scholarly journals Sanger sequencing as a first-line approach for molecular diagnosis of Andersen-Tawil syndrome

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1016 ◽  
Author(s):  
Armando Totomoch-Serra ◽  
Manlio F. Marquez ◽  
David E. Cervantes-Barragán
Keyword(s):  
Molecular Diagnosis ◽  
Sanger Sequencing ◽  
Heterozygous Mutation ◽  
Coding Region ◽  
First Line ◽  
Base Pairs ◽  
Exon 2 ◽  
Clinical Criteria ◽  
Exon 1 ◽  
Next Generation Sequencing Ngs

In 1977, Frederick Sanger developed a new method for DNA sequencing based on the chain termination method, now known as the Sanger sequencing method (SSM).  Recently, massive parallel sequencing, better known as next-generation sequencing (NGS),  is replacing the SSM for detecting mutations in cardiovascular diseases with a genetic background. The present opinion article wants to remark that “targeted” SSM is still effective as a first-line approach for the molecular diagnosis of some specific conditions, as is the case for Andersen-Tawil syndrome (ATS). ATS is described as a rare multisystemic autosomal dominant channelopathy syndrome caused mainly by a heterozygous mutation in the KCNJ2 gene. KCJN2 has particular characteristics that make it attractive for “directed” SSM. KCNJ2 has a sequence of 17,510 base pairs (bp), and a short coding region with two exons (exon 1=166 bp and exon 2=5220 bp), half of the mutations are located in the C-terminal cytosolic domain, a mutational hotspot has been described in residue Arg218, and this gene explains the phenotype in 60% of ATS cases that fulfill all the clinical criteria of the disease. In order to increase the diagnosis of ATS we urge cardiologists to search for facial and muscular abnormalities in subjects with frequent ventricular arrhythmias (especially bigeminy) and prominent U waves on the electrocardiogram.

scholarly journals Complete Thyroxine-Binding Globulin (TBG) Deficiency Produced by a Mutation in Acceptor Splice Site Causing Frameshift and Early Termination of Translation (TBG-Kankakee)12

1998 ◽  
Vol 83 (10) ◽  
pp. 3604-3608
Author(s):  
Gisah A. Carvalho ◽  
Roy E. Weiss ◽  
Samuel Refetoff
Keyword(s):  
Splice Site ◽  
Messenger Rna ◽  
Restriction Site ◽  
Splice Junction ◽  
Early Termination ◽  
Coding Region ◽  
Acceptor Splice Site ◽  
Exon 2 ◽  
Gene Level ◽  
Exon 1

Fourteen T4-binding globulin (TBG) variants have been identified at the gene level. They are all located in the coding region of the gene and 6 produce complete deficiency of TBG (TBG-CD). We now describe the first mutation in a noncoding region producing TBG-CD. The proband was treated for over 20 yr with L-T4 because of fatigue associated with a low concentration of serum total T4. Fifteen family members were studied showing low total T4 inherited as an X chromosome-linked trait, and affected males had undetectable TBG in serum. Sequencing of the entire coding region and promoter of the TBG gene revealed no abnormality. However, an A to G transition was found in the acceptor splice junction of intron II that produced a new HaeIII restriction site cosegregating with the TBG-CD phenotype. Sequencing exon 1 to exon 3 of TBG complementary DNA reverse transcribed from messenger RNA of skin fibroblasts from an affected male, confirmed a shift in the ag acceptor splice site. This results in the insertion of a G in exon 2 and causes a frameshift and a premature stop at codon 195. This early termination of translation predicts a truncated TBG lacking 201 amino acids.

Genetic and Phenotypic Analysis of Families with Inherited Hypo- and Dys-Fibrinogenemia. Fibrinogen Bratislava.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1794-1794
Author(s):  
Angelika Batorova ◽  
Daniela Horvathova ◽  
Martin Mistrik ◽  
Philippe de Moerloose ◽  
Marguerite Neerman-Arbez
Keyword(s):  
Genetic Analysis ◽  
Fibrinogen Level ◽  
Novel Mutation ◽  
Heterozygous Mutation ◽  
Blood Coagulation Disorders ◽  
Phenotypic Analysis ◽  
Spontaneous Bleeding ◽  
Exon 2 ◽  
Exon 1 ◽  
History Of

Abstract Inherited hypofibrinogenemia (hypo-FBG) and dysfibrinogenemia (dys-FBG) are rare blood coagulation disorders caused by quantitative or qualitative defects of fibrinogen. We reviewed the clinical course in 47 individuals with dys-FBG and 16 patients with hypo-FBG with median fibrinogen coagulant/antigen levels of 0.76/2.8 and 1.1/1.2 g/L, respectively. Genetic analysis was performed in 5 families (16 individuals) with dys-FBG and 4 families (8 individuals) with hypo-FBG. In the dysfibrinogenemia group 21 (45%) individuals were asymptomatic, 24(51%) patients suffered from bleeding and/or prolonged wound healing (only four had serious bleeding) and 2(4%) patients had a history of thrombosis. A total of 96 surgeries were performed without preoperative fibrinogen replacement in 31 dys-FBG patients, only 9 (9%) procedures were complicated with bleeding, two requiring fibrinogen substitution. Genetic analysis in dysfibrinogenemia has revealed heterozygous mutation in FGA exon 2 (Aα Arg16 His) known to cause delayed fibrinopeptide A cleavage by thrombin in 6 individuals (3 families). Five patients from two other families were heterozygous for a novel mutation in FGA exon 2 (Aα Gly13Glu). Fibrinogen coag/Ag median levels were comparable for both mutant genotypes: 0.5/2.9 g/L and 0.56/2.8 g/L, respectively. In the hypofibrinogenemia group 6/14 (43%) patients had mild spontaneous bleeding, 8/36 (22%) surgeries performed in 12 patients w/o replacement were complicated with bleeding. A novel mutation in FGG exon 1 (Trp3 Stop) was identified in heterozygosity for 3 patients (3 families) with FBG coag/Ag median level of 1.1/1.2 g/L. An additional unrelated patient with a fibrinogen level of 0.7 g/L and serious postpartum bleeding was heterozygous for a novel mutation in FGG exon 7 (Trp253Cys) - Fibrinogen Bratislava.

scholarly journals Functional analysis of the AUG- and CUG-initiated forms of the c-Myc protein.

1994 ◽  
Vol 5 (5) ◽  
pp. 597-609 ◽  
Author(s):  
E M Blackwood ◽  
T G Lugo ◽  
L Kretzner ◽  
M W King ◽  
A J Street ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Chromosomal Translocation ◽  
Regulatory Elements ◽  
Genetic Alterations ◽  
Coding Region ◽  
Exon 2 ◽  
Translational Initiation ◽  
Selective Growth Advantage ◽  
Exon 1 ◽  
Normal Human

Activation of the c-myc proto-oncogene by chromosomal translocation or proviral insertion frequently results in the separation of the c-myc coding region from its normal regulatory elements. Such rearrangements are often accompanied by loss or mutation of c-myc exon 1 sequences. These genetic alterations do not affect synthesis of the major c-myc protein, p64, which is initiated from the first AUG codon in exon 2. However they can result in mutation or loss of the CUG codon located in exon 1 that normally serves as an alternative translational initiation codon for synthesis of an N-terminally extended form of c-Myc (p67). It has been hypothesized that p67 is a functionally distinct form of c-Myc whose specific loss during c-myc rearrangements confers a selective growth advantage. Here we describe experiments designed to test the functional properties of the two c-Myc protein forms. We introduced mutations within the translational initiation codons of a normal human c-myc cDNA that alter the pattern of Myc protein synthesis (p64 vs. p67). The functions of each of these proteins were experimentally addressed using co-transformation and transcriptional activation assays. Both the p64 and p67 c-Myc proteins were independently able to collaborate with bcr-abl in the transformation of Rat-1 fibroblasts. In addition, both the exon 1- and exon 2-initiated forms of the c-Myc protein stimulated transcription of a Myc/Max-responsive reporter construct to a similar level. Given the apparent absence of functional differences between p64 and p67, we conclude that the basis for c-Myc oncogenic activation lies primarily in the overall deregulation of its expression and not in alterations in the protein. The existence of the CUG translational initiator may reflect a mechanism for the continued synthesis of c-Myc protein under conditions where AUG initiation is inhibited.

scholarly journals Characteristics of defensin1 gene and designing structure to create resistant transgenic corn lines to weevils

2016 ◽  
Vol 14 (2) ◽  
pp. 279-286
Author(s):  
Vì Thị Xuân Thủy ◽  
Lò Thị Mai Thu ◽  
Hồ Mạnh Tường ◽  
Lê Văn Sơn ◽  
Nguyễn Vũ Thanh Thanh ◽  
...  
Keyword(s):  
Amino Acid Sequences ◽  
Disulfide Bridges ◽  
Coding Region ◽  
Exon 2 ◽  
Transformation Vector ◽  
Plant Defensins ◽  
Maize Sample ◽  
Exon 1 ◽  
Hybrid Maize ◽  
Group 1

Plant defensins are multifunctional proteins, inhibiting the growth of fungal, anti-bacterial, altering membrane channels, inhibiting activity of trypsin and α-amylase. Plant defensin consists of 18 groups in which the group 1 includes  defensins to inhibit either α-amylase enzyme or trypsin. Defensins bind to the active site of α-amylase in the weevil gut, thus inhibit starch digestion in weevils. In this report, we present the results of cloning and determining the ZmDEF1 gene sequence isolated from mRNA and DNA of Sonla province local maize and LVN99 hybrid maize cultivar. The coding region of ZmDEF1 gene isolated from some maize samples had the size of 243 nucleotides, encoding 80 amino acids. Gen ZmDEF1 isolated from DNA had the size 345bp consists of two exons and one in tron (102 bp). The nucleotide sequences of ZmDEF1 gene (DNA) of the samples have 6 positions nucleotide difference, on exon 1 has two points difference (position 43, 53), on intron has a difference (position 150), on exon 2 has 3 nucleotide site difference (203, 263 and 297 position). Deduced amino acid sequences of defensin of the Sonla local maize sample has 8 cysteines to make 4 disulfide bridges, while LVN99 hybrid maize has 7 cysteines, which can formed only 3 disulfide bridges. Transformation vector pBetaPhaso-ZmDEF1 has been designed successfully, in which ZmDEF1 is controlled by seed specific Phasoline promoter. The correct insertion and expression of ZmDEF1 was examinated in transgenic tobacco plants throught PCR and RT-PCR, respectively. These results provide an firm evident for using the designed transformation vector to produce transgenic maỉze lines with an improved resistant ability  to weevils.

scholarly journals The Drosophila melanogaster actin 5C gene uses two transcription initiation sites and three polyadenylation sites to express multiple mRNA species

1986 ◽  
Vol 6 (6) ◽  
pp. 2080-2088
Author(s):  
B J Bond ◽  
N Davidson
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Initiation ◽  
Splice Acceptor Site ◽  
Acceptor Site ◽  
Base Pairs ◽  
Exon 2 ◽  
Rna Molecules ◽  
Exon 1 ◽  
Polyadenylation Sites ◽  
Tata Sequence

At least six mRNAs are made from the Drosophila melanogaster act5C gene. We investigated the structures of these RNAs in detail and determined that they are heterogeneous at both their 5' and 3' ends. At the 5' end there were two nonhomologous leader exons which were alternately spliced to the remainder of the gene. These leader exons mapped to 1.7 and 0.7 kilobases, respectively, upstream of a common splice acceptor site which was eight base pairs 5' to the translation initiator AUG. Exon 1 is 147 bases in length, while exon 2 is 111 bases. A consensus TATA sequence was found roughly 30 base pairs upstream from exon 1, but none was found in the analogous position upstream of exon 2. The transcript length diversity arose principally from the use of three polyadenylation sites. This gave rise to RNA molecules with 3'-untranslated regions of roughly 375, 655, and 945 base pairs. With two start sites and three termination sites, this gene has the potential to produce six different transcripts. All six possible transcripts were present in whole fly mRNA. Transcripts containing the two different leader exons were found in roughly the same relative quantities through development. In contrast, the various 3' ends were differentially represented through development.

scholarly journals The Drosophila melanogaster actin 5C gene uses two transcription initiation sites and three polyadenylation sites to express multiple mRNA species.

1986 ◽  
Vol 6 (6) ◽  
pp. 2080-2088 ◽  
Author(s):  
B J Bond ◽  
N Davidson
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Initiation ◽  
Splice Acceptor Site ◽  
Acceptor Site ◽  
Base Pairs ◽  
Exon 2 ◽  
Rna Molecules ◽  
Exon 1 ◽  
Polyadenylation Sites ◽  
Tata Sequence

At least six mRNAs are made from the Drosophila melanogaster act5C gene. We investigated the structures of these RNAs in detail and determined that they are heterogeneous at both their 5' and 3' ends. At the 5' end there were two nonhomologous leader exons which were alternately spliced to the remainder of the gene. These leader exons mapped to 1.7 and 0.7 kilobases, respectively, upstream of a common splice acceptor site which was eight base pairs 5' to the translation initiator AUG. Exon 1 is 147 bases in length, while exon 2 is 111 bases. A consensus TATA sequence was found roughly 30 base pairs upstream from exon 1, but none was found in the analogous position upstream of exon 2. The transcript length diversity arose principally from the use of three polyadenylation sites. This gave rise to RNA molecules with 3'-untranslated regions of roughly 375, 655, and 945 base pairs. With two start sites and three termination sites, this gene has the potential to produce six different transcripts. All six possible transcripts were present in whole fly mRNA. Transcripts containing the two different leader exons were found in roughly the same relative quantities through development. In contrast, the various 3' ends were differentially represented through development.

scholarly journals The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rajiv Sharma ◽  
Daniel P. Dever ◽  
Ciaran M. Lee ◽  
Armon Azizi ◽  
Yidan Pan ◽  
...  
Keyword(s):  
Genetic Diseases ◽  
Basic Research ◽  
Gene Correction ◽  
Coding Region ◽  
Hematopoietic Stem ◽  
Hematopoietic Reconstitution ◽  
Exon 1 ◽  
Template Library ◽  
Donor Template

AbstractTargeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

scholarly journals Transcriptional Pausing and Activation at Exons-1 and -2, Respectively, Mediate the MGMT Gene Expression in Human Glioblastoma Cells

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 888
Author(s):  
Mohammed A. Ibrahim Al-Obaide ◽  
Kalkunte S. Srivenugopal
Keyword(s):  
Dna Methyltransferase ◽  
Glioblastoma Cells ◽  
Rt Pcr ◽  
Repair Gene ◽  
Exon 2 ◽  
Mgmt Gene ◽  
Dna Repair Gene ◽  
Exon 1 ◽  
Transcriptional Pausing ◽  
Transcription Assays

Background: The therapeutically important DNA repair gene O6-methylguanine DNA methyltransferase (MGMT) is silenced by promoter methylation in human brain cancers. The co-players/regulators associated with this process and the subsequent progression of MGMT gene transcription beyond the non-coding exon 1 are unknown. As a follow-up to our recent finding of a predicted second promoter mapped proximal to the exon 2 [Int. J. Mol. Sci.2021, 22(5), 2492], we addressed its significance in MGMT transcription. Methods: RT-PCR, RT q-PCR, and nuclear run-on transcription assays were performed to compare and contrast the transcription rates of exon 1 and exon 2 of the MGMT gene in glioblastoma cells. Results: Bioinformatic characterization of the predicted MGMT exon 2 promoter showed several consensus TATA box and INR motifs and the absence of CpG islands in contrast to the established TATA-less, CpG-rich, and GAF-bindable exon 1 promoter. RT-PCR showed very weak MGMT-E1 expression in MGMT-proficient SF188 and T98G GBM cells, compared to active transcription of MGMT-E2. In the MGMT-deficient SNB-19 cells, the expression of both exons remained weak. The RT q-PCR revealed that MGMT-E2 and MGMT-E5 expression was about 80- to 175-fold higher than that of E1 in SF188 and T98G cells. Nuclear run-on transcription assays using bromo-uridine immunocapture followed by RT q-PCR confirmed the exceptionally lower and higher transcription rates for MGMT-E1 and MGMT-E2, respectively. Conclusions: The results provide the first evidence for transcriptional pausing at the promoter 1- and non-coding exon 1 junction of the human MGMT gene and its activation/elongation through the protein-coding exons 2 through 5, possibly mediated by a second promoter. The findings offer novel insight into the regulation of MGMT transcription in glioma and other cancer types.

scholarly journals Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 29
Author(s):  
Lilia González-Cerón ◽  
José Cebrián-Carmona ◽  
Concepción M. Mesa-Valle ◽  
Federico García-Maroto ◽  
Frida Santillán-Valenzuela ◽  
...  
Keyword(s):  
Amino Acid ◽  
B Cell ◽  
Plasmodium Vivax ◽  
Nucleotide Diversity ◽  
Protective Antigen ◽  
Balancing Selection ◽  
Southern Mexico ◽  
Exon 2 ◽  
Exon 1 ◽  
Tajima’S D

Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima’s D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima’s D, β-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.

scholarly journals Stromal MED12 exon 2 mutations in complex fibroadenomas of the breast

2020 ◽  
pp. jclinpath-2020-207062
Author(s):  
Edaise M da Silva ◽  
Francisco Beca ◽  
Ana Paula Martins Sebastiao ◽  
Melissa P Murray ◽  
Catarina Silveira ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Laser Capture Microdissection ◽  
Sanger Sequencing ◽  
Mediator Complex ◽  
Telomerase Reverse Transcriptase ◽  
Exon 2 ◽  
Stromal Component ◽  
Hotspot Mutations ◽  
Laser Capture

AimsHere we explore the presence of mediator complex subunit 12 (MED12) exon 2 and telomerase reverse transcriptase (TERT) promoter hotspot mutations in complex fibroadenomas (CFAs) of the breast.MethodsThe stromal components from 18 CFAs were subjected to Sanger sequencing of MED12 exon 2 and the TERT promoter hotspot loci. The epithelial and stromal components of two MED12 mutated CFAs were subjected to laser capture microdissection, and Sanger sequencing of MED12 exon 2, TERT promoter and PIK3CA exons 9 and 20, separately.ResultsMED12 exon 2 mutations were identified in the stroma of 17% of CFAs. The analyses of epithelial and stromal components, microdissected separately, revealed that MED12 mutations were restricted to the stroma. No TERT promoter or PIK3CA mutations in exons 9 and 20 were detected in analysed CFAs.ConclusionsLike conventional fibroadenomas, MED12 exon 2 mutations appear to be restricted to the stromal component of CFAs, supporting the notion that CFAs are stromal neoplasms.

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