The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock
Genetic variability in the genes of circadian clock is manifested as the phenotypic variability of physiological functions and behavior as well as disorders of the function of not only the clock but also other systems, leading to the development of a pathologies. We analyzed the influence of SNPs lo...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2016-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/485 |
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| author | O. A. Podkolodnaya D. A. Rasskazov N. L. Podkolodnyy N. N. Podkolodnaya V. V. Suslov L. K. Savinkova P. M. Ponomarenko M. P. Ponomarenko |
| author_facet | O. A. Podkolodnaya D. A. Rasskazov N. L. Podkolodnyy N. N. Podkolodnaya V. V. Suslov L. K. Savinkova P. M. Ponomarenko M. P. Ponomarenko |
| author_sort | O. A. Podkolodnaya |
| collection | DOAJ |
| description | Genetic variability in the genes of circadian clock is manifested as the phenotypic variability of physiological functions and behavior as well as disorders of the function of not only the clock but also other systems, leading to the development of a pathologies. We analyzed the influence of SNPs localized in the [–70, –20] region from the transcription start site of the gene on TBP / promoter affinity in two groups of genes that are components of the system of human circadian clock. The first group comprises the genes of the circadian oscillator core (11 genes); the second, the genes of the nearest regulatory environment of the circadian oscillator (21 genes). A group for comparison included genes with another function (31 genes). The SNP_TATA_Comparator web service was used for prediction of the effect of SNPs in the regions of positioning of RNA polymerase II on the dissociation constant for TBP / promoter. It was shown that the number of SNP markers reducing the TBP / promoter affinity in the first group of genes significantly lower than the number of SNP markers increasing affinity (α < 10–3). The reverse was true of the comparison group: SNP markers reduced TBP / promoter affinity to a significantly greater extent than the SNP marker increased affinity (α < 10–6). This property may be a characteristic feature of genes of the circadian oscillator. These predictions are important for identification of candidate SNP markers of various pathologies associated with the dysfunction of circadian clock genes for further testing them in experimental and clinical studies, as well as for verification of mathematical models of the circadian oscillator. |
| format | Article |
| id | doaj-art-987757715a6a4f1a98d488d3a2f9c2b6 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2016-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-987757715a6a4f1a98d488d3a2f9c2b62025-02-01T09:58:02ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592016-01-0119668269010.18699/VJ15.089428The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clockO. A. Podkolodnaya0D. A. Rasskazov1N. L. Podkolodnyy2N. N. Podkolodnaya3V. V. Suslov4L. K. Savinkova5P. M. Ponomarenko6M. P. Ponomarenko7Institute of Cytology and Genetics SB RA S, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Institute of Computational Mathematics and Mathematical Geophysics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RA S, Novosibirsk, RussiaChildren’s Hospital Los Angeles, University of Southern California, USAInstitute of Cytology and Genetics SB RA S, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, RussiaGenetic variability in the genes of circadian clock is manifested as the phenotypic variability of physiological functions and behavior as well as disorders of the function of not only the clock but also other systems, leading to the development of a pathologies. We analyzed the influence of SNPs localized in the [–70, –20] region from the transcription start site of the gene on TBP / promoter affinity in two groups of genes that are components of the system of human circadian clock. The first group comprises the genes of the circadian oscillator core (11 genes); the second, the genes of the nearest regulatory environment of the circadian oscillator (21 genes). A group for comparison included genes with another function (31 genes). The SNP_TATA_Comparator web service was used for prediction of the effect of SNPs in the regions of positioning of RNA polymerase II on the dissociation constant for TBP / promoter. It was shown that the number of SNP markers reducing the TBP / promoter affinity in the first group of genes significantly lower than the number of SNP markers increasing affinity (α < 10–3). The reverse was true of the comparison group: SNP markers reduced TBP / promoter affinity to a significantly greater extent than the SNP marker increased affinity (α < 10–6). This property may be a characteristic feature of genes of the circadian oscillator. These predictions are important for identification of candidate SNP markers of various pathologies associated with the dysfunction of circadian clock genes for further testing them in experimental and clinical studies, as well as for verification of mathematical models of the circadian oscillator.https://vavilov.elpub.ru/jour/article/view/485circadian rhythmthe promotersnptata-binding protein (tbp)the affinity of tbp / promotergene expression |
| spellingShingle | O. A. Podkolodnaya D. A. Rasskazov N. L. Podkolodnyy N. N. Podkolodnaya V. V. Suslov L. K. Savinkova P. M. Ponomarenko M. P. Ponomarenko The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock Вавиловский журнал генетики и селекции circadian rhythm the promoter snp tata-binding protein (tbp) the affinity of tbp / promoter gene expression |
| title | The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock |
| title_full | The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock |
| title_fullStr | The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock |
| title_full_unstemmed | The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock |
| title_short | The effects of SN Ps in the regions of positioning RNA polymerase II on the TBP/promoter affinity in the genes of human circadian clock |
| title_sort | effects of sn ps in the regions of positioning rna polymerase ii on the tbp promoter affinity in the genes of human circadian clock |
| topic | circadian rhythm the promoter snp tata-binding protein (tbp) the affinity of tbp / promoter gene expression |
| url | https://vavilov.elpub.ru/jour/article/view/485 |
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