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

BACKGROUND: The 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 the...

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Autores principales: Chadaeva, Irina V., Ponomarenko, Petr M., Rasskazov, Dmitry A., Sharypova, Ekaterina B., Kashina, Elena V., Zhechev, Dmitry A., Drachkova, Irina A., Arkova, Olga V., Savinkova, Ludmila K., Ponomarenko, Mikhail P., Kolchanov, Nikolay A., Osadchuk, Ludmila V., Osadchuk, Alexandr V.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836831/
https://www.ncbi.nlm.nih.gov/pubmed/29504899
http://dx.doi.org/10.1186/s12864-018-4478-3
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author Chadaeva, Irina V.
Ponomarenko, Petr M.
Rasskazov, Dmitry A.
Sharypova, Ekaterina B.
Kashina, Elena V.
Zhechev, Dmitry A.
Drachkova, Irina A.
Arkova, Olga V.
Savinkova, Ludmila K.
Ponomarenko, Mikhail P.
Kolchanov, Nikolay A.
Osadchuk, Ludmila V.
Osadchuk, Alexandr V.
author_facet Chadaeva, Irina V.
Ponomarenko, Petr M.
Rasskazov, Dmitry A.
Sharypova, Ekaterina B.
Kashina, Elena V.
Zhechev, Dmitry A.
Drachkova, Irina A.
Arkova, Olga V.
Savinkova, Ludmila K.
Ponomarenko, Mikhail P.
Kolchanov, Nikolay A.
Osadchuk, Ludmila V.
Osadchuk, Alexandr V.
author_sort Chadaeva, Irina V.
collection PubMed
description BACKGROUND: The 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. RESULTS: A 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. CONCLUSIONS: According 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 MATERIAL: The online version of this article (10.1186/s12864-018-4478-3) contains supplementary material, which is available to authorized users.
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spelling pubmed-58368312018-03-07 Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters Chadaeva, Irina V. Ponomarenko, Petr M. Rasskazov, Dmitry A. Sharypova, Ekaterina B. Kashina, Elena V. Zhechev, Dmitry A. Drachkova, Irina A. Arkova, Olga V. Savinkova, Ludmila K. Ponomarenko, Mikhail P. Kolchanov, Nikolay A. Osadchuk, Ludmila V. Osadchuk, Alexandr V. BMC Genomics Research BACKGROUND: The 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. RESULTS: A 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. CONCLUSIONS: According 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 MATERIAL: The online version of this article (10.1186/s12864-018-4478-3) contains supplementary material, which is available to authorized users. BioMed Central 2018-02-09 /pmc/articles/PMC5836831/ /pubmed/29504899 http://dx.doi.org/10.1186/s12864-018-4478-3 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Chadaeva, Irina V.
Ponomarenko, Petr M.
Rasskazov, Dmitry A.
Sharypova, Ekaterina B.
Kashina, Elena V.
Zhechev, Dmitry A.
Drachkova, Irina A.
Arkova, Olga V.
Savinkova, Ludmila K.
Ponomarenko, Mikhail P.
Kolchanov, Nikolay A.
Osadchuk, Ludmila V.
Osadchuk, Alexandr V.
Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters
title Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters
title_full Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters
title_fullStr Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters
title_full_unstemmed Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters
title_short Candidate SNP markers of reproductive potential are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters
title_sort candidate snp markers of reproductive potential are predicted by a significant change in the affinity of tata-binding protein for human gene promoters
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836831/
https://www.ncbi.nlm.nih.gov/pubmed/29504899
http://dx.doi.org/10.1186/s12864-018-4478-3
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