Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters

Abstract

BackgroundThe progress of medicine, science, technology, education, and culture improves, year by year, quality of life and life expectancy of the populace. The modern human has a chance to further improve the quality and duration of his/her life and the lives of his/her loved ones by bringing their lifestyle in line with their sequenced individual genomes. With this in mind, one of genome-based developments at the junction of personalized medicine and bioinformatics will be considered in this work, where we used two Web services: (i) SNP_TATA_Comparator to search for alleles with a single nucleotide polymorphism (SNP) that alters the affinity of TATA-binding protein (TBP) for the TATA boxes of human gene promoters and (ii) PubMed to look for retrospective clinical reviews on changes in physiological indicators of reproductive potential in carriers of these alleles.ResultsA total of 126 SNP markers of female reproductive potential, capable of altering the affinity of TBP for gene promoters, were found using the two above-mentioned Web services. For example, 10 candidate SNP markers of thrombosis (e.g., rs563763767) can cause overproduction of coagulation inducers. In pregnant women, Hughes syndrome provokes thrombosis with a fatal outcome although this syndrome can be diagnosed and eliminated even at the earliest stages of its development. Thus, in women carrying any of the above SNPs, preventive treatment of this syndrome before a planned pregnancy can reduce the risk of death. Similarly, seven SNP markers predicted here (e.g., rs774688955) can elevate the risk of myocardial infarction. In line with Bowles’ lifespan theory, women carrying any of these SNPs may modify their lifestyle to improve their longevity if they can take under advisement that risks of myocardial infarction increase with age of the mother, total number of pregnancies, in multiple pregnancies, pregnancies under the age of 20, hypertension, preeclampsia, menstrual cycle irregularity, and in women smokers.ConclusionsAccording to Bowles’ lifespan theory—which links reproductive potential, quality of life, and life expectancy—the above information was compiled for those who would like to reduce risks of diseases corresponding to alleles in own sequenced genomes. Candidate SNP markers can focus the clinical analysis of unannotated SNPs, after which they may become useful for people who would like to bring their lifestyle in line with their sequenced individual genomes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4478-3) contains supplementary material, which is available to authorized users.

Natural Selection Equally Supports the Human Tendencies in Subordination and Domination: A Genome-Wide Study With in silico Confirmation and in vivo Validation in Mice

“…Nevertheless, in the case of human reproductive potential, which is considered the target of natural selection, we observed a diametrically opposite pattern, namely: five candidate SNP markers were decreasing the TBP–promoter affinity and 19 candidate SNP markers were increasing this affinity (Chadaeva et al, 2018). Besides, we found (Ponomarenko P. et al, 2017) only a minority (12 of 28) of candidate SNP markers of familial Alzheimer’s disease that can decrease the TBP–promoter affinity; this finding is consistent with natural selection for its very slow pathogenesis, whose clinical manifestation is observed only at the age of over 65 (Table 2).…”

Unannotated single nucleotide polymorphisms in the TATA box of erythropoiesis genes show in vitro positive involvements in cognitive and mental disorders

“…Using publicly available online databases, in this work we selected unannotated SNPs of the promoters of genes associated with erythropoiesis, which were analyzed by means of our public Web service SNP_TATA_Z-tester [ 31 ], developed within the framework of the three-step biophysical model for TBP binding to TATA-like boxes [ 25 ], namely: (i) TBP slides along DNA ↔ (ii) TBP stops at a TBP-binding site [TATA-box] ↔ (iii) the TBP–promoter complex is fixed by a 90 O bend of DNA, − as in vitro independently observed experimentally in solution [ 32 ]. The Web service has been used by us previously to predict candidate SNP markers in TATA boxes in the context of real-world promoters of genes related to reproductive potential [ 33 ], aggressiveness [ 34 ], Alzheimer’s disease [ 35 ], obesity [ 36 ], chronopathologies [ 37 ], and autoimmune diseases [ 37 ].…”

Сandidate SNP-markers of rheumatoid arthritis that can significantly alter the affinity of the TATA-binding protein for human gene promoters

“…На этой основе мы создали Webсервис SNP_TATA_Comparator (Ponomaren ko et al, 2015) для применения указанного уравнения свя зывания ТВР с ДНК в процессе анализа референсного генома че ловека (Telenti et al, 2016). С помощью SNP_TATA_Com pa ra tor ранее уже был сделан прогноз кандидатных SNP маркеров агрессивности, женского репродуктивного по тенциала, предрасположенности к социальному подчи нению и доминированию, а также ожирения, нарушений циркадного ритма, аутоиммунных заболеваний и болезни Альцгеймера (Arkova et al, 2015;Chadaeva et al, 2016Chadaeva et al, , 2018Chadaeva et al, , 2019Ponomarenko P. et al, , 2017. В настоящей работе мы представля ем обновление SNP_TATA_Ztester этого Webсервиса (Ponomarenko et al, 2015) и результаты его применения к исследованию РА в качестве продолжения серии наших биоинформатических прогнозов.…”