Hypothetical SNP markers that significantly affect the affinity of the TATA-binding protein to VEGFA, ERBB2, IGF1R, FLT1,
详细信息 查看全文
- 作者：I. I. Turnaev ; D. A. Rasskazov ; O. V. Arkova ; M. P. Ponomarenko…
- 关键词：tumor ; chemotherapy ; target oncogene ; promoter ; single nucleotide polymorphism (SNP) ; TATA ; binding protein (TBP) ; affinity change ; Z score
- 刊名：Molecular Biology
- 出版年：2016
- 出版时间：January 2016
- 年：2016
- 卷：50
- 期：1
- 页码：141-152
- 全文大小：652 KB
- 参考文献：1.Mallal S., Nolan D., Witt C., Masel G., Martin A.M., Moore C., Sayer D., Castley A., Mamotte C., Maxwel D., James I., Christiansen F.T. 2002. Association between presence of HLA-B 5701. HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. Lancet. 359, 727–732.PubMed
2.Podkolodnyi N.L., Afonnikov D.A., Vas’kin Yu.Yu., Bryzgalov L.O., Ivanisenko V.A., Demenkov P.S., Ponomarenko M.P., Rasskazov D.A., Gunbin K.V., Protsuk I.V., Shutov I.Yu., Leont’ev P.N., Fursov M.Yu., Bondar’ N.P., Antontseva E.V., et al. 2014. Program complex SNP–MED for analysis of single-nucleotide polymorphism (SNP) effects on the function of genes associated with socially significant diseases. Russ. J. Genet.: Appl. Res. 4 (3), 159–167.CrossRef
3.Trovato G.M. 2014. Sustainable medical research by effective and comprehensive medical skills: Overcoming the frontiers by predictive, preventive and personalized medicine. EPMA J. 5, 14.CrossRef PubMed PubMedCentral
4.Colonna V., Ayub Q., Chen Y., Pagani L., Luisi P., Pybus M., Garrison E., Xue Y., Tyler-Smith C.; 1000 Genomes Project Consortium, Abecasis G.R., Auton A., Brooks L.D., DePristo M.A., Durbin R.M., Handsaker R.E., Kang H.M., Marth G.T., McVean G.A. 2014. Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences. Genome Biol. 15, R88.CrossRef PubMed PubMedCentral
5.NCBI Resource Coordinators. 2013. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 41, D8–D20.CrossRef PubMedCentral
6.Flicek P., Amode M.R., Barrell D., Beal K., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., Gordon L., Hendrix M., Hourlier T., Johnson N., Kahari A., et al. 2011. Ensembl 2011. Nucleic Acids Res. 39, D800–D806.CrossRef PubMed PubMedCentral
7.Harrow J., Frankish A., Gonzalez J.M., Tapanari E., Diekhans M., Kokocinski F., Aken B.L., Barrell D., Zadissa A., Searle S., Barnes I., Bignell A., Boychenko V., Hunt T., Kay M., et al. 2012. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760–1774.CrossRef PubMed PubMedCentral
8.Dreszer T.R., Karolchik D., Zweig A.S., Hinrichs A.S., Raney B.J., Kuhn R.M., Meyer L.R., Wong M., Sloan C.A., Rosenbloom K.R., Roe G., Rhead B., Pohl A., Malladi V.S., Li C.H., et al. 2012. The UCSC Genome Browser database: Extensions and updates. 2011. Nucleic Acids Res. 40, D918–D923.CrossRef PubMed PubMedCentral
9.Abbas A., Lechevrel M., Sichel F. 2006. Identification of new single nucleotide polymorphisms (SNP) in alcohol dehydrogenase class IVADH7 gene within a French population. Arch. Toxicol. 80, 201–205.CrossRef PubMed
10.Willems P., Verhagen O., Segeren C., Veenhuizen P., Guikema J., Wiemer E., Groothuis L., Jong T.B., Kok H., Bloem A., Bos N., Vellenga E., Mensink E., Sonneveld P., Lokhorst H., et al. 2000. Consensus strategy to quantitate malignant cells in myeloma patients is validated in a multicenter study. Blood. 96, 63–70.PubMed
11.Pardo L.M., MacKay I., Oostra B., van Duijn C.M., Aulchenko Y.S. 2005. The effect of genetic drift in a young genetically isolated population. Ann. Hum. Genet. 69, 288–295.CrossRef PubMed
12.Ou Q.S., Cheng Z.J., Yang B., Jiang L., Chen J. 2011. Analysis of the ratio of mitchondrial DNA with A1555G mutant to wild type in deaf patients of Fujian province in China by a new method and its relationship with the severity of hearing loss. Chin. Med. J. 124, 3347–3352.PubMed
13.Kravtsov A.L., Lyapin M.N., Shmel’kova T.P., Golovko E.M., Milyukova T.A., Kostyukova T.A., Ezhov I.N. 2011. Flow cytometric determination of DNA contents in individual Vibrio cholerae cells: Comparative analysis of heterogeneity in cells of strains with different biological properties. Zh. Mikrobiol. Epidemiol. Immunobiol. 5, 7–11.PubMed
14.Vasiliev G.V., Merkulov V.M., Kobzev V.F., Merkulova T.I., Ponomarenko M.P., Kolchanov N.A. 1999. Point mutations within 663–666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site. FEBS Lett. 462, 85–88.CrossRef PubMed
15.Ponomarenko J.V., Orlova G.V., Merkulova T.I., Gorshkova E.V., Fokin O.N., Vasiliev G.V., Frolov A.S., Ponomarenko M.P. 2002. rSNP_Guide: An integrated database-tools system for studying SNPs and sitedirected mutations in transcription factor binding sites. Hum. Mutat. 20, 239–248.CrossRef PubMed
16.Amberger J., Bocchini C.A., Scott A.F., Hamosh A. 2009. McKusick’s Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res. 37, D793–D796.CrossRef PubMed PubMedCentral
17.Mitsuyasu H., Izuhara K., Mao X.Q., Gao P.S., Arinobu Y., Enomoto T., Kawai M., Sasaki S., Dake Y., Hamasaki N., Shirakawa T., Hopkin J.M. 1998. Ile50Val variant of IL4R-alpha upregulates IgE synthesis and associates with atopic asthma. Nat. Genet. 19, 119–120.CrossRef PubMed
18.Guo L., Du Y., Chang S., Zhang K., Wang J. 2014. rSNPBase: A database for curated regulatory SNPs. Nucleic Acids Res. 42, D1033–1039.CrossRef PubMed PubMedCentral
19.Savinkova L.K., Ponomarenko M.P., Ponomarenko P.M., Drachkova I.A., Lysova M.V., Arshinova T.V., Kolchanov N.A. 2009. TATA box polymorphisms in human gene promoters and associated hereditary pathologies. Biochemistry (Moscow). 74 (2), 117–129.CrossRef
20.Babu M.M., Luscombe N.M., Aravind L., Gerstein M., Teichmann S.A. 2004. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14, 283–291.CrossRef PubMed
21.Ponomarenko M., Mironova V., Gunbin K., Savinkova L. 2013. Hogness Box. In: Brenner’s Encyclopedia of Genetics, 2nd ed., vol. 3. Eds. Maloy S., Hughes K. San Diego: Academic Press, pp. 491–494.CrossRef
22.Martianov I., Viville S., Davidson I. 2002. RNA polymerase II transcription in murine cells lacking the TATA binding protein. Science. 298, 1036–1039.CrossRef PubMed
23.Muller F., Lakatos L., Dantonel J., Strahle U., Tora L. 2001. TBP is not universally required for zygotic RNA polymerase II transcription in zebrafish. Curr. Biol. 11, 282–287.CrossRef PubMed
24.Rhee H.S., Pugh B.F. 2012. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 483, 295–301.CrossRef PubMed PubMedCentral
25.Choukrallah M.A., Kobi D., Martianov I., Pijnappel W.W., Mischerikow N., Ye T., Heck A.J., Timmers H.T., Davidson I. 2012. Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome. Nucleic Acids Res. 40, 1446–1459.CrossRef PubMed PubMedCentral
26.Yang M.Q., Laflamme K., Gotea V., Joiner C.H., Seidel N.E., Wong C., Petrykowska H.M., Lichtenberg J., Lee S., Welch L., Gallagher P.G., Bodine D.M., Elnitski L. 2011. Genome-wide detection of a TFIID localization element from an initial human disease mutation. Nucleic Acids Res. 39, 2175–2187.CrossRef PubMed PubMedCentral
27.Hahn S., Buratowski S., Sharp P.A., Guarente L. 1989. Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc. Natl. Acad. Sci. U. S. A. 86, 5718–5722.CrossRef PubMed PubMedCentral
28.Wiley S.R., Kraus R.J., Mertz J.E. 1992. Functional binding of the “TATA” box binding component of transcription factor TFIID to the–30 region of TATA-less promoters. Proc. Natl. Acad. Sci. U. S. A. 89, 5814–5818.CrossRef PubMed PubMedCentral
29.Wolner B.S., Gralla J.D. 2000. Roles for non-TATA core promoter sequences in transcription and factor binding. Mol. Cell. Biol. 20, 3608–3615.CrossRef PubMed PubMedCentral
30.Pugh B.F. 2000. Control of gene expression through regulation of the TATA-binding protein. Gene. 255, 1–14.CrossRef PubMed
31.Stewart J.J., Stargell L.A. 2001. The stability of the TFIIA–TBP–DNA complex dependent on the sequence of the TATAAA element. J. Biol. Chem. 276, 30078–30084.CrossRef PubMed
32.Mogno I., Vallania F., Mitra R.D., Cohen B.A. 2010. TATA is a modular component of synthetic promoters. Genome Res. 20, 1391–1397.CrossRef PubMed PubMedCentral
33.Ponomarenko P.M., Ponomarenko M.P., Drachkova I.A., Lysova M.V., Arshinova T.V., Savinkova L.K., Kolchanov N.A. 2009. Prediction of the affinity of the TATA-binding protein to TATA boxes with single nucleotide polymorphisms. Mol. Biol. (Moscow). 43 (3), 472–479.CrossRef
34.Ponomarenko P.M., Savinkova L.K., Drachkova I.A., Lysova M.V., Arshinova T.V., Ponomarenko M.P., Kolchanov N.A. 2008. Stepwise TBP/TATA-box binding model allows prediction of human hereditary disease by a single nucleotide polymorphism. Dokl. Ross. Akad. Nauk. 419, 828–832.
35.Drachkova I.A., Savinkova L.K., Ponomarenko M.P., Lysova M.V., Arshinova T.V., Kolchanov N.A. 2007. Interaction of a recombinant TATA-bindng protein with the TATA boxes of of mammalian gene promoters. Ekol. Genet. 5, 44–49.
36.Savinkova L.K., Drachkova I.A., Arshinova T.V., Ponomarenko P.M., Ponomarenko M.P., Kolchanov N.A. 2013. An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA-binding protein. PLoS ONE. 8, e54626.CrossRef
37.Drachkova I.A., Savinkova L.K., Arshinova T.V., Ponomarenko M.P., Peltek S.E., Kolchanov N.A. 2014. The mechanism by which TATA-box polymorphisms associated with human hereditary diseases influence interactions with the TATA-binding protein. Hum. Mutat. 35, 601–608.CrossRef PubMed
38.Arkova O.V., Kuznetsov N.A., Fedorova O.S., Kolchanov N.A., Savinkova L.K. 2014. Real-time analysis of TBP interaction with the TATA box of the human triosephosphate isomerase gene promoter in the normal and pathological states. Acta Naturae. 6, 40–44.
39.Drachkova I.A., Shekhovtsov C.V., Pel’tek S.E., Ponomarenko P.M., Arshinova T.V., Ponomarenko M.P., Merkulova T.I., Savinkova L.K., Kolchanov N.A. 2012. Analysis of the interaction of human TATA-binding protein with the TATA element of the NOS2A gene promoter using surface plasmon resonance. Vavilov. Zh. Genet. Selekts. 16, 391–396.
40.Suslov V.V., Ponomarenko P.M., Efimov V.M., Savinkova L.K., Ponomarenko M.P., Kolchanov N.A. 2010. SNPs in the HIV-1 TATA box and the AIDS pandemic. J. Bioinform. Comput. Biol. 8, 607–625.CrossRef PubMed
41.Suslov V.V., Ponomarenko P.M., Ponomarenko M.P., Drachkova I.A., Arshinova T.V., Savinkova L.K., Kolchanov N.A. 2010. TATA box polymorphisms in genes of commercial and laboratory animals and plants associated with selectively valuable traits. Russ. J. Genet. 46 (4), 394–403.CrossRef
42.Mironova V.V., Omel’yanchuk N.A., Ponomarenko P.M., Ponomarenko M.P., Kolchanov N.A. 2010. Efficiency of TBP binding with the plant ARF gene promoter correlates with the type of effect (activation/ repression) of ARF proteins on transcription. Dokl. Ross. Akad. Nauk. 433, 549–554.
43.Ponomarenko P.M., Ponomarenko M.P. 2015. Sequence-based prediction of transcription up-regulation by auxin in plants. J. Bioinform. Comput. Biol. 13, 1540009.CrossRef PubMed
44.Ponomarenko P.M., Suslov V.V., Savinkova L.K., Ponomarenko M.P., Kolchanov N.A. 2010. A precise equation of equilibrium of four steps of TBP binding with the TATA box for prognosis of phenotypic manifestation of mutations. Biophysics (Moscow). 55 (3), 353–357.
45.Ponomarenko M.P., Suslov V.V., Gunbin K.V., Ponomarenko P.M., Vishnevskii O.V., Kolchanov N.A. 2014. Identification of the relationship between the variability of the expression of signaling pathway genes in the human brain and affinity of TATA-binding protein to their promoters. Vavilov. Zh. Genet. Selekts. 18, 1219–1230.
46.Rasskazov D.A., Gunbin K.V., Ponomarenko P.M., Vishnevskii O.V., Ponomarenko M.P., Afonnikov D.A. 2013. SNP_TATA_Comparator: Web-service for comparison of SNPs within gene promoters associated with human diseases using the equilibrium equation of the TBP/TATA complex. Vavilov. Zh. Genet. Selekts. 17, 599–606.
47.Antontseva E.V., Bryzgalov L.O., Matveeva M.Yu., Kashina E.V., Cherdyntseva N.V., Merkulova T.I. 2012. Search for regulatory SNPs associated with colon cancer in the APC and MLH1 genes. Russ. J. Genet.: Appl. Res. 2 (3), 222–228.CrossRef
48.Rasskazov D.A., Antontseva E.V., Bryzgalov L.O., Matveeva M.Yu., Kashina E.V., Ponomarenko P.M., Orlova G.V., Ponomarenko M.P., Afonnikov D.A., Merkulova T.I. 2014. rSNP_guide-based evaluation of SNPs in promoters of the human APC and MLH1 genes associated with colon cancer. Russ. J. Genet.: Appl. Res. 4 (4), 245–253.CrossRef
49.Bryzgalov L.O., Antontseva E.V., Matveeva M.Y., Shilov A.G., Kashina E.V., Mordvinov V.A., Merkulova T.I. 2013. Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data. PLoS ONE. 8, e78833.CrossRef
50.Al-Shakfa F., Dulucq S., Brukner I., Milacic I., Ansari M., Beaulieu P., Moghrabi A., Laverdiere C., Sallan S.E., Silverman L.B., Neuberg D., Kutok J.L., Sinnett D., Krajinovic M. 2009. DNA variants in region for noncoding interfering transcript of dihydrofolate reductase gene and outcome in childhood acute lymphoblastic leukemia. Clin. Cancer Res. 15, 6931–6938.CrossRef PubMed
51.Polyanovski O.L., Lebedenko E.N., Deyev, S.M. 2012. ERBB oncogene proteins as targets for monoclonal antibodies. Biochemistry (Moscow). 77 (3), 227–245.CrossRef
52.Ni Y., Hall A.W., Battenhouse A., Iyer V.R. 2012. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet. 13, 46.CrossRef PubMed PubMedCentral
53.Hu J., Locasale J.W., Bielas J.H., O’Sullivan J., Sheahan K., Cantley L.C., Vander Heiden M.G., Vitkup D. 2013. Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nat. Biotechnol. 31, 522–529.CrossRef PubMed PubMedCentral
54.Hein M., Graver S. 2013. Tumor cell response to bevacizumab single agent therapy in vitro. Cancer Cell Int. 13, 94.CrossRef PubMed PubMedCentral
55.Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Podkolodnaya O.A., Vorobyev D.G., Kolchanov N.A., Overton G.C. 1999. Oligonucleotide frequency matrices addressed to recognizing functional DNA sites. Bioinformatics. 15, 631–643.CrossRef PubMed
56.Chen C.Y., Chang I.S., Hsiung C.A., Wasserman W.W. 2014. On the identification of potential regulatory variants within genome wide association candidate SNP sets. BMC Med. Genomics. 7, 34.CrossRef PubMed PubMedCentral
57.Akimov I.A., Chernolovskaya E.L. 2010. Silencing of the CCNB1, Her2, and PKC genes by small interfering RNA differently retards the division of different human cancer cell lines. Mol. Biol. (Moscow). 44 (1), 89–96.CrossRef
58.Zukunft J., Lang T., Richter T., Hirsch-Ernst K.I., Nussler A.K., Klein K., Schwab M., Eichelbaum M., Zanger U.M. 2005. A natural CYP2B6 TATA box polymorphism (–82TC) leading to enhanced transcription and relocation of the transcriptional start site. Mol. Pharmacol. 67, 1772–1782.CrossRef PubMed
59.Chambers S.K., Clouser M.C., Baker A.F., Roe D.J., Cui H., Brewer M.A., Hatch K.D., Gordon M.S., Janicek M.F., Isaacs J.D., Gordon A.N., Nagle R.B., Wright H.M., Cohen J.L., Alberts D.S. 2010. Overexpression of tumor vascular endothelial growth factor A may portend an increased likelihood of progression in a phase II trial of bevacizumab and erlotinib in resistant ovarian cancer. Clin. Cancer Res. 16, 5320–5328.CrossRef PubMed PubMedCentral
60.Eniu A. 2007. Integrating biological agents into systemic therapy of breast cancer: Trastuzumab, lapatinib, bevacizumab. J. BUON. 12, S119–S126.PubMed
61.Nam S., Chang H.R., Jung H.R., Gim Y., Kim N.Y., Grailhe R., Seo H.R., Park H.S., Balch C., Lee J., Park I., Jung S.Y., Jeong K.C., Powis G., Liang H., et al. 2015. A pathway-based approach for identifying biomarkers of tumor progression to trastuzumab-resistant breast cancer. Cancer Lett. 356, 880–890.CrossRef PubMed
62.Clarke J.M., Hurwitz H.I. 2013. Targeted inhibition of VEGF receptor 2: An update on ramucirumab. Expert Opin. Biol. Ther. 13, 1187–1196.CrossRef PubMed PubMedCentral
63.Aprile G., Bonotto M., Ongaro E., Pozzo C., Giuliani F. 2013. Critical appraisal of ramucirumab (IMC-1121B) for cancer treatment: From benchside to clinical use. Drugs. 73, 2003–2015.CrossRef PubMed
64.Inno A., Di Salvatore M., Cenci T., Martini M., Orlandi A., Strippoli A., Ferrara A.M., Bagala C., Cassano A., Larocca L.M., Barone C. 2011. Is there a role for IGF1R and c-MET pathways in resistance to cetuximab in metastatic colorectal cancer? Clin. Colorect. Cancer. 10, 325–332.CrossRef
65.Kalra N., Zhang J., Yu Y., Ho M., Merino M., Cao L., Hassan R. 2012. Efficacy of anti-insulin-like growth factor I receptor monoclonal antibody in is highly correlated with insulin growth factor-I receptor sites/cell. Int. J. Cancer. 131, 2143–2152.CrossRef PubMed PubMedCentral
66.ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature. 489, 57–74.CrossRef
67.Kim T.H., Barrera L.O., Zheng M., Qu C., Singer M.A., Richmond T.A., Wu Y., Green R.D., Ren B. 2005. A high-resolution map of active promoters in the human genome. Nature. 436, 876–880.CrossRef PubMed PubMedCentral
68.Carninci P., Sandelin A., Lenhard B., Katayama S., Shimokawa K., Ponjavic J., Semple C.A., Taylor M.S., Engstrom P.G., Frith M.C., Forrest A.R., Alkema W.B., Tan S.L., Plessy C., Kodzius R., et al. 2006. Genomewide analysis of mammalian promoter architecture and evolution. Nat. Genet. 38, 626–635.CrossRef PubMed
69.Sandelin A., Carninci P., Lenhard B., Ponjavic J., Hayashizaki Y., Hume D.A. 2007. Mammalian RNA polymerase II core promoters: Insights from genomewide studies. Nat. Rev. Genet. 8, 424–436.CrossRef PubMed
70.Yang C., Bolotin E., Jiang T., Sladek F.M., Martinez E. 2007. Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene. 389, 52–65.CrossRef PubMed PubMedCentral
71.Drachkova I.A., Ponomarenko P.M., Arshinova T.V., Ponomarenko M.P., Suslov V.V., Savinkova L.K., Kolchanov N.A. 2011. In vitro examining the existing prognoses how TBP binds to TATA with SNP associated with human diseases. Health. 3, 577–583.CrossRef
72.Reijnen M.J., Sladek F.M., Bertina R.M., Reitsma P.H. 1992. Disruption of a binding site for hepatocyte nuclear factor 4 results in hemophilia B Leyden. Proc. Natl. Acad. Sci. U. S. A. 89, 6300–6303.CrossRef PubMed PubMedCentral
73.Zhao Y.Y., Zhou J., Narayanan C.S., Cui Y., Kumar A. 1999. Role of C/A polymorphism at–20 on the expression of human angiotensinogen gene. Hypertension. 33, 108–115.CrossRef PubMed
74.Horan M., Millar D.S., Hedderich J., Lewis G., Newsway V., Mo N., Fryklund L., Procter A.M., Krawczak M., Cooper D.N. 2003. Human growth hormone 1 (GH1) gene expression: Complex haplotype-dependent influence of polymorphic variation in the proximal promoter and locus control region. Hum. Mutat. 21, 408–423.CrossRef PubMed
75.Bieberstein N.I., Carrillo Oesterreich F., Straube K., Neugebauer K.M. 2012. First exon length controls active chromatin signatures and transcription. Cell Rep. 2, 62–68.CrossRef PubMed
76.Ioshikhes I., Trifonov E.N., Zhang M.Q. 1999. Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure. Proc. Natl. Acad. Sci. U. S. A. 96, 2891–2895.CrossRef PubMed PubMedCentral
77.Richmond T.J., Davey C.A. 2003. The structure of DNA in the nucleosome core. Nature. 423, 145–150.CrossRef PubMed
78.Zwarts K.Y., Clee S.M., Zwinderman A.H., Engert J.C., Singaraja R., Loubser O., James E., Roomp K., Hudson T.J., Jukema J.W., Kastelein J.J., Hayden M.R. 2002. ABCA1 regulatory variants influence coronary artery disease independent of effects on plasma lipid levels. Clin. Genet. 61, 115–125.CrossRef PubMed
79.Hornung G., Bar-Ziv R., Rosin D., Tokuriki N., Tawfik D.S., Oren M., Barkai N. 2012. Noise-mean relationship in mutated promoters. Genome Res. 22, 2409–2417.CrossRef PubMed PubMedCentral
80.Levitsky V.G., Ponomarenko M.P., Ponomarenko J.V., Frolov A.S., Kolchanov N.A. 1999. Nucleosomal DNA property database. Bioinformatics. 15, 582–592.CrossRef PubMed
81.Levitsky V.G., Ignatieva E.V., Ananko E.A., Turnaev I.I., Merkulova T.I., Kolchanov N.A., Hodgman T.C. 2007. Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions. BMC Bioinform. 8, 481.CrossRef
82.Oshchepkov D.Y., Vityaev E.E., Grigorovich D.A., Ignatieva E.V., Khlebodarova T.M. 2004. SITECON: A tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition. Nucleic Acids Res. 32, W208–W212.CrossRef PubMed PubMedCentral
83.Andersen M.C., Engstrom P.G., Lithwick S., Arenillas D., Eriksson P., Lenhard B., Wasserman W.W., Odeberg J. 2008. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol. 4, e5.CrossRef
84.Macintyre G., Bailey J., Haviv I., Kowalczyk A. 2010. is-rSNP: A novel technique for in silico regulatory SNP detection. Bioinformatics. 26, i524–i530.CrossRef PubMed PubMedCentral
85.Boyle A.P., Hong E.L., Hariharan M., Cheng Y., Schaub M.A., Kasowski M., Karczewski K.J., Park J., Hitz B.C., Weng S., Cherry J.M., Snyder M. 2012. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 22, 1790–1797.CrossRef PubMed PubMedCentral
86.Riva A. 2012. Large-scale computational identification of regulatory SNPs with rSNP-MAPPER. BMC Genomics. 13, S7.CrossRef PubMed PubMedCentral
87.Fu Y., Liu Z., Lou S., Bedford J., Mu X., Yip K.Y., Khurana E., Gerstein M. 2014. FunSeq2: A framework for prioritizing noncoding regulatory variants in cancer. Genome Biol. 15, 480.CrossRef PubMed PubMedCentral
88.Chen C.C., Xiao S., Xie D., Cao X., Song C.X., Wang T., He C., Zhong S. 2013. Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions. PLoS Comput. Biol. 9, e1003367.CrossRef
89.International HapMap 3 Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature. 467, 52–58.CrossRef
90.Peltoketo H., Piao Y., Mannermaa A., Ponder B.A., Isomaa V., Poutanen M., Winqvist R., Vihko R. 1994. A point mutation in the putative TATA box, detected in nondiseased individuals and patients with hereditary breast cancer, decreases promoter activity of the 17 beta-hydroxysteroid dehydrogenase type 1 gene 2 (EDH17B2) in vitro. Genomics. 23, 250–252.CrossRef PubMed
91.Wu K.S., Zhou X., Zheng F., Xu X.Q., Lin Y.H., Yang J. 2010. Influence of interleukin-1 beta genetic polymorphism, smoking and alcohol drinking on the risk of non-small cell lung cancer. Clin. Chim. Acta. 411, 1441–1446.CrossRef PubMed
92.Wang Y., Kato N., Hoshida Y., Yoshida H., Taniguchi H., Goto T., Moriyama M., Otsuka M., Shiina S., Shiratori Y., Ito Y., Omata M. 2003. Interleukin-1beta gene polymorphisms associated with hepatocellular carcinoma in hepatitis C virus infection. Hepatology. 37, 65–71.CrossRef PubMed
93.Landrum M.J., Lee J.M., Riley G.R., Jang W., Rubinstein W.S., Church D.M., Maglott D.R. 2014. ClinVar: Public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 42, D980–D985.CrossRef PubMed PubMedCentral
94.De Vivo I., Huggins G.S., Hankinson S.E., Lescault P.J., Boezen M., Colditz G.A., Hunter D.J. 2002. A functional polymorphism in the promoter of the progesterone receptor gene associated with endometrial cancer risk. Proc. Natl. Acad. Sci. U. S. A. 99, 12263–12268.CrossRef PubMed PubMedCentral
95.Pianezza M.L., Sellers E.M., Tyndale R.F. 1998. Nicotine metabolism defect reduces smoking. Nature, 393, 750.CrossRef PubMed
96.Philips S., Richter A., Oesterreich S., Rae J.M., Flockhart D.A., Perumal N.B., Skaar T.C. 2012. Functional characterization of a genetic polymorphism in the promoter of the ESR2 gene. Horm. Cancer. 3, 37–43.CrossRef PubMed PubMedCentral
97.Yoo S.S., Jin C., Jung D.K., Cho Y.Y., Choi J.E., Lee W.K., Lee S.Y., Lee J., Cha S.I., Kim C.H., Seok Y. Lee E., Park J.Y. 2015. Putative functional variants of XRCC1 identified by RegulomeDB were not associated with lung cancer risk in a Korean population. Cancer Genet. 208, 19–24.CrossRef PubMed - 作者单位：I. I. Turnaev (1)
D. A. Rasskazov (1)
O. V. Arkova (1)
M. P. Ponomarenko (1) (2)
P. M. Ponomarenko (3)
L. K. Savinkova (1) (2)
N. A. Kolchanov (1)
1. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
2. Novosibirsk State University, Novosibirsk, 630090, Russia
3. Children’s Hospital Los Angeles, University of Southern California, California, CA, 90027, USA - 刊物类别：Biomedical and Life Sciences
- 刊物主题：Life Sciences
Life Sciences
Biochemistry
Human Genetics
Russian Library of Science - 出版者：MAIK Nauka/Interperiodica distributed exclusively by Springer Science+Business Media LLC.
- ISSN：1608-3245
文摘
The following hypothesis has been proposed: IF an SNP can significantly increase the expression of an oncogene by increasing the affinity of the TATA-binding protein (TBP) to its promoter, THEN this SNP can also reduce the apparent bioactivity of inhibitors of this oncogene during antitumor chemotherapy and vice versa. In the context of this hypothesis, the previously proposed method (http://beehive.bionet.nsc. ru/cgi-bin/mgs/tatascan/start.pl) was applied to analyze all SNPs found within the [–70;–20] regions (which harbor all proven TBP-binding sites) of the promoters of VEGFA, EGFR, ERBB2, IGF1R, FLT1, KDR, and MET oncogenes according to the human reference genome, hg19. For 83% of these SNPs, their effect on TBP affinity to the oncogene promoters required for assembly of preinitiation complexes was not significant. rs36208385, rs36208384, rs370995111, rs372731987, rs111811434, rs369547510, rs76407893, rs369728300, and rs72001900 can potentially serve as SNP markers to reduce the apparent bioactivity of oncogene inhibitors, while rs141092704, rs184083669, rs145139616, rs200697953, rs187746433, rs199730913, rs377370642, rs114484350, rs374921120, rs146790957, rs376727645, and rs72001900 can be the markers for enhancing this activity.