Novel regulatory SNPs in the promoter region of the TNFRSF18 gene in a Gabonese population

Velavan, Thirumalaisamy P.; Bechlars, Silke; Huang, Xiangsheng; Kremsner, Peter G.; Kun, Jürgen F. J.

doi:10.1590/s0100-879x2011007500036

Cited by 8 publications

(3 citation statements)

References 6 publications

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“…Finally, the two bottom lines of Table 1 show two examples of the known SNP markers of so-called silent SNPs: −20A→T within the promoter of the human CYP21A2 gene [ 83 ] and rs111426889, which precedes the alternative TSS located at position −120 upstream of the major TSS for transcript number 3 of the TNFRSF18 gene [ 84 ]. These silent SNPs are useful for monitoring of migration flows and ethnic composition of regional human subpopulations.…”

Section: Resultsmentioning

confidence: 99%

How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

Пономаренко

Рассказов

Arkova

et al. 2015

BioMed Research International

116

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The use of biomedical SNP markers of diseases can improve effectiveness of treatment. Genotyping of patients with subsequent searching for SNPs more frequent than in norm is the only commonly accepted method for identification of SNP markers within the framework of translational research. The bioinformatics applications aimed at millions of unannotated SNPs of the “1000 Genomes” can make this search for SNP markers more focused and less expensive. We used our Web service involving Fisher's Z-score for candidate SNP markers to find a significant change in a gene's expression. Here we analyzed the change caused by SNPs in the gene's promoter via a change in affinity of the TATA-binding protein for this promoter. We provide examples and discuss how to use this bioinformatics application in the course of practical analysis of unannotated SNPs from the “1000 Genomes” project. Using known biomedical SNP markers, we identified 17 novel candidate SNP markers nearby: rs549858786 (rheumatoid arthritis); rs72661131 (cardiovascular events in rheumatoid arthritis); rs562962093 (stroke); rs563558831 (cyclophosphamide bioactivation); rs55878706 (malaria resistance, leukopenia), rs572527200 (asthma, systemic sclerosis, and psoriasis), rs371045754 (hemophilia B), rs587745372 (cardiovascular events); rs372329931, rs200209906, rs367732974, and rs549591993 (all four: cancer); rs17231520 and rs569033466 (both: atherosclerosis); rs63750953, rs281864525, and rs34166473 (all three: malaria resistance, thalassemia).

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Section: Resultsmentioning

confidence: 99%

How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

Пономаренко

Рассказов

Arkova

et al. 2015

BioMed Research International

116

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“…The single-nucleotide polymorphisms (SNPs) in the promoter region of the genes such as STAT6 , Foxp3 , and TNFRSF18 were well characterized for their functional role [4, 10, 83]. One gene of interest that plays a key role in the function of Tregs is the IL-10 gene locus.…”

Section: Regulatory Gene Polymorphismsmentioning

confidence: 99%

Regulatory T Cells and Parasites

Velavan

Ojurongbe

2011

Journal of Biomedicine and Biotechnology

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Human host encounters a wide array of parasites; however, the crucial aspect is the failure of the host immune system to clear these parasites despite antigen recognition. In the recent past, a new immunological concept has emerged, which provides a framework to better understand several aspects of host susceptibility to parasitic infection. It is widely believed that parasites are able to modulate the magnitude of effector responses by inducing regulatory T cell (Tregs) population and several studies have investigated whether this cell population plays a role in balancing protective immunity and pathogenesis during parasite infection. This review discusses the several mechanism of Treg-mediated immunosuppression in the human host and focuses on the functional role of Tregs and regulatory gene polymorphisms in infectious diseases.

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“…The human TNFRSF18 gene (glucocorticoid-induced TNFR-related protein) contains the known SNP marker of resistance to parasites (rs111426889) ( 142 ) due to overexpression of this gene ( 79 ). A primary keyword search yielded a minireview ( 143 ) showing that TNFRSF18 overexpression can cause development of some autoimmune diseases with fourfold prevalence among women ( 10 ).…”

Section: Resultsmentioning

confidence: 99%

Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

et al. 2016

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Some variations of human genome [for example, single nucleotide polymorphisms (SNPs)] are markers of hereditary diseases and drug responses. Analysis of them can help to improve treatment. Computer-based analysis of millions of SNPs in the 1000 Genomes project makes a search for SNP markers more targeted. Here, we combined two computer-based approaches: DNA sequence analysis and keyword search in databases. In the binding sites for TATA-binding protein (TBP) in human gene promoters, we found candidate SNP markers of gender-biased autoimmune diseases, including rs1143627 [cachexia in rheumatoid arthritis (double prevalence among women)]; rs11557611 [demyelinating diseases (thrice more prevalent among young white women than among non-white individuals)]; rs17231520 and rs569033466 [both: atherosclerosis comorbid with related diseases (double prevalence among women)]; rs563763767 [Hughes syndrome-related thrombosis (lethal during pregnancy)]; rs2814778 [autoimmune diseases (excluding multiple sclerosis and rheumatoid arthritis) underlying hypergammaglobulinemia in women]; rs72661131 and rs562962093 (both: preterm delivery in pregnant diabetic women); and rs35518301, rs34166473, rs34500389, rs33981098, rs33980857, rs397509430, rs34598529, rs33931746, rs281864525, and rs63750953 (all: autoimmune diseases underlying hypergammaglobulinemia in women). Validation of these predicted candidate SNP markers using the clinical standards may advance personalized medicine.

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Novel regulatory SNPs in the promoter region of the TNFRSF18 gene in a Gabonese population

Cited by 8 publications

References 6 publications

How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

Regulatory T Cells and Parasites

Candidate SNP Markers of Gender-Biased Autoimmune Complications of Monogenic Diseases Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

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