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Biomedical and candidate SNP markers of chronopathologies can significantly change the affinity of the ТАТА-binding protein to the promoters of human genes

  • Published:
Russian Journal of Genetics: Applied Research

Abstract

The computational analysis of millions of unannotated SNPs from the 1000 Genomes Project may speed up the search for biomedical SNP markers. We combined the analysis of SNPs at the binding sites of the TATA-binding protein (TBP) using a previously described Web service (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl) with a keyword search for biochemical markers of chronopathologies that correspond to the clinical manifestations of these SNPs. We found 32 known and candidate SNP markers of circadian-rhythm disturbances in the [–70;–20] region of the promoters of 14 human genes (location of proven binding sites of TBP). These SNPs include rs17231520 and rs569033466 (both confer risk of chronopathologies in the liver); rs35036378 (behavioral chronoaberrations); rs549858786 (rheumatoid arthritis with a chronoaberration of IL1B expression); rs563207167, rs11557611, and rs5505 (all three: chronopathologies of the tumor—host balance, blood pressure, and the reproductive system); rs1143627 (bipolar disorder with circadian dependence of diagnosis and treatment); rs16887226 and rs544850971 (both: lowered resistance to endotoxins because of the imbalance between the circadian and immune systems); rs367732974 and rs549591993 (both: circadian dependence of heart attacks); rs563763767 (circadian dependence of myocardial infarction); rs2276109 and rs572527200 (both: circadian dependence of asthma attacks); rs34223104, rs563558831, and rs10168 (circadian optima of treatment with methotrexate and cyclophosphamide); and rs397509430, rs33980857, rs34598529, rs33931746, rs33981098, rs34500389, rs63750953, rs281864525, rs35518301, and rs34166473 (all: neurosensory hearing loss and restless legs syndrome). For these SNPs, we evaluated the α (significance) of changes in the affinity of TBP for promoters, where increased affinity corresponds to overexpression of the genes, and decreased affinity to deficient expression (Z-test). Verification of these 32 SNP markers according to the clinical standards and protocols may advance the field of predictive preventive personalized medicine.

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia

    D. A. Rasskazov, N. L. Podkolodnyy, O. A. Podkolodnaya, N. N. Tverdokhleb, V. V. Suslov, L. K. Savinkova & M. P. Ponomarenko

  2. Institute of Computational Mathematics and Mathematical Geophysics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 63900, Russia

    N. L. Podkolodnyy

  3. Novosibirsk State University, Novosibirsk, 63900, Russia

    N. L. Podkolodnyy, O. A. Podkolodnaya & M. P. Ponomarenko

  4. Children’s Hospital Los Angeles, University of Southern California, Los Angeles, 90027, United States

    P. M. Ponomarenko

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  1. D. A. Rasskazov
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  2. N. L. Podkolodnyy
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Original Russian Text © D.A. Rasskazov, N.L. Podkolodnyy, O.A. Podkolodnaya, N.N. Tverdokhleb, V.V. Suslov, L.K. Savinkova, P.M. Ponomarenko, M.P. Ponomarenko, 2015, published in Vavilovskii Zhurnal Genetiki i Selektsii, 2015, Vol. 19, No. 6, pp. 691–698.

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Rasskazov, D.A., Podkolodnyy, N.L., Podkolodnaya, O.A. et al. Biomedical and candidate SNP markers of chronopathologies can significantly change the affinity of the ТАТА-binding protein to the promoters of human genes. Russ J Genet Appl Res 6, 738–748 (2016). https://doi.org/10.1134/S207905971607011X

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  • DOI: https://doi.org/10.1134/S207905971607011X

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