Systematic analysis of disease-related regulatory mutation classes reveals distinct effects on transcription factor binding

In Silico Biology

Volumn 9, Issue 4, 2009, Pages 209-224

  Laurila, Kirsti ^a   Lähdesmäki, Harri ^a,b  

^a TAMPERE UNIVERSITY OF TECHNOLOGY   (Finland)

^b AALTO UNIVERSITY   (Finland)

Author keywords

Binding affinity; Regulatory mutation; Transcription factors

Indexed keywords

ALPHA FETOPROTEIN; HEMOGLOBIN GAMMA CHAIN; TRANSCRIPTION FACTOR; VASCULOTROPIN RECEPTOR 1;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONTROLLED STUDY; DNA STRUCTURE; GENE MUTATION; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MUTATIONAL ANALYSIS; PROBABILITY; PROTEIN DNA BINDING;

BASE SEQUENCE; BINDING SITES; DATABASES, NUCLEIC ACID; DISEASE; DNA; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION REGULATION; HUMANS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; TRANSCRIPTION FACTORS;

EID: 70449427464     PISSN: 14343207     EISSN: None     Source Type: Journal    
DOI: 10.3233/ISB-2009-0398     Document Type: Article

References (46)

1. 558. J. Clin. Invest. 94, 1205-1211.
2. Theuns, J., Brouwers, N., Engelborghs, S., Sleegers, K., Bogaerts, V., Corsmit, E., de Pooter, T., van Duijn, C. M., de Deyn, P. P. and van Broeckhoven, C. (2006). Promoter mutations that increase amyloid precursor-protein expression are associated with Alzheimer disease. Am. J. Hum. Genet. 26, 936-946.
3. Matsuda, M., Sakamoto, N. and Fukumaki, Y. (1992). δ-Thalassemia caused by disruption of the site for an erythroid-specific transcription factor, GATA-1, in the δ-globin gene promoter. Blood 80, 1347-1351.
4. Wittwer, J., Marti-Jaun, J. and Hersberger, M. (2006). Functional Polymorphism in ALOX15 Results in Increased Allele-Spesific Transcription in Macrophages Through Binding of the Transcription Factor SPI1. Hum. Mutat. 27, 78-87.
5. Andersen, M. C., Engström, P. G., Lithwick, S., Arenillas, D., Eriksson, P., Lenhard, B.,Wasserman,W.W. and Odeberg, J. (2008). In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput. Biol. 4, e5.
6. Laurila, K. and Lähdesmäki, H. (2008). Effects of Disease-Related Mutations on Transcription Factor Binding. In: Proceedings of the Fifth TICSPWorkshop on Computational Systems Biology (WCSB 2008), pp. 89-92.
7. Pabo, C. O. and Sauer, R. T. (1992). Transcription factors: Structural Families and Principles of DNA recognition. Annu. Rev. Biochem. 61 1053-1095.
8. Harrington, R. E. (1992). DNA curving and bending in protein-DNA recognition. Mol. Microbiol. 6, 2549-2555.
9. Suzuki, M., Loakes, D. and Yagi, N.(1996). DNA conformation and its changes upon binding transcription factors. Adv. Biophys. 32, 53-72.
10. Travers, A. A. (2004). The structural basis of DNA flexibity. Philos. Transact. A Math. Phys. Eng. Sci. 15, 1423-1438.
11. G.γ gene. Proc. Natl. Acad. Sci. USA 81, 4894-4898.
12. Solis, C., Aizencang, G. I., Astrin, K. H., Bishop, D. F. and Desnick, R. J. (2001). Uroporphyrinogen III synthase erythroid promoter mutations in adjacent GATA-1 and CP2 elements cause congenital erythropoietic porphyria. J. Clin. Invest. 107, 753-762.
13. Ponomarenko, J. V., Merkulova, T. I., Vasiliev, G. V., Levashova, Z. B., Orlova, G. V., Lavryushev, S. V., Fokin, O. N., Ponomarenko, M. P., Frolov, A. S. and Sarai, A. (2001). rSNP Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res. 29, 312-316.
14. Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel. J. A., Thomas, N. S., Abeysinghe, S., Krawczak, M. and Cooper, D. N. (2003). The Human Gene Mutation Database (HGMD®: 2003 Update. Hum. Mutat. 21 577-581.
15. Stormo, G.D. (2000). DNA binding sites: Representation and discovery. Bioinformatics 16, 16-23.
16. Staden, R. (1984). Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res. 12, 505-519.
17. Matys, V., Fricke, E., Geffers, R., Gössling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A. E., Kel-Margoulis, O. V., Kloos, D. U., Land, S., Lewicki-Potapov, B., Michael, H., Münch, P., Reuter, I., Rotert, S., Saxel, H., Scheer, M., Thiele, S. and Wingender, E. (2003). TRANSFAC: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378.
18. Sandelin, A., Alkema, W., Engström, P., Wasserman, W. W. and Lenhard, B. (2004). JASPAR: An open access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94.
19. Darling, D. A. (1957). The Kolmogorov-Smirnov, Cramer-von Mises Tests. Ann. Math. Statist. 28, 823-838.
20. Efron, B. and Tibshirani, R. J. (1993). An Introduction to the Bootstrap. Boca Raton: Chapman & Hall/CRC.
21. Segal, E., Raveh-Sadka, T., Schroeder, M., Unnerstall, U. and Gaul, U. (2008). Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451, 535-540.
22. Menendez, D., Krysiak, O., Inga, A., Krysiak, B., Resnick, M. A. and Schönfelder, G. (2006). A SNP in the flt-1 promoter integrates the VEGF system into the p53 transcriptional network. Proc. Natl. Acad. Sci. USA 103, 1406-1411.
23. Alj, Y., Georgiakaki, M., Savouret, J.-F., Mal, F., Attali, P., Pelletier, G., Fourré C., Milgrom, E., Buffet, C., Guiochon- Mantel, A. and Perlemuter, G. (2004). Hereditary persistence of alpha-fetoprotein is due to both proximal and distal hepatocyte nuclear factor-1 site mutations. Gastroenterology 126, 308-317.
24. McVey, J. H., Michaelides, K., Hansen, L. P., Ferguson-Smith, M., Tilghman, S., Krumlauf, R. and Tuddenham, E. G. (1993). A G→A substitution in an HNF I binding site in the human afetoprotein gene is associated with hereditary persistence of αfetoprotein (HPAFP). Hum. Mol. Genet. 2, 379-384.
25. Hata, J., Matsuda, K., Ninomiya, T., Yonemoto, K., Matsushita, T., Ohnishi, Y., Saito, S., Kitazono, T., Ibayashi, S., Iida, M., Kiyohara, Y., Nakamura, Y. and Kubo, M. (2007). Functional SNP in a Sp1-binding site of AGTRL1 gene is associated with suspectibility to brain infarction. Hum. Mol. Gen. 16, 630-639.
26. Ishigami, T., Umemura, S., Tamura, K., Hibi, K., Nyui, N., Kihara, M., Yabana, M., Watanabe, Y., Sumida, Y., Nagahara, T., Ochiai, H. and Ishii, M. (1997). Essential hypertension and 5′ upstream core promoter region of human angiotensinogen gene. Hypertension 30, 1325-1330.
27. Dachet, C., Poirier, O., Cambien, F., Chapman, J. and Rouis, M. (2000). New functional polymorphism CETP/-629, in cholesteryl ester transfer protein (CETP) gene related to CETP mass and high density lipoprotein cholesterol levels: Role of Sp1/Sp3 in transcriptional regulation. Arterioscler. Thromb. Vasc. Biol. 20, 507-515.
28. Carew, J. A., Pollak, E. S., High, K. A. and Bauer, K. A. (1998). Severe Factor VII Deficiency Due to a Mutation Disrupting an Sp1 Binding Site in the Factor VII Promoter. Blood 92, 1639-1645.
29. Di Pierro, E., Moriondo, V. and Cappellini, M. D. (2004). Human gene mutations. Gene symbol: FECH. Disease: Porphyria, erythropoietic. Hum. Genet. 114, 221.
30. Ludlow, L. B., Schick, B. P., Budarf, M. L., Driscoll, D. A., Zackai, E. H., Cohen, A. and Konkle, B. A. (1996). Identification of a mutation in a GATA binding site of the platelet glycoprotein Ibβ promoter resulting in the Bernard-Soulier Syndrome. J. Biol. Chem. 271, 22076-22080.
31. Jacquelin, B., Tarantino, M. D., Kritzik, M., Rozenshteyn, D., Koziol, J. A., Nurden, A. T. and Kunicki, T. J. (2001). Allele-dependent transcriptional regulation of the human integrin alpha2 gene. Blood 15, 1721-1726.
32. Jansen, H., Verhoeven, A. J. M., Weeks, L., Kastelein, J. J. P., Halley, D. J. J., van den Ouweland, A., Jukema, J. W., Seidell, J. C. and Birkenhäger, J. C. (1997). Common C-to-T substitution at position -480 of the hepatic lipase promoter associated with a lowered lipase activity in coronary artery disease patients. Arterioscler. Thromb. Vasc. Biol. 17, 2837-2842.
33. Okamoto, K., Makino, S., Yoshikawa, Y., Takaki, A., Nagatsuka, Y., Ota, M., Tamiya, G., Kimura, A., Bahram, S. and Inoko, H. (2003). Identification of IBL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am. J. Hum. Genet. 72, 303-312.
34. Berg, L.-P., Scopes, D. A., Alhaq, A., Kakkar, V. V. and Cooper, D. N. (1994). Disruption of a binding site for hepatocyte nuclear factor 1 in the protein C gene promoter is associated with hereditary thrombophilia. Hum. Mol. Genet. 3, 2147-2152.
35. Zhang, X., Miao, X., Tan, W., Ning, B., Liu, Z., Hong, Y., Song, W., Guo, Y., Zhang, X., Shen, Y., Qiang, B., Kadlubar, F. F. and Lin, D. (2005) Identification of Functional Genetic Variants in Cyclooxygenase-2 and Their Association With Risk of Esophageal Cancer. Gastroenterology 129, 556-576.
36. Nicolś, M., NoéV. and Ciudad, C. J. (2003). Transcriptional regulation of the human Sp1 gene promoter by the specificity protein (Sp) family members nuclear factor Y (NF-Y) and E2F. Biochem. J. 371 265-275.
37. Masotti, C., Armelin-Correa, L. M., Splendore, A., Lin, C. J., Barbosa, A., Sogayar, M. C. and Passos-Bueno, M. R. (2005). A functional SNP in the promoter region of TCOF1 is associated with reduced gene expression and YY2 DNA-protein interaction. Gene. 359, 44-52.
38. Knight, J. C., Udalova, I., Hill, A. V., Greenwood, B. M., Peshu, N., Marsh, K. and Kwiatkowski, D. (1999). A polymorphism that affects OCT-1 binding to the TNF promoter region is associated with severe malaria. Nat. Genet. 22, 145-150.
39. de Laat, W. and Grosveld, F. (2003). Spatial organization of gene expression: The active chromatin hub. Chromosome Res.11, 447-459.
40. Wasserman, W. W. and Sandelin, A. (2004). Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet. 5, 276-287.
41. Berger, M. F., Philippakis, A. A., Qureshi, A. M., He, F. S., Estep, P. W. III and Bulyk, M. L. (2006). Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotech. 24, 1429-1435.
42. Narlikar, L., Gordân, R. and Hartemink, A. J. (2007). A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput. Biol. 3, 2199-2208.
43. Kim, H., Kechris, K. J. and Hunter, L. (2007). Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions. In: Bioinformatics Research and Applications. Third International Symposium on Bioinformatics Research and Applications (ISBRA). Lecture Notes in Computer Science. 4463, pp. 338-349.
44. Lähdesmäki, H., Rust, A. G. and Shmulevich, I. (2008). Probabilistic inference of transcription factor binding from multiple data sources. PLoS ONE. 3, e1820.
45. Suzuki, M. and Yagi, N. (1994). DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. Proc. Natl. Acad. Sci. USA. 91, 12357-12361.
46. Torkamani, A. and Schork, N. J. (2008). Predicting functional regulatory polymorphisms. Bioinformatics 24, 1787-1792.