmentally persistent (represented by serogroup 1/2a food isolates) phenotype. The combined presence of SSI-1 and inlA PMSC mutations have potential for use as genetic markers for risk assessment when L. monocytogenes is recovered from foods, indicating low potential for pathogenesis.

Download Full-text

Identification and characterization of BrxR as a regulatory gene in the BREX phage restriction system

10.1101/2021.12.19.473356 ◽

2021 ◽

Author(s):

Yvette Luyten ◽

Deanna Hausman ◽

Juliana C. Young ◽

Lindsey A. Doyle ◽

Natalia C. Ubilla-Rodriguez ◽

...

Keyword(s):

Stop Codon ◽

Regulatory Gene ◽

Premature Stop Codon ◽

Type I ◽

Coding Sequence ◽

Functional Roles ◽

Wide Range ◽

Prime End ◽

Identification And Characterization

Bacteriophage exclusion (BREX) phage restriction systems are found in a wide range of bacteria. Various BREX systems encode unique combinations of proteins that usually include a site-specific methyltransferase; none appear to contain a nuclease. Here we describe the identification and characterization of a Type I BREX system from Acinetobacter and the effect of deleting each BREX ORF on growth, methylation and phage restriction. The analysis identified a previously uncharacterized gene at the 5-prime end of the BREX operon that is dispensable for methylation but involved in restriction. Biochemical and crystallographic analyses of this factor, which we term BrxR (BREX Regulator), demonstrate that it forms a homodimer and specifically binds a pseudo-palindromic DNA target site upstream of its transcription start site. Precise deletion of the BrxR gene causes cell toxicity, reduces phage restriction, and significantly increases the expression of BrxC. In contrast, the introduction of a premature stop codon into the BrxR gene has little effect, implying that the BrxR coding sequence and BrxR protein have independent functional roles in BREX regulation. We speculate that the BrxR coding sequence is involved in cis regulation of BREX activity and that the BrxR protein may play an additional regulatory role, perhaps during horizontal transfer of the system.

Download Full-text

NTPDase5/PCPH as a New Target in Highly Aggressive Tumors: A Systematic Review

BioMed Research International ◽

10.1155/2014/123010 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 2

Author(s):

Paula Andreghetto Bracco ◽

Ana Paula Santin Bertoni ◽

Márcia Rosângela Wink

Keyword(s):

Cancer Progression ◽

Stop Codon ◽

Active Form ◽

Premature Stop Codon ◽

Diagnostic Tools ◽

Therapy Targets ◽

Base Pair Deletion ◽

Wide Range ◽

Resistance To Stress ◽

Single Base Pair

The protooncogenePCPHwas recently identified as being the ectonucleoside triphosphate diphosphohydrolase 5 (ENTPD5). This protooncogene is converted into an oncogene by a single base pair deletion, resulting in frame change and producing a premature stop codon, leading to a mutated protein (mt-PCPH) with only 27 kDa, which is much smaller than the original 47 kDa protein. Overexpression of the PCPH as well as the mutated PCPH increases the cellular resistance to stress and apoptosis. This is intriguing considering that the active form, that is, the oncogene, is the mutated PCPH. Several studies analyzed the expression of NTPDase5/mt-PCPH in a wide range of tumor cells and evaluated its role and mechanisms in cancer and other pathogenic processes. The main point of this review is to integrate the findings and proposed theories about the role played by NTPDase5/mt-PCPH in cancer progression, considering that these proteins have been suggested as potential early diagnostic tools and therapy targets.

Download Full-text

A Novel Loss-of-Sclerostin Function Mutation in a First Egyptian Family with Sclerosteosis

BioMed Research International ◽

10.1155/2015/517815 ◽

2015 ◽

Vol 2015 ◽

pp. 1-8 ◽

Cited By ~ 5

Author(s):

Alaaeldin Fayez ◽

Mona Aglan ◽

Nora Esmaiel ◽

Taher El Zanaty ◽

Mohamed Abdel Kader ◽

...

Keyword(s):

Bone Density ◽

Autosomal Recessive ◽

Frameshift Mutation ◽

Stop Codon ◽

Premature Stop Codon ◽

In Silico Analysis ◽

Genomic Sequencing ◽

Gene Coding ◽

Autosomal Recessive Condition ◽

Silico Analysis

Sclerosteosis is a rare autosomal recessive condition characterized by increased bone density. Mutations inSOSTgene coding for sclerostin are linked to sclerosteosis. Two Egyptian brothers with sclerosteosis and their apparently normal consanguineous parents were included in this study. Clinical evaluation and genomic sequencing of theSOSTgene were performed followed by in silico analysis of the resulting variation. A novel homozygous frameshift mutation in theSOSTgene, characterized as one nucleotide cytosine insertion that led to premature stop codon and loss of functional sclerostin, was identified in the two affected brothers. Their parents were heterozygous for the same mutation. To our knowledge this is the first Egyptian study of sclerosteosis andSOSTgene causing mutation.

Download Full-text

Incomplete Segregation of MSH6 Frameshift Variants with Phenotype of Lynch Syndrome

10.20944/preprints201704.0027.v1 ◽

2017 ◽

Author(s):

Raffaella Liccardo ◽

Marina De Rosa ◽

Giovanni Battista Rossi ◽

Nicola Carlomagno ◽

Paola Izzo ◽

...

Keyword(s):

Lynch Syndrome ◽

In Silico ◽

Stop Codon ◽

Direct Sequencing ◽

Premature Stop Codon ◽

In Silico Analysis ◽

Frameshift Deletion ◽

The Family ◽

Novel Variants ◽

Repair Genes

Background: Lynch syndrome, the most frequent form of hereditary colorectal cancer and involves mutations in mismatch repair genes. The aim of this study was to identify mutations in MSH6 from 97 subjects negative for mutations in MLH1 and MSH2. Methods: By direct sequencing, we identified 27 MSH6 variants, of which, nine were novel. To verify the pathogenicity of these novel variants we performed in silico and segregation analyses. Results: Three novel variants were predicted by in silico analysis as damaging mutations and segregated with the disease phenotype. While, a novel frameshift deletion variant that was predicted to yield a premature stop codon, did not segregate with the LS phenotype in 3 of 4 cases in the family. Interestingly, another frame-shift variant identified in this study, already described in the literature, also did not segregate with the LS phenotype in 1 of 2 affected subjects in the family. In all affected subjects of both families, no mutation was detected in other MMR genes. Therefore, it is expected that within these families other genetic factors contribute to the disease either alone or in combination with MSH6 variants. Conclusion: We conclude that caution should be exercised in counseling for MSH6-associated LS family members.

Download Full-text

The B-hordein prolamin family of barley

Genome ◽

10.1139/gen-2013-0016 ◽

2013 ◽

Vol 56 (3) ◽

pp. 179-185 ◽

Cited By ~ 9

Author(s):

Olin D. Anderson

Keyword(s):

Stop Codon ◽

Premature Stop Codon ◽

In Silico Analysis ◽

Gene Families ◽

Full Length ◽

C Terminus ◽

Est Assembly ◽

Silico Analysis ◽

Total Ests ◽

Relative Gene

The spectrum of B-hordein prolamins and genes in the single barley cultivar Barke is described from an in silico analysis of 1452 B-hordein ESTs and available genomic DNA. Eleven unique B-hordein proteins are derived from EST contigs. Ten contigs encode apparent full-length B-hordeins and the eleventh contains a premature stop codon that will lead to a truncated B-hordein. The 11 sequences are placed within the two previously described classes, i.e., the B1- and B3-type B-hordeins. The number of ESTs assigned to each sequence is used as an estimate of relative gene transcription and expression. Three of the sequences account for 79% of the total ESTs, with one sequence comprises 32% of the total ESTs and has a variant C-terminus caused by an undefined sequence change history near the 3′ coding terminus. The 70× difference in EST distribution among sequences points to the importance of understanding differential rates of expression within closely related gene families. Analysis of available genomic sequences confirms the EST assembly and reveals one full-length and two partial sequences of pseudogenes as evidenced by no matching ESTs for the sequences and premature stop codons and frame shifts.

Download Full-text

NKCC1: Newly Found as a Human Disease-Causing Ion Transporter

Function ◽

10.1093/function/zqaa028 ◽

2020 ◽

Vol 2 (1) ◽

Author(s):

Rainelli Koumangoye ◽

Lisa Bastarache ◽

Eric Delpire

Keyword(s):

De Novo ◽

Stop Codon ◽

Neurodevelopmental Disorder ◽

Premature Stop Codon ◽

Dominant Negative ◽

De Novo Mutation ◽

Dominant Negative Effect ◽

Salt Wasting ◽

Wide Range ◽

Negative Effect

Abstract Among the electroneutral Na+-dependent chloride transporters, NKCC1 had until now evaded identification as a protein causing human diseases. The closely related SLC12A transporters, NKCC2 and NCC have been identified some 25 years ago as responsible for Bartter and Gitelman syndromes: two renal-dependent salt wasting disorders. Absence of disease was most surprising since the NKCC1 knockout mouse was shown in 1999 to be viable, albeit with a wide range of deleterious phenotypes. Here we summarize the work of the past 5 years that introduced us to clinical cases involving NKCC1. The most striking cases are of 3 children with inherited mutations, who have complete absence of NKCC1 expression. These cases establish that lack of NKCC1 causes deafness; CFTR-like secretory defects with mucus accumulation in lung and intestine; severe xerostomia, hypotonia, dysmorphic facial features, and severe neurodevelopmental disorder. Another intriguing case is of a patient with a dominant deleterious SLC12A2 allele. This de novo mutation introduced a premature stop codon leading to a truncated protein. This mutant transporter seems to exert dominant-negative effect on wild-type transporter only in epithelial cells. The patient who suffers from lung, bladder, intestine, pancreas, and multiple endocrine abnormalities has, however, normal hearing and cognition. Finally, new reports substantiate the haploinsufficiency prediction of the SLC12A2 gene. Cases with single allele mutations in SLC12A2 have been linked to hearing loss and neurodevelopmental disorders.

Download Full-text