Functional Significance Of Polymorphism Research Articles

Polymorphism of the vitamin D receptor gene in kazakh with bronchial asthma

Introduction.The polymorphism of the vitamin D receptor (VDR) gene is associated with bronchial asthma (BA). Based on this, studies on the prevalence of VDR polymorphism in representatives of different races and peoples with AD and in healthy people are timely.Aims.To determine the TaqI polymorphism of the vitamin D receptor gene (TT, TS and CC) in children and adolescents with a verified diagnosis of AD on the example of the Kazakh population of Western Kazakhstan.Materials and methods. The study involved 54 Kazakh children with BA (Me age 12.8 years, fluctuations range 5–17 years). The control group consisted of residents of the same region without BA: Kazakhs – 66 children, Russians – 40 children. In each of these groups, children were born in the third generation of families without mixed marriages. The examination was performed by collecting venous blood with the informed consent of the legal representative of the child/adolescent. The samples were stored at a temperature of -80 ºC until the start of the analysis with further DNA sequencing and PCR at the INVITRO laboratory.Results.In Kazakh children without BA TT alleles were recorded in 57.6%, TC – in 34.8%, CC – in 7.6%. In Russian children without BA, the TT allele was found in 35.0%, TC – 55.0%, CC – 10%. In children of Kazakhs with BA, the TT allele was in 74.0% of cases, TC in 26.0%, and CC was absent. The first stage of the study with a limited number of observations did not allow obtaining a statistically significant difference between the individual indicated groups. However, taking into account the probable protective effect of the CC allele, the differences in the frequency of the TT alleles and in total TC and CC and CC and in total TT and TC turned out to be significant: 0.000 and 0.030, respectively. When studying the distribution of alleles within the groups, it turned out that for Kazakhs in the control group and, especially, in AD, a decrease in the frequencies of TC alleles and, most clearly, CC alleles is typical.Conclusion.The protective value of the CC allele cannot be ruled out. But it is not yet possible to formulate a final opinion on the functional significance of polymorphism. Further research will help to understand the relationship between the structural features of the VDR and BA.

Electromobility Shift Assay Reveals Evidence in Favor of Allele-Specific Binding of RUNX1 to the 5′ Hypersensitive Site 4-Locus Control Region

In our previous studies on the Iranian β-thalassemia (β-thal) patients, we identified an association between the severity of the β-thal phenotype and the polymorphic palindromic site at the 5′ hypersensitive site 4-locus control region (5′HS4-LCR) of the β-globin gene cluster. Furthermore, a linkage disequilibrium was observed between this region and XmnI-HBG2 in the patient population. Based on this data, it was suggested that the well-recognized phenotype-ameliorating role assigned to positive XmnI could be associated with its linked elements in the LCR. To investigate the functional significance of polymorphisms at the 5′HS4-LCR, we studied its influence on binding of transcription factors. Web-based predictions of transcription factor binding revealed a binding site for runt-related transcription factor 1 (RUNX1), when the allele at the center of the palindrome (TGGGG(A/G)CCCCA) was A but not when it was G. Furthermore, electromobility shift assay (EMSA) presented evidence in support of allele-specific binding of RUNX1 to 5′HS4. Considering that RUNX1 is a well-known regulator of hematopoiesis, these preliminary data suggest the importance of further studies to confirm this interaction and consequently investigate its functional and phenotypical relevance. These studies could help us to understand the molecular mechanism behind the phenotype modifying role of the 5′HS4-LCR polymorphic palindromic region (rs16912979), which has been observed in previous studies.

Characterization and functional significance of polymorphisms in porcine Toll-like receptor (TLR) 5 gene

Li, H.-t., Wang, L., Liu, D. and Yang, X.-q. 2012. Characterization and functional significance of polymorphisms in porcine Toll-like receptor (TLR) 5 gene. Can. J. Anim. Sci. 92: 409–415. Toll-like receptor (TLR) 5 plays an important role in host defenses by recognizing bacterial flagellin and signaling to initiate immune responses. Polymorphisms in the TLR5 gene have a profound influence on receptor function and host susceptibility/resistance to infectious disease, as suggested by studies in humans and other species. In the present study, we characterized polymorphisms and determined their functional significance in the porcine TLR5 gene. Four novel non-synonymous single nucleotide polymorphisms (SNPs), c.176C>T (p.R59M), c.902C>T (p.S301F), c.959T>A (p.F320Y), and c.1796C>T (p.T599M) (reference sequence: GenBank No. AB208697), were first identified by sequencing the complete coding sequences (CDS) of the TLR5 gene in the Min pig, an indigenous Chinese pig breed known for its high general resistance to disease. SNP c.1796C>T (p.T599M) is located in one of the six predicted N-glycosylation sites in the extracellular domain of the TLR5 protein. By measuring protein activation, as represented by nuclear factor κB activity, in transiently transfected PK-15 cells with TLR5 expression vectors carrying site-directed mutations, we demonstrated that the previously discovered SNP c.1205C>T, leading to the amino acid substitution of proline by leucine, attenuated the responses of the receptor to flagellin (P<0.01). Further functional investigation on SNP c.1205C>T is necessary to determine its possible role in disease susceptibility in pigs and may facilitate pig breeding aimed at improving disease resistance.

Using blocks of linked single nucleotide polymorphisms as highly polymorphic genetic markers for parentage analysis

Single nucleotide polymorphisms (SNPs) are plentiful in most genomes and amenable to high throughput genotyping, but they are not yet popular for parentage or paternity analysis. The markers are bi-allelic, so individually they contain little information about parentage, and in nonmodel organisms the process of identifying large numbers of unlinked SNPs can be daunting. We explore the possibility of using blocks of between three and 26 linked SNPs as highly polymorphic molecular markers for reconstructing male genotypes in polyandrous organisms with moderate (five offspring) to large (25 offspring) clutches of offspring. Haplotypes are inferred for each block of linked SNPs using the programs Haplore and Phase 2.1. Each multi-SNP haplotype is then treated as a separate allele, producing a highly polymorphic, 'microsatellite-like' marker. A simulation study is performed using haplotype frequencies derived from empirical data sets from Drosophila melanogaster and Mus musculus populations. We find that the markers produced are competitive with microsatellite loci in terms of single parent exclusion probabilities, particularly when using six or more linked SNPs to form a haplotype. These markers contain only modest rates of missing data and genotyping or phasing errors and thus should be seriously considered as molecular markers for parentage analysis, particularly when the study is interested in the functional significance of polymorphisms across the genome.

Identification and functional significance of polymorphisms in the μ-opioid receptor gene ( Oprm) promoter of C57BL/6 and DBA/2 mice

C57BL/6J and DBA/2J mice demonstrate differences in morphine preference when tested in a two-bottle choice paradigm. Quantitative trait loci (QTL) mapping suggested the proximal region of chromosome 10 was responsible for 41% of the observed genetic variance. The μ-opioid receptor (MOR) gene ( Oprm) maps to this region and is a prime candidate for explaining the QTL. We hypothesized that variations in Oprm between these strains are responsible for differences in morphine preference. We identify five single nucleotide polymorphisms (SNPs) in the Oprm promoter; three within or near putative transcription factor binding sites. Promoter fragments were amplified from genomic DNA by polymerase chain reaction (PCR) and subcloned into luciferase reporter vectors. A significant difference in basal Oprm promoter activity was seen with C57BL/6 and DBA/2 ∼1675 constructs in MOR-positive BE(2)-C cells, but not in MOR-negative Neuro-2a cells. In BE(2)-C cells, average DBA/2 ∼1675 construct activity was 1.3–2.0× greater than average C57BL/6 activity suggesting that the SNPs might alter MOR expression in these two mouse strains. Significant differences in promoter activities between the two cell lines suggest that cell-type-specific transcription factors are involved. No significant differences in construct activity were found between untreated and morphine-treated BE(2)-C or Neuro-2a cells, suggesting that morphine does not regulate transcription of Oprm.

Functional significance of polymorphism among MHC class II gene promoters.

The functional significance of polymorphism among MHC class II promoters in man and mouse is here reviewed, mainly in terms of the hypothesis of differential expression. The hypothesis proposes that differences between antigen-presenting cells in MHC class II expression exert a co-dominant effect on the Th1-Th2 cytokine balance, such that class II molecules of one type come to control to a greater extent the production of one group of cytokines, and those of another type the production of the alternative group. The survey deals with the influence of signal strength and antigen-presenting cell type on T-cell subset differentiation; functional differences between MHC class II molecules not obviously related to determinant selection; disease protection mediated by HLA alleles; mechanisms possibly responsible for allotypic and isotypic bias; overdominance (heterozygous advantage) in selection for expression of class II alleles; MHC class II promoter structure and function; inter-locus and inter-allele variability within human MHC class II gene upstream regulatory regions; a comparison of these polymorphisms in mouse and man; read-out of class II promoter function; and a comparison with expression of MHC class I. We conclude that the evidence that this variation is functionally active (i.e. controls expression) is increasing, but is not yet compelling. The crucial test still to come, we suggest, is whether or not the biological effects attributable to this polymorphism will line up with molecular studies on expression.