Sequence variants in the FcεRI alpha chain gene

2002 ◽  
Vol 93 (1) ◽  
pp. 37-41 ◽  
Author(s):  
Toshiki Shikanai ◽  
Eric S. Silverman ◽  
Brian W. Morse ◽  
Craig M. Lilly ◽  
Hiroshi Inoue ◽  
...  
Keyword(s):  
Promoter Region ◽  
Population Substructure ◽  
Chain Gene ◽  
Polymorphism Analysis ◽  
Sequence Variants ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Alpha Chain ◽  
Asthmatic Patients ◽  
Single Stranded Conformational Polymorphism

There is a relationship between IgE levels and expression of high-affinity IgE receptors (FcεRI). Because the alpha chain is the only portion of the receptor that binds directly to IgE, we reasoned that sequence variants in the FcεRI alpha gene may exist that alter these binding events. We screened all of the exons and the promoter region of the FcεRI alpha chain gene with genomic DNA from 389 asthmatic and 341 normal control subjects for mutations by using single-stranded conformational polymorphism analysis. No nonsynonomous single nucleotide polymorphisms (SNPs) were identified in the coding region. Three SNPs were found in the promoter region: an A/C transversion at −770 from the translation start site; a G/A transition at −664; and a T/C transition at −335. No differences in allele frequencies were detected between asthmatic subjects and controls. Homozygosity for the C variant at locus −335 was more common in Caucasian asthmatic patients with IgE levels in the lower quartile than in the upper quartile ( P = 0.032). An analysis of highly polymorphic SNPs indicated that this association is unlikely to be due to population substructure. We conclude that homozygosity for the C allele of FcεRI alpha chain variant is associated with lower IgE levels.

Nucleotide variation in the ovine KRT31 promoter region and its association with variation in wool traits in Merino-cross lambs

2019 ◽  
Vol 157 (2) ◽  
pp. 182-188
Author(s):  
W. Chai ◽  
H. Zhou ◽  
H. Gong ◽  
J. Wang ◽  
Y. Luo ◽  
...  
Keyword(s):  
Promoter Region ◽  
Wool Fibre ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Banding Patterns ◽  
Keratin Gene ◽  
Single Stranded Conformational Polymorphism ◽  
Exon 1 ◽  
Polymerase Chain ◽  
Fleece Weight

AbstractKeratins are the main structural proteins of wool fibres, and it is thought that variation in the keratins may affect wool fibre characteristics. Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analyses were used to investigate four regions of the ovine keratin gene KRT31 including a portion of the promoter, the exon 1, exon 3 and exon 7 regions. Initially, in a screening panel of 300 New Zealand Romney, Merino and White Dorper sheep obtained from 26 farms, three, two, two and two PCR-SSCP banding patterns were observed for these four regions, respectively. The promoter region, the exon 1 and exon 3 regions contained two single nucleotide polymorphisms (SNPs) and the exon 7 region contained one SNP. The effect of the variation found in the promoter region on wool traits was subsequently investigated in 485 Southdown × Merino-cross lambs from seven sire-lines. The three variants identified in the original 300 sheep (named A, B and C) were observed with frequencies of 56, 29 and 15%, respectively. The presence of A and B had no significant effect on wool traits, but the presence of C was found to be associated with an increase in greasy fleece weight (GFW), clean fleece weight (CFW) and mean staple length (MSL). There was an effect of genotype on CFW and MSL, with BC sheep producing wool of higher CFW and MSL than AA, AB, AC and BB sheep. These results suggest that ovine KRT31 might be a useful candidate gene for improving wool traits.

scholarly journals Variation in the Promoter Region of the MC4R Gene Elucidates the Association of Body Measurement Traits in Hu Sheep

2019 ◽  
Vol 20 (2) ◽  
pp. 240
Author(s):  
Girmay Shishay ◽  
Guiqiong Liu ◽  
Xunping Jiang ◽  
Yun Yu ◽  
Wassie Teketay ◽  
...  
Keyword(s):  
Promoter Region ◽  
Gene Promoter ◽  
Body Measurement ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Mc4r Gene ◽  
Real Time Quantitative Pcr ◽  
Regulatory Variants ◽  
Significant Difference ◽  
Body Measurement Traits

The melanocortin 4 receptor (MC4R) gene is expressed in the appetite-regulating areas of the brain and is engaged in the leptin signaling pathway. Although previous studies have identified variants in the coding region of the sheep MC4R gene showing significant associations with birth weight, weaning weight, and backfat thickness, no such associations have been reported for the promoter region. Besides, the essential promoter region of the sheep MC4R has not been delineated. In this study, to better understand the transcriptional regulation of MC4R and to elucidate the association between regulatory variants and haplotypes with body measurement traits in sheep, we cloned and characterized the MC4R promoter. We found that the minimal promoter of the gene is located within the region −1207/−880 bp upstream of the first exon. Real-time quantitative PCR (RT-qPCR) data revealed the mRNA expression of the MC4R gene had a significant difference between sex and age. In the association analysis, eight single nucleotide polymorphisms (SNPs) had a significant association with one or more traits (p < 0.05); of these, two SNPs were novel. Notably, individuals with haplotype H1H2 (CT-GA-GT-GA-GT-GA-GA-CG) were heavier in body weight than other haplotypes. Altogether, variations in the MC4R gene promoter, most notably haplotype H1H2, may greatly benefit marker-assisted selection in sheep.

scholarly journals Polymorphism analysis and expression patterns of the <i>IGF1</i> gene in the Shitou goose

2021 ◽  
Vol 64 (2) ◽  
pp. 315-323
Author(s):  
Jun Tang ◽  
Mao Guo ◽  
Jing Fu ◽  
Hongjia Ouyang ◽  
Yunbo Tian ◽  
...  
Keyword(s):  
Growth And Development ◽  
Expression Patterns ◽  
Subcutaneous Fat ◽  
Breast Muscle ◽  
Growth Stages ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Growing Age ◽  
Leg Muscle

Abstract. Insulin-like growth factor 1 (IGF1) is one of the endocrine hormones that plays an important role in regulating growth and development of animals. In this study, polymorphism in the 5′UTR and 3′UTR coding region and of the IGF1 gene was detected by DNA sequencing technology, and the abundance of IGF1 mRNA in various tissues at three growth stages of the Shitou goose was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Moreover, the differential expression of IGF1 in various tissues between the Shitou goose and Wuzong goose was revealed. Two single nucleotide polymorphisms (SNPs) were found in the exon3 region of IGF1 in the Shitou goose. IGF1 mRNA was extensively expressed in various tissues of Shitou geese with high abundant expression in the liver, breast muscle and leg muscle at three growth stages. IGF1 mRNA expression showed a trend of first increase and then decrease in the pituitary, liver, subcutaneous fat and abdominal fat tissues, but it decreased in the breast muscle and leg muscle of a Shitou goose with growing age. Expression of IGF1 in the liver, leg muscle and pituitary tissues of the Shitou goose was significantly higher than that of the Wuzong goose. This provides a foundation for further study of regulatory mechanisms of IGF1 in the growth and development of geese.

scholarly journals Sequence Variation in the Bovine Lipin-1 Gene (LPIN1) and Its Association with Milk Fat and Protein Contents in New Zealand Holstein-Friesian × Jersey (HF × J)-cross Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3223
Author(s):  
Xiaohua Du ◽  
Huitong Zhou ◽  
Xia Liu ◽  
Yunhai Li ◽  
Jonathan G. H. Hickford
Keyword(s):  
New Zealand ◽  
Dairy Cows ◽  
Milk Production ◽  
Milk Fat ◽  
Sequence Variation ◽  
Polymorphism Analysis ◽  
Sequence Variants ◽  
Coding Region ◽  
Holstein Friesian ◽  
Lipin 1

Lipin-1 is known to play a regulatory role in tissues that function in lipid metabolism. In dairy cows, the lipin-1 gene (LPIN1) is highly expressed in the mammary gland, but its function in milk production is less understood. In this study, we used PCR-single strand conformation polymorphism analysis to investigate sequence variation in three regions of bovine LPIN1 in New Zealand Holstein-Friesian × Jersey (HF × J)-cross dairy cows, including part of the 5′ non-coding region, the region containing the LPIN1β-spliced exon, and the sixth coding exon that encodes the putative transcriptional activating domain of the protein. No variation was found in the LPIN1β-spliced exon, but two sequence variants containing one single nucleotide polymorphism (SNP) were identified in the 5′ non-coding region and four sequence variants containing four non-synonymous SNPs were identified in the sixth coding exon. Among the three common variants of the sixth coding exon, variant C was found to be associated with an increase in milk fat percentage (presence 4.96 ± 0.034% vs. absence 4.81 ± 0.050%; p = 0.006) and milk protein percentage (presence 4.09 ± 0.017% vs. absence 3.99 ± 0.025%; p = 0.001), but no associations (p > 0.01) were detected for milk yield. These results suggest that variation in LPIN1 affect the synthesis of fat and proteins in milk and has potential as a gene-marker to improve milk production traits.

scholarly journals β2-Adrenoreceptor Polymorphisms in Asthmatic Patients

2003 ◽  
Vol 8 (1) ◽  
pp. 22-28 ◽  
Author(s):  
Saeed Binaei ◽  
Sahar M. Rashed ◽  
Michael L. Christensen
Keyword(s):  
Smooth Muscles ◽  
Upstream Region ◽  
Significant Implication ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Nocturnal Asthma ◽  
Asthmatic Patients ◽  
Asthma Patients ◽  
Bronchial Dilatation ◽  
Β2 Agonists

β2-adrenergic receptors (β2AR) are GTP-binding protein (G-protein) coupled receptors widely distributed in human tissue. Inhaled β2-agonist drugs exert their primary effect on the β2AR of bronchial smooth muscles, causing relaxation and bronchial dilatation. Polymorphisms in the β2AR gene have been identified, which may affect responsiveness to β2-agonists and disease severity in asthmatics. Nine single nucleotide polymorphisms (SNPs) within the coding region and eight SNPs within in the 5′ upstream region of the β2AR gene have been identified. The two most studied polymorphisms are mutations in the coding region at codon 16, Arg to Gly (Arg16Gly) and at codon 27, Gln to Glu (Gln27Glu). Evidence suggests that carriers of Gly16, as well as carriers of Gln27, are prone to down-regulation of β2AR. Patients who are homozygous for Arg16 and/or Glu 27 may be more susceptible to tachyplaxis with chronic use of β2-agonists. Although β2AR polymorphism is not related to the severity of asthma, patients with nocturnal asthma have higher frequency of Gly16. A polymorphism in the 5′ upstream region, 5′ leader cistron (5′LC), encodes for a protein that regulates mRNA transcription. The Cys19 polymorphism in the 5′LC is associated with higher expression of β2AR. More recent studies have focused on combinations of polymorphisms across the gene region (haplotypes). The interaction of multiple SNPs within a haplotype may control β2AR function resulting in different phenotypic response in patients with asthma. β2AR polymorphism may have a significant implication in the pathophysiology of asthma and therapeutic response.

scholarly journals A Case-Control Study of the Association between Polymorphisms in the Fibrinogen Alpha Chain Gene and Schizophrenia

2017 ◽  
Vol 2017 ◽  
pp. 1-5 ◽  
Author(s):  
Wenwang Rao ◽  
Na Zhou ◽  
Huiping Zhang ◽  
Rui Liu ◽  
Shangchao Zhang ◽  
...  
Keyword(s):  
Case Control Study ◽  
Case Control ◽  
Chain Gene ◽  
Nucleotide Polymorphisms ◽  
Alpha Chain ◽  
Potential Biomarker ◽  
Healthy Control ◽  
A Minor ◽  
Intron 4 ◽  
Control Study

Our previous studies using the mass spectrum analysis provided evidence that fibrinopeptide A (FPA) could be a potential biomarker for schizophrenia diagnosis. We sought further to demonstrate that variants in the fibrinogen alpha chain gene (FGA) coded FPA might confer vulnerability to schizophrenia. 1,145 patients with schizophrenia and 1,016 healthy volunteers from the Han population in Northeast China were recruited. The association of three tag single nucleotide polymorphisms (SNPs) (rs2070011 in the 5′UTR, rs2070016 in intron 4, and rs2070022 in the 3′UTR) in FGA and schizophrenia was examined using a case-control study design. Genotypic distributions of these three SNPs were not found to be significantly different between cases and controls (rs2070011: χ2=1.28, P=0.528; rs2070016: χ2=4.11, P=0.128; rs2070022: χ2=1.23, P=0.541). There were also no significant differences in SNP allelic frequencies between cases and controls (all P>0.05). Additionally, the frequency of haplotypes consisting of alleles of these three SNPs was not significantly different between cases and healthy control subjects (global χ2=9.27, P=0.159). Our study did not show a significant association of FGA SNPs with schizophrenia. Future studies may need to test more FGA SNPs in a larger sample to identify those SNPs with a minor or moderate effect on schizophrenia.

Variation in the ovine keratin-associated protein 15-1 gene affects wool yield

2018 ◽  
Vol 156 (7) ◽  
pp. 922-928 ◽  
Author(s):  
W. Li ◽  
H. Gong ◽  
H. Zhou ◽  
J. Wang ◽  
X. Liu ◽  
...  
Keyword(s):  
Fibre Diameter ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Banding Patterns ◽  
Single Stranded Conformational Polymorphism ◽  
Associated Proteins ◽  
Polymerase Chain ◽  
Wool Yield

AbstractKeratin-associated proteins (KAPs) are constituents of wool and hair fibres and are believed to play an important role in determining the characteristics of the fibres. In the current study, a polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) approach was used to screen for variation in the ovine KAP15-1 gene (KRTAP15-1). Four PCR-SSCP banding patterns, representing four different variants (named A to D), were detected. Four single nucleotide polymorphisms were found within the coding region and three of these were non-synonymous. The effect of this genetic variation on wool traits was investigated in 396 Merino × Southdown-cross sheep. Of the three variants found in these sheep (A, B and C), the presence of B was found to be associated with decreased wool yield, while C was associated with increased wool yield and decreased fibre diameter standard deviation. Sheep of genotype AC had a higher wool yield than those of genotype AA or AB.

scholarly journals Molecular Cloning and Polymorphism Analysis of PmFGF18 from Pinctada fucata martensii

2020 ◽  
Vol 8 (11) ◽  
pp. 896
Author(s):  
Ruijuan Hao ◽  
Chuchu Mo ◽  
Linda Adzigbli ◽  
Chuangye Yang ◽  
Yuewen Deng ◽  
...  
Keyword(s):  
Promoter Region ◽  
Growth Traits ◽  
Pearl Oyster ◽  
Pinctada Fucata ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Full Length Sequence ◽  
Slow Growing

Fibroblast growth factor 18 (FGF18) plays an important functional role in skeletal growth and development. The FGF18 gene was characterized in pearl oyster Pinctada fucata martensii (PmFGF18) with the full-length sequence containing an open reading frame of 714 bp encoding 237 amino acids. The domain analysis of PmFGF18 showed a distinctive FGF domain, with a high similarity to FGF18 protein sequences from Crassostrea gigas (43.35%) and C. virginica (37.43%). PmFGF18 expression was revealed in all analyzed tissues with a significantly higher expression level in the fast-growing group than the slow-growing group. The analysis of PmFGF18 polymorphism demonstrated 33 SNPs (single nucleotide polymorphisms) in the CDS and promoter region of PmFGF18 sequence. Association analysis revealed 19 SNPs (2 SNPs from CDS and 17 SNPs from the promoter region) associating significantly with growth traits. Among the associated SNPs, one SNP g.50918198 A > C was verified in the other breeding line. Therefore, PmFGF18 can be utilized as a candidate gene for growth, and its related SNPs could be used in selective breeding of P. f. martensii for the improvement of growth traits.

scholarly journals Analysis of the relationship between single nucleotide polymorphism of the CD209, IL-10, IL-28 and CCR5 D32 genes with the human predisposition to developing tick-borne encephalitis

2017 ◽  
Vol 71 (1) ◽  
pp. 0-0 ◽  
Author(s):  
Piotr Czupryna ◽  
Miłosz Parczewski ◽  
Sambor Grygorczuk ◽  
Sławomir Pancewicz ◽  
Joanna Zajkowska ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Promoter Region ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Tick Borne Encephalitis ◽  
Base Pair Deletion ◽  
Thermal Cycler ◽  
The Relationship

<b>Introduction: </b>It is known that in the pathogenesis of tick-borne encephalitis (TBE) various molecules play a significant role. The most prominent factors include IL-10, IL-28B, CD-209 and CCR5. It is reasonable to search for genetic predispositions to the development of various clinical forms of TBE related to the genetic variation of IL-10, IL-28B, CD-209 and CCR5. In this study we aimed to search for the relationship between single nucleotide polymorphism in the promoter region of the CD209, IL-10, IL-28 and 32 base pair deletion in CCR5 coding region (Δ 32) with the human predisposition to development of various clinical presentations of TBE. We tried to assess the relation between the presence of particular alleles and genotypes with laboratory and clinical parameters. <b>Material/Methods </b>59 patients with TBE and 57 people, bitten by a tick who never developed TBE (Polish cohort), were included in the study. To assess the distribution of single nucleotide polymorphisms, TaqMan SNP genotyping assays were used for IL10: rs1800872 and rs1800896, for CD 209 rs4804803 and rs2287886, rs12979860 for IL 28B SNPs according to the manufacturer’s protocol using real-time PCR technology on the StepOne thermal cycler. <b>Results </b>Comparison between TBE patients and CG showed that in SNP rs2287886 CD 209 AG heterozygotes were more frequent in the TBE group, while homozygotes GG were more frequent in the CG group. <b>Conclusions </b> SNP rs2287886 CD 209 AG heterozygotes predispose humans to develop TBE. Single nucleotide polymorphism in the promoter region of the CD209, IL-10, IL-28 and CCR5 D32 genes does not correlate with the severity of TBE.

scholarly journals A frame shift mutation in the fibrinogen A alpha chain gene in a kindred with renal amyloidosis

Blood ◽  
1996 ◽  
Vol 87 (10) ◽  
pp. 4197-4203 ◽  
Author(s):  
T Uemichi ◽  
JJ Liepnieks ◽  
T Yamada ◽  
MA Gertz ◽  
N Bang ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Mutant Gene ◽  
Single Strand Conformation Polymorphism ◽  
Plasma Fibrinogen ◽  
Chain Gene ◽  
Renal Amyloidosis ◽  
Polymorphism Analysis ◽  
Alpha Chain ◽  
Frame Shift ◽  
Frame Shift Mutation

A new American kindred with amyloidosis was found by single-strand conformation polymorphism analysis to have a mutation in the fibrinogen A alpha chain gene. Affected members in this kindred have autosomal dominant amyloid nephropathy. DNA sequencing showed a single nucleotide deletion at the third base of codon 524 of the fibrinogen A alpha chain genes (4904delG) that resulted in a frame shift and premature termination of the protein at codon 548. Antiserum was produced to a portion of the abnormal peptide predicted by the DNA sequence and amyloid deposits were immuno-histologically proven to contain this abnormal peptide. Two of the propositus' 4 children were positive for the mutant fibrinogen A alpha chain gene by restriction fragment length polymorphism analysis based on polymerase chain reaction. These two mutant gene carriers now in the second decade of life show no clinical symptoms of amyloidosis as yet but have lower plasma fibrinogen concentrations when compared with their normal siblings. This the first description of a kindred with renal amyloidosis and low plasma fibrinogen and also the first report of amyloidosis caused by a frame shift mutation.

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