Detection of insertion polymorphisms in 5' flank and second intron of the porcine growth hormone gene.
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Alleles↗
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Results for “intronic polymorphism”
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Whole exon 5 and intron 5 replaced by RHCE in DVa(Hus).
The DVa(Hus) was previously investigated through cDNA analysis, which revealed an RHD-CE(5)-D hybrid allele. However, the 5' and 3' breakpoints remain unknown. In this article, gene recombinations between the RHD and RHCE alleles were investigated by a combination approach of a sequence-specific primer PCR (PCR-SSP) and an RHD full-length coding region sequencing method on two Chinese subjects with weak D phenotypes. The hybrid Rhesus box of each individual was also investigated through an established PCR-based method. As a result, two partial D phenotypes, DVa(Hus) and DVI type III, were identified, each carrying one hybrid RHD-CE-D allele. The two samples were also serotyped with Rh phontypes of DccEe and DCcee, respectively. Other sequencing analyses of the DVaHus sample showed that the sequence of intron 4 is identical with RHD, whereas the whole sequence of exon 5 and intron 5 is identical with RHCE except for seven polymorphisms in the intron 5. We may concluded that in the case of this Chinese DVa(Hus), the whole exon 5 and complete intron 5 of a total segment of 1801 nucleotides were replaced by RHCE suggesting that the breakpoints of the replaced region are the 5' end of the exon 5 and the 3' end of the intron 5.
Alleles↗
Novel single nucleotide polymorphisms of the human nuclear factor kappa-B 2 gene identified by sequencing the entire gene.
The nuclear factor kappa-B 2 (NFKB2) gene is a member of the NFKB/Rel gene family, which is known to be a pivotal regulator of the acute phase of the inflammatory response and of immune responses. We identified three novel single nucleotide polymorphisms (SNPs) and determined their allelic frequencies, as determined by the sequencing of 48 alleles of the entire gene in a Japanese population sample. Two of the three polymorphisms were identified at nucleotide (nt) position 1837 (T/C) and nt position, 1867 (GG/G) in the upstream region of the gene. The other polymorphism was identified at nt position 2584 (G/T) within intron 1. These polymorphisms will be useful in genetic studies of the processes involved in inflammatory responses and in bone differentiation.
Japan↗
Intraspecific nuclear DNA variation in Drosophila.
We have summarized and analyzed all available nuclear DNA sequence polymorphism studies for three species of Drosophila, D. melanogaster (24 loci), D. simulans (12 loci), and D. pseudoobscura (5 loci). Our major findings are: (1) The average nucleotide heterozygosity ranges from about 0.4% to 2% depending upon species and function of the region, i.e., coding or noncoding. (2) Compared to D. simulans and D. pseudoobscura (which are about equally variable), D. melanogaster displays a low degree of DNA polymorphism. (3) Noncoding introns and 3' and 5' flanking DNA shows less polymorphism than silent sites within coding DNA. (4) X-linked genes are less variable than autosomal genes. (5) Transition (Ts) and transversion (Tv) polymorphisms are about equally frequent in non-coding DNA and at fourfold degenerate sites in coding DNA while Ts polymorphisms outnumber Tv polymorphisms by about 2:1 in total coding DNA. The increased Ts polymorphism in coding regions is likely due to the structure of the genetic code: silent changes are more often Ts's than are replacement substitutions. (6) The proportion of replacement polymorphisms is significantly higher in D. melanogaster than in D. simulans. (7) The level of variation in coding DNA and the adjacent noncoding DNA is significantly correlated indicating regional effects, most notably recombination. (8) Surprisingly, the level of polymorphism at silent coding sites in D. melanogaster is positively correlated with degree of codon usage bias. (9) Three proposed tests of the neutral theory of DNA polymorphisms have been performed on the data: Tajima's test, the HKA test, and the McDonald-Kreitman test. About half of the loci fail to conform to the expectations of neutral theory by one of the tests. We conclude that many variables are affecting levels of DNA polymorphism in Drosophila, from properties of nucleotides to population history and, perhaps, mating structure. No simple, all encompassing explanation satisfactorily accounts for the data.
Animals↗
GCF2/LRRFIP1 represses tumor necrosis factor alpha expression.
Tumor necrosis factor alpha (TNF-alpha) is an important mediator of inflammation, apoptosis, and the development of secondary lymphoid structures. Multiple polymorphic microsatellites have been identified in and around the gene, and there are also multiple single-base pair biallelic polymorphisms in the introns and promoter. The TNF-alpha -308 promoter polymorphism is a G-to-A transition which has been statistically associated with various autoimmune disorders. Some studies have found that it may directly mediate the increased transcription of TNF-alpha in some circumstances. This study characterizes proteins interacting at the polymorphic promoter site. Affinity purification of binding proteins and confirmatory chromatin immunoprecipitation assays were used to identify the proteins. Electrophoretic mobility shift analyses and surface plasmon resonance were used to define binding characteristics. Proteins interacting at this site include GCF2/LRRFIP1 and Ets-1. GCF2/LRRFIP1 appears to act as a repressor and occupies the -308 site in cells that do not make TNF-alpha. Cells competent to produce TNF-alpha have Ets-1 bound to the -308 promoter site. Active transcription is accompanied by NF-kappaB and c-Jun binding to the proximal promoter. Thus, dynamic changes on the TNF-alpha promoter, particularly at the -308 site, accompany the transition from repressed to active transcription. GCF2/LRRFIP1 is the first TNF-alpha repressor identified.
Base Sequence↗
Identification of a novel type 1 diabetes susceptibility gene, T-bet.
The gene encoding interferon (IFN)-gamma, IFNG, is known as one of the candidate susceptibility genes for type 1 diabetes. In addition, cytokines, including IFN-gamma, play important roles in the pathogenesis of type 1 diabetes. Therefore, we focused on the Th1-specific T-box transcription factor gene (T-bet), which contributes to the induction of the hallmark Th1 cytokine, IFN-gamma. We first screened for polymorphisms in the T-bet gene and detected two microsatellite repeat polymorphisms located in intron 1 and the 3'- flanking region, and two single nucleotide polymorphisms, including a His33Gln substitution within the coding region. By association studies, the Gln-positive phenotype and (CA)14 allele in 3'-flanking region of T-bet were found to be associated with type 1 diabetes in the Japanese population. Furthermore, Gln33 T-bet showed a significantly higher transcriptional activity of the IFNG gene via a dual luciferase reporter assay. Our study suggests the first evidence of an association between type 1 diabetes and polymorphisms in the T-bet gene, and that variation in T-bet transcriptional activity may play a role in the development of type 1 diabetes, possibly through the effect on IFN-gamma production in Th1 cells.
Adolescent↗
Intronic ANG II type 2 receptor gene polymorphism 1675 G/A modulates receptor protein expression but not mRNA splicing.
The X-linked ANG II type 2 receptor (AT2) is supposed to be involved in cardiovascular disorders. Two studies associated the A allele of the AT2 gene polymorphism (PM) 1675 G/A with left ventricular hypertrophy in men and coronary ischemia in women. Because the PM is located in the short intron 1 of the AT2 gene within a sequence motif similar to the splice branch site consensus, we tested whether it might affect pre-mRNA splicing and/or modulate AT2 receptor expression. We first analyzed the AT2 mRNA splice pattern by RT-PCR in myocardial samples from 12 explanted human hearts and compared it with the respective genotypes. All 12 patients, 10 hemizygous males (7 A, 3 G allele carriers) and 2 homozygous females (2 G/G allele carriers), exhibited the same myocardial AT2 splice pattern with a relative abundance of transcript exon 1/2/3 compared with exon 1/3. Next, AT2 minigene constructs were cloned from both alleles, comprising the core promoter and the complete transcribed region up to the translation start codon, upstream of a luciferase reporter gene. These constructs were transfected into human (HT1080) and rat (PC12W) cell lines and rat vascular smooth muscle cells, and luciferase activities were assessed, as well as the splice patterns of the chimeric AT2/luciferase mRNAs. In all transfected cell types, the mRNA expressed from the AT2 constructs was spliced like the endogenous myocardial AT2 mRNA. However, luciferase activities driven by the G allele construct were significantly higher than those expressed from the A allele. Taken together, these data indicate that individuals carrying the G allele may express higher levels of AT2 receptor protein, which may be protective during the development of ventricular hypertrophy and coronary ischemia.
Animals↗
Association between the NOS3 (-786 T/C) and the ACE (I/D) DNA genotypes and early coronary artery disease.
DNA polymorphisms at the endothelium constitutive nitric oxide synthase gene (NOS3) have been linked to the risk of developing coronary artery disease (CAD). In vitro, a polymorphism in the 5' region of the NOS3 gene (-786 T/C) influences promoter activity. This polymorphism has been associated with coronary spasms among Japanese. The genetic variation at the angiotensin-converting enzyme (ACE) is associated with plasma ACE activities and has also been linked with susceptibility to cardiovascular disease. Our objective was to determine if DNA polymorphisms in the NOS3 and ACE genes were associated with early CAD. We analyzed the -786 T/C polymorphism in the 5' flanking region and the 27-bp repeat polymorphism in NOS3 intron 4, as well as the ACE-I/D polymorphism. A total of 170 male smokers (CAD patients) younger than 50 years and 300 male smokers (healthy controls) were genotyped. Frequencies were compared by the chi(2) test, and odds ratios (ORs) and their 95% confidence intervals (CI) were also calculated. Only the -786 T/C polymorphism in the 5' flanking region of the NOS3 gene was significantly associated with early CAD in our population. The frequency of the CC genotype was significantly increased (P = 0.039) in patients compared to controls (OR = 1.67; 95% CI = 1.01, 2.72). We found a synergistic effect between the NOS3-CC and the ACE-DD genotypes in the risk of developing early CAD. The frequency of CC + DD was significantly increased among patients (P = 0.002). Thus, those with a NOS3-CC and an ACE-DD genotype would have a significantly increased risk of suffering an early episode of coronary artery disease (OR = 2.82; 95% CI = 1.40, 5.70). Although based on a limited number of patients, our work suggests that individuals who are NOS3-CC + ACE-DD are at a higher risk for early CAD, probably as a consequence of increased endothelial dysfunction.
Adult↗
Recurrent early pregnancy loss and endothelial nitric oxide synthase gene polymorphisms.
OBJECTIVE(S): Studies on the relation between endothelial nitric oxide synthase (eNOS) activity in implantation and maintenance of pregnancy highlights the importance of eNOS gene polymorphisms in recurrent early pregnancy loss (REPL). We investigated the relationship between idiopathic REPL and polymorphisms in eNOS among South Indian women. METHODS: A case-control study comprising 145 females with REPL and 99 control females. The polymorphisms studied include a 27 bp intron 4 repeat, Glu298Asp variation of exon 7 and a novel 140 A --> G polymorphism in intron 6. A polymerase chain reaction-based di-deoxy dye terminator sequencing method was used for genotyping. RESULTS: A novel A --> G polymorphism was identified in intron 6. The more frequent b allele of intron 4 repeat was present at a frequency of 0.84 in cases as compared to 0.86 in controls (O.R 1.17); the G allele of exon 7 coding for the wild-type glutamate containing isoform was present at a frequency of 0.79 in cases and 0.83 in controls (O.R 1.30, CI 0.6-2.8). The intron 6 variant A allele was present at a frequency of 0.58 in cases and 0.45 in controls (O.R 0.59, CI 0.33-1.08). Overall, the polymorphism in intron 6, in homozygous condition, exhibited a significant association to the risk of REPL (O.R 0.43, CI 0.21-0.89), P: 0.021). CONCLUSIONS: The present study identifies and validates a novel polymorphism in the eNOS gene which was found associated with the risk of REPL.
Abortion, Habitual↗
Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat.
Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena species for amplification-product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification-product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60) followed by intron markers (0.46), exon markers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of intron markers were polymorphic. Polymorphic-sequence-tagged sites for plant-breeding applications can be created easily by targeting noncoding gene regions.
Avena↗
Genetic analysis of the ferrochelatase gene in eight Japanese patients from seven families with erythropoietic protoporphyria.
A decrease in the activity of ferrochelatase (FECH; EC 4.99.1.1), the terminal enzyme of the heme biosynthetic pathway, results in erythropoietic protoporphyria (EPP; MIM 177000). We analyzed the FECHgene in eight Japanese EPP patients from seven non-consanguineous families and found two distinct genomic DNA abnormalities. In six patients from five families, there was a G-to-A point-mutation at the first position of the intron 9 donor site; it resulted in aberrant splicing and skipping of exon 9 in FECH mRNA. In one patient, we found an A-to-G point-mutation 4 bases from the 3" terminus of intron 4 that led to the in-frame insertion of 3 bases in mRNA. No allelic anomalies, except for 3 single nucleotide polymorphisms were detected in another patient. We analyzed intron polymorphism at IVS3-48, known to be associated with the phenotypic expression of EPP, in these eight patients and 152 healthy Japanese volunteers. All patients were C/C homozygous for IVS3-48. The allelic frequency of IVS3-48C polymorphism in the healthy Japanese volunteers was 67.8% (103/152).
Adolescent↗
Polymorphic tandem repeat region in interleukin-1 alpha intron 6.
Analysis of polymerase chain reaction amplified products from the sixth intron of the human interleukin-1 alpha gene reveals a high polymorphism (polymorphism information content = 0.51) in a Caucasian population. Altogether, seven alleles have been defined ranging from 620 to 1220bp. This polymorphism is probably attributable to a variable number of 46-bp tandem repeats, each containing potential regulatory sequences.
Base Sequence↗
Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes.
Despite the fact that D. melanogaster and D. simulans have been the central model system for molecular population genetics, few data are available for noncoding regions. Here, we present an analysis of population genetic data from intergenic regions and comparisons of these data to previously collected data from introns and exons. Polymorphisms and fixations were categorized as A/T to G/C or G/C to A/T changes and were polarized by inferring the ancestral state using both parsimony and maximum likelihood. Noncoding fixations in both D. melanogaster and D. simulans were consistent with equilibrium base-composition evolution. However, polarized noncoding polymorphisms, revealed a different pattern. Although A/T to G/C and G/C to A/T polymorphisms in D. simulans were consistent with equilibrium, we observed a highly significant dearth of A/T to G/C polymorphisms in D. melanogaster introns but not in intergenic sequences. Such data could be explained by recent evolution of mutational biases associated with transcription or by lineage-specific selection on base composition. These data reveal the complexity of evolutionary processes acting even on noncoding DNA in Drosophila.
Animals↗
A polymorphic dinucleotide repeat in the third intron of TAP1.
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ATP Binding Cassette Transporter, Subfamily B, Mem↗
Characterization of porcine leptin receptor polymorphisms and their association with reproduction and production traits.
Fatness in pigs is of prime economic importance due to market incentives for production of lean pork and elevated fatness increasing the feed costs. Leptin (LEP) action, mediated through its specific receptors (LEPR), was reported to be involved in the regulation of fatness via feed intake, energy expenditure, and whole-body energy balance in pigs. In this study, we have designed 17 primer sets based on the human and mouse LEPR sequences and successfully amplified coding regions of 15 porcine LEPR exon fragments by polymerase chain reactions (PCR). Four single nucleotide polymorphisms (SNP) of Intron 2, Exons 2, 6, and 18 were found in Landrace, Yorkshire, and Duroc by mutagenetically separated-PCR (MS-PCR) and PCR-restriction fragment length polymorphisms (PCR-RFLP). Chi-square statistics was used to calculate homogeneity of genotypic frequencies of 4 gene polymorphisms for three breeds of animals. Effects of Intron 2, Exon 2, and Exon 18 polymorphisms on the reproduction trait such as litter sizes of sows were evident (p < 0.05) in Duroc and Yorkshire. There was no (p > 0.05) significant influence on the production trait of average daily gain due to four candidate gene polymorphisms in three porcine breeds. However, effects of Exon 6 and 18 polymorphisms on the production trait of backfat thickness were significant (p < 0.05) in Landrace and Yorkshire, respectively. Effects of Exon 18 polymorphisms on feed efficiency were also evident (p < 0.05) in Duroc.
Animals↗
Relation of BsmI vitamin D receptor gene polymorphism to bone mineral density and occurrence of osteoporosis in postmenopausal Chinese women in Taiwan.
Osteoporosis is a common disorder with a strong genetic component. Our aim was to evaluate the correlation of the vitamin D receptor gene intron 8 BsmI polymorphism with bone mineral density (BMD) and their relationship to osteoporosis. We determined the vitamin D receptor gene intron 8 BsmI polymorphfsm using polymerase chain reaction-based restriction analysis in 171 postmenopausal Chinese women in Taiwan. The polymorphism was detected using the restriction enzyme BsmI, where the B allele indicated absence of the cuttable site and the b allele its presence. BMD of the lumbar spine and proximal femur were measured using dual-energy X-ray absorptiometry. The allelic frequencies for postmenopausal Chinese women in Taiwan were 12.3% for B and 87.7% for b in BsmI restriction fragment length polymorphisms. The prevalence of each genotype in the study population was: 6.4% BB, 11.7% Bb and 81.9% bb. The three genotypic groups differed significantly in BMD at the lumbar spine and the femoral neck. These differences corresponded to significant gene-dose effects at the lumbar spine and femoral neck (p<0.001 for both sites). The relative risk for the development of osteoporosis was about 2-3 times as great as that predicted by the differences between genotypes in BMD, and remained significant even after adjustment for age, height and weight. The vitamin D receptor gene intron 8 BsmI polymorphism is associated with reduced BMD and predisposes women to osteoporosis.
Aged↗
Heparan sulfate proteoglycan 2 polymorphism in Alzheimer's disease and correlation with neuropathology.
A genetic association of an intronic single nucleotide polymorphism site of heparan sulfate proteoglycan 2 (HSPG2) with Alzheimer's disease (AD) was investigated among Finnish AD patients (n=213) and controls (n=269). No association of the HSPG2 polymorphism alone was observed with AD. However, an association of HSPG2 A allele with AD was detected in apolipoprotein (APOE) epsilon4 allele carriers. The odds ratio for AD was doubled in subjects carrying both epsilon4 and HSPG2 A alleles (OR=6.6) when compared to subjects with epsilon4 allele alone (OR=3.1). The impact of HSPG2 polymorphism on beta amyloid and tau pathology was studied using immunohistochemistry. Paired helical filament labeling was significantly more pronounced in AD patients carrying both epsilon4 and HSPG A alleles when compared to epsilon4 carriers lacking the HSPG2 A allele. In conclusion, HSPG2 A allele may possess an additive risk effect among the APOE epsilon4 carriers in AD.
Adult↗
Comparison of two polymorphisms of the interleukin-1 gene family: interleukin-1 receptor antagonist polymorphism contributes to susceptibility to severe sepsis.
OBJECTIVES: To determine whether the allele frequencies and genotype distribution of an interleukin (IL)-1beta TaqI polymorphism and an interleukin-1 receptor antagonist polymorphism are associated with susceptibility to and outcome of severe sepsis. In addition, we analyze a possible linkage disequilibrium between a previously described NcoI polymorphism within the tumor necrosis factor (TNF) locus and the two IL-1 gene family polymorphisms. DESIGN: Prospective, consecutive entry study of patients with diagnosis of severe sepsis. SETTING: Intensive care unit (ICU) of a university hospital. PATIENTS: Ninety-three patients with diagnosis of severe sepsis admitted to the ICU between June 1993 and June 1996. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: The polymorphic region within intron 2 of the IL-1ra gene containing variable numbers of a tandem repeat of 86 base pairs was amplified by means of the polymerase chain reaction. Alleles A1-5 are identified according to the size of the amplified DNA product. The region that contains the biallelic TaqI site within exon 5 of the IL-1beta gene was analyzed by polymerase chain reaction amplification and subsequent digestion using the TaqI restriction enzyme. A NcoI TNF-beta polymorphism was determined. The allele frequency of the allele IL-1raA2 was increased in 93 patients with severe sepsis compared with normal individuals (p < .01). No association with patients' outcome was observed. Allele frequencies or genotype distribution of the IL-1beta TaqI polymorphism did not differ between patients and controls. In addition, the allele TNFB2 of the NcoI TNF-beta polymorphism was associated with nonsurvival. Occurrence of the TNFB1 and TNFB2 alleles and genotypes was unrelated to alleles and genotypes of the two IL-1 gene family polymorphisms. CONCLUSION: In contrast to the TNF-beta NcoI polymorphism, which has been associated with patients' nonsurvival, the allele IL-1raA2 of the polymorphism within the intron 2 of IL-1ra may contribute to susceptibility to sepsis.
Case-Control Studies↗