Structural and biochemical insights into the association between ERAP1 polymorphism and autoimmune diseases
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Found SNPs between Purenkong and Jinpumkong 2 using direct sequencing method and to map these genes to soybean linkage map.To discover SNPs,a total of 76 protein related genes were selected and primers were designed.Among 49 loci showing high-quality sequence,11 SNPs were identified in 7 loci between the parental genotypes.Average SNP frequency between the parental genotypes was one SNP per 2 400 bp.With SNP genotyping in 90 RILs,these genes were mapped in exiting linkage map.
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Non-coding RNAs play an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD).This study was performed to investigate the role of PVT1 and miR-146a single nucleotide polymorphisms (SNPs) in the lung function of COPD smokers.Real-time PCR and Western blot analyses were performed to measure the expression of miR-146 and PVT1 SNPs and determine the effect of these SNPs on the pathogenesis of COPD.A total of 100 COPD smokers were enrolled in this study and divided into four groups as follows: Rs2910164CC/GC + Rs13281615GG; Rs2910164CC/GC + Rs13281615GA/AA; Rs2910164GG + Rs13281615GG; and Rs2910164GG + Rs13281615GA/AA.No obvious differences in terms of age, sex, and body height and weight were found among the four groups.However, the Rs2910164GG + Rs13281615GA/AA was associated with the highest stage of the Global Initiative for Chronic Obstructive Lung Disease and the highest values of the forced vital capacity, forced expiratory volume, and diffusing capacity of carbon monoxide, while the lowest values of these parameters were observed in the Rs2910164CC/GC + Rs13281615GG group.In addition, the highest and lowest COX2 levels were observed in the Rs2910164GG + Rs13281615GA/AA and Rs2910164CC/GC + Rs13281615GG groups, respectively.PVT1 directly and negatively regulated the miR-146a expression, which in turn directly and negatively regulated COX2 expression.Thus, the combined actions of SNP in PVT1 Rs13281615 and miR-146a Rs2910164 affected the lung function in COPD smokers.
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Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation in humans. However, the factors that affect SNP density are poorly understood. The goal of this study was to estimate the relative effects of mutability and selection on SNP density in transcribed regions of human genes. It is important for prediction of the regions that harbor functional polymorphisms.We used frequency-validated SNPs resulting from single-nucleotide substitutions. SNPs were subdivided into five functional categories: (i) 5' untranslated region (UTR) SNPs, (ii) 3' UTR SNPs, (iii) synonymous SNPs, (iv) SNPs producing conservative missense mutations, and (v) SNPs producing radical missense mutations. Each of these categories was further subdivided into nine mutational categories on the basis of the single-nucleotide substitution type. Thus, 45 functional/mutational categories were analyzed. The relative mutation rate in each mutational category was estimated on the basis of published data. The proportion of segregating sites (PSSs) for each functional/mutational category was estimated by dividing the observed number of SNPs by the number of potential sites in the genome for a given functional/mutational category. By analyzing each functional group separately, we found significant positive correlations between PSSs and relative mutation rates (Spearman's correlation coefficient, at least r = 0.96, df = 9, P < 0.001). We adjusted the PSSs for the mutation rate and found that the functional category had a significant effect on SNP density (F = 5.9, df = 4, P = 0.001), suggesting that selection affects SNP density in transcribed regions of the genome. We used analyses of variance and covariance to estimate the relative effects of selection (functional category) and mutability (relative mutation rate) on the PSSs and found that approximately 87% of variation in PSS was due to variation in the mutation rate and approximately 13% was due to selection, suggesting that the probability that a site located in a transcribed region of a gene is polymorphic mostly depends on the mutability of the site.
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Although much progress has been made in understanding the pathogenesis of Crohn’s disease, the precise etiology of Crohn’s disease still remains unknown. In our serial studies on Crohn’s disease, we found a decrease in NK and ADCC activities as well as a decrease in the phagocytic activity by monocytes, whereas an increased superoxide production activity by monocytes was evident. On the other hand, the characterization of lymphocyte subsets has demonstrated no abnormalities. According to these findings, I would like to propose a new tentative hypothesis for the pathogenesis of Crohn’s disease. It has been suggested that impaired killing system activities, such as phagocytic as well as NK and ADCC activities, are primarily responsible for the promotion and perpetuation of chronic inflammation and ulceration. When our attention is directed to the common target substances of these protective mechanisms, viral antigens appear as the most likely causative organism. Therefore, a lot of attention must be focused on viral infection as a causative factor. Furthermore, effects of psychological and physical stress on the disease onset or the recurrence of inflammatory bowel disease are also discussed.
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A set of 47 SNP (single nucleotide polymorphisms) markers (Cabezas et al. 2011) was tested for their usefulness to improve a genetic map from the cross of GF.GA‑52-42 x 'Solaris' previously established with SSR markers (Schwander et al. 2012). 55.3 % of the SNPs showed informative segregation and 26 SNP markers were localized on 16 of the 19 linkage groups of grapevine. Five chromosome regions with large gaps of recombining SSR markers could be equipped by positioning a SNP marker there. One SNP marker, VV10992, was found linked to the major resistance locus Rpv10 and should be applicable for marker-assisted selection.
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AIM: To identify the susceptible gene (s) for type 2 diabetes in the prevousely mapped region, 1p36.33-p36.23, in Han population of North China using single nucleotide polymorphisms (SNPs) and to analyze the haplotypes of the gene (s) related to type 2 diabetes.METHODS: Twenty three SNPs located in 10 candidate genes in the mapped region were chosen from public SNP domains with bioinformatic methods, and the single base extension (SBE) method was used to genotype the loci for 192 sporadic type 2 diabetes patients and 172 normal individuals, all with Hah ethical origin, to perform this casecontrol study. The haplotypes with significant difference in the gene (s) were further analyzed.RFSULTS: Among the 23 SNPs, 8 were found to be common in Chinese Han population. Allele frequency of one SNP,rs436045 in the protein kinase C/ζgene (PRKCZ) was statistically different between the case and control groups (P＜0.05). Furthermore, haplotypes at five SNP sites of PRKCZ gene were identified.CONCLUSION: PRKCZgene may be associated with type 2 diabetes in Hah population in North China. The haplotypes at five SNP sites in this gene may be responsible for this association.
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Abstract We conducted genome-wide linkage scans using both microsatellite and single-nucleotide polymorphism (SNP) markers. Regions showing the strongest evidence of linkage to alcoholism susceptibility genes were identified. Haplotype analyses using a sliding-window approach for SNPs in these regions were performed. In addition, we performed a genome-wide association scan using SNP data. SNPs in these regions with evidence of association ( P ≦ 0.0001) were identified. We found that the general patterns for nonparametric linkage (NPL) scores from SNP and microsatellite genome scans are fairly consistent; however, the peaks of the NPL scores are mostly higher in the SNP-based scan than those using microsatellite markers, which might be located at different regions. Furthermore, SNPs identified from linkage screens were not so strongly associated with alcoholism (the most significant SNP had a p -value of 0.030) as those identified from association genomic screening (the most significant SNP had a p -value of 2.0 × 10 -8 ).
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Gene expression profiles and single-nucleotide polymorphism (SNP) profiles are modern data for genetic analysis. It is possible to use the two types of information to analyze the relationships among genes by some genetical genomics approaches. In this study, gene expression profiles were used as expression traits. And relationships among the genes, which were co-linked to a common SNP(s), were identified by integrating the two types of information. Further research on the co-expressions among the co-linked genes was carried out after the gene-SNP relationships were established using the Haseman-Elston sib-pair regression. The results showed that the co-expressions among the co-linked genes were significantly higher if the number of connections between the genes and a SNP(s) was more than six. Then, the genes were interconnected via one or more SNP co-linkers to construct a gene-SNP intermixed network. The genes sharing more SNPs tended to have a stronger correlation. Finally, a gene-gene network was constructed with their intensities of relationships (the number of SNP co-linkers shared) as the weights for the edges.
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Summary Extreme lordosis, also called swayback, lowback or softback, can occur as a congenital trait or as a degenerative trait associated with ageing. In this study, the hereditary aspect of congenital swayback was investigated using whole genome association studies of 20 affected and 20 unaffected American Saddlebred (ASB) Horses for 48 165 single‐nucleotide polymorphisms (SNPs). A statistically significant association was identified on ECA20 (corrected P = 0.017) for SNP BIEC2‐532523. Of the 20 affected horses, 17 were homozygous for this SNP when compared to seven homozygotes among the unaffected horses, suggesting a major gene with a recessive mode of inheritance. The result was confirmed by testing an additional 13 affected horses and 166 unaffected horses using 35 SNPs in this region of ECA20 (corrected P = 0.036). Combined results for 33 affected horses and 287 non‐affected horses allowed identification of a region of homozygosity defined by four SNPs in the region. Based on the haplotype defined by these SNPs, 80% of the 33 affected horses were homozygous, 21% heterozygous and 9% did not possess the haplotype. Among the non‐affected horses, 15% were homozygous, 47% heterozygous and 38% did not possess the haplotype. The differences between the two groups were highly significant ( P < 0.00001). The region defined by this haplotype includes 53 known and predicted genes. Exons from three candidate genes, TRERF1 , RUNX2 and CNPY3 were sequenced without finding distinguishing SNPs. The mutation responsible for swayback may lie in other genes or in regulatory regions outside exons. This information can be used by breeders to reduce the occurrence of swayback among their livestock. This condition may serve as a model for investigation of congenital skeletal deformities in other species.
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