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

Пономаренко, М. П.; Arkova, Olga; Рассказов, Д. А.; Пономаренко, П. М.; Савинкова, Л. К.; Колчанов, Н. А.

doi:10.3389/fimmu.2016.00130

Cited by 17 publications

(11 citation statements)

References 165 publications

(216 reference statements)

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“…The predictions in the cases of candidate SNP markers of obesity-related disorders (97), autoimmunerelated pathologies (108), chronopathologies (109), aggressiveness-related comorbidities (105), and sporadic AD (49) as well as resistance to antitumor chemotherapy (110) and social dominance/submission (111) were made using Web-service SNP_TATA_ Comparator (51). Below we selectively review these results in greater detail.…”

Section: Biomedical Predictions Using a Abstract Search For Known Bimentioning

confidence: 99%

SNP TATA Comparator genomewide landmarks for preventive personalized medicine

et al. 2017

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Year after year, conditions, quality, and duration of human lives have been improving due to the progress of science, technology, education, and medicine, which however has a downside. Owing to improvement in children's nutrition, developmental acceleration occurs that imbalances a child's system. Because of virtual worlds of the Internet, social experience of teenagers expands and clashes with puberty of adolescents. Due to the comfort of cities, urbanization emerges and causes stress to adults because of artificial light, noise, pollution, violations of personal space, and family disruption. At old age, all these factors taken together contribute to loneliness, cancer, diabetes, drug addiction, and sporadic Alzheimer's disease, which shorten the lifespan, as reviewed in the US, 1990-2010. That is why, a person may ask oneself: "What can I do now to keep my health in my old age?" To help them, we provide this comprehensive review on predictive preventive personalized medicine. This branch of molecular medicine uses single nucleotide polymorphisms to prevent diseases on the basis of the difference between the individual and reference human genomes.

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Section: Biomedical Predictions Using a Abstract Search For Known Bimentioning

confidence: 99%

SNP TATA Comparator genomewide landmarks for preventive personalized medicine

et al. 2017

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“…It should be emphasized that known SNP markers of monogenic diseases cause these diseases, whereas candidate SNP markers of polygenic diseases whose symptoms include aggressiveness can only serve as genomewide informative landmarks suggestive of either increased or decreased risk of aggressiveness (in these diseases relative to the norm) among patients with the minor alleles of these SNPs [67]. For example, here we predicted a candidate SNP marker (rs201381696) of aggressiveness in obesity.…”

Section: Discussionmentioning

confidence: 98%

“…That is why we apply this approach to studies of unannotated SNPs detected by the 1000 Genomes project [11] which are less known at present. Recently, we predicted candidate SNP markers of complications of hereditary diseases in obesity [66], of autoimmune comorbidities of these diseases [67], and of circadian rhythm disorders [68]. …”

Section: Introductionmentioning

confidence: 99%

Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic 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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BackgroundAggressiveness in humans is a hereditary behavioral trait that mobilizes all systems of the body—first of all, the nervous and endocrine systems, and then the respiratory, vascular, muscular, and others—e.g., for the defense of oneself, children, family, shelter, territory, and other possessions as well as personal interests. The level of aggressiveness of a person determines many other characteristics of quality of life and lifespan, acting as a stress factor. Aggressive behavior depends on many parameters such as age, gender, diseases and treatment, diet, and environmental conditions. Among them, genetic factors are believed to be the main parameters that are well-studied at the factual level, but in actuality, genome-wide studies of aggressive behavior appeared relatively recently. One of the biggest projects of the modern science—1000 Genomes—involves identification of single nucleotide polymorphisms (SNPs), i.e., differences of individual genomes from the reference genome. SNPs can be associated with hereditary diseases, their complications, comorbidities, and responses to stress or a drug. Clinical comparisons between cohorts of patients and healthy volunteers (as a control) allow for identifying SNPs whose allele frequencies significantly separate them from one another as markers of the above conditions. Computer-based preliminary analysis of millions of SNPs detected by the 1000 Genomes project can accelerate clinical search for SNP markers due to preliminary whole-genome search for the most meaningful candidate SNP markers and discarding of neutral and poorly substantiated SNPs.ResultsHere, we combine two computer-based search methods for SNPs (that alter gene expression) {i} Web service SNP_TATA_Comparator (DNA sequence analysis) and {ii} PubMed-based manual search for articles on aggressiveness using heuristic keywords. Near the known binding sites for TATA-binding protein (TBP) in human gene promoters, we found aggressiveness-related candidate SNP markers, including rs1143627 (associated with higher aggressiveness in patients undergoing cytokine immunotherapy), rs544850971 (higher aggressiveness in old women taking lipid-lowering medication), and rs10895068 (childhood aggressiveness-related obesity in adolescence with cardiovascular complications in adulthood).ConclusionsAfter validation of these candidate markers by clinical protocols, these SNPs may become useful for physicians (may help to improve treatment of patients) and for the general population (a lifestyle choice preventing aggressiveness-related complications).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3353-3) contains supplementary material, which is available to authorized users.

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“…It has been widely used as an internal control for experimental testing (Mihi et al 2011). TBP is an indispensable basal transcription factor, and the RNA polymerase II binds to the TBP-DNA complex to initiate transcription (Ponomarenko et al 2016). A knockout (Martianov et al 2002) or knockdown (Muller et al 2001) of the TBP gene is lethal, and TBP expression might not be subjected to significant regulation.…”

Section: Discussionmentioning

confidence: 99%

Identification of optimal reference genes for examination of gene expression in different tissues of fetal yaks

Li¹,

Wu²,

Guo³

et al. 2017

CZECH J ANIM SCI

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Li M., Wu X., Guo X., Bao P., Ding X., Chu M., Liang C., Yan P. (2017): Identification of optimal reference genes for examination of gene expression in different tissues of fetal yaks. Czech J. Anim. Sci., 62, 426-434.Reverse transcription quantitative real-time PCR (RT-qPCR) is widely used to study the relative abundance of mRNA transcripts because of its sensitivity and reliable quantification. However, the reliability of the interpretation of expression data is influenced by several complex factors, including RNA quality, transcription activity, and PCR efficiency, among others. To avoid experimental errors arising from potential variation, the selection of appropriate reference genes to normalize gene expression is essential. In this study, 10 commonly used reference genes -ACTB, B2M, HPRT1, GAPDH, 18SrRNA, 28SrRNA, PPIA, UBE2D2, SDHA, and TBPwere selected as candidate reference genes for six fetal tissues (heart, liver, spleen, lung, kidney, and forehead skin) of yak (Bos grunniens). The transcription stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper. The results showed that the combination of TBP and ACTB provided high-quality data for further study. In contrast, the commonly used reference genes 28SrRNA, SDHA, GAPDH, and B2M should not be used for endogenous controls because of their unstable expression in this study. The reference genes that could be used in future gene expression studies in yaks were indentified.

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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

Cited by 17 publications

References 165 publications

SNP TATA Comparator genomewide landmarks for preventive personalized medicine

SNP TATA Comparator genomewide landmarks for preventive personalized medicine

Candidate SNP markers of aggressiveness-related complications and comorbidities of genetic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Identification of optimal reference genes for examination of gene expression in different tissues of fetal yaks

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