Functional analysis of human promoter polymorphisms

Human Molecular Genetics

Volumn 12, Issue 18, 2003, Pages 2249-2254

  Hoogendoorn, Bastiaan ^a   Coleman, Sharon L ^a   Guy, Carol A ^a   Smith, Kaye ^a   Bowen, Tim ^a   Buckland, Paul R ^a   O'Donovan, Michael C ^a  

^a CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

LUCIFERASE;

ARTICLE; CONTROLLED STUDY; DNA FLANKING REGION; DNA POLYMORPHISM; DNA VECTOR; EUKARYOTIC PROMOTER DATABASE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC DATABASE; GENETIC SCREENING; GENETIC SELECTION; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; HAPLOTYPE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; MOLECULAR CLONING; PRIORITY JOURNAL; PROMOTER REGION; REPORTER GENE; SINGLE NUCLEOTIDE POLYMORPHISM;

5' FLANKING REGION; 5' UNTRANSLATED REGIONS; BASE SEQUENCE; CELL LINE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CHROMOSOMES; DATABASES, FACTUAL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENES, REPORTER; GENETIC VECTORS; HAPLOTYPES; HUMANS; LUCIFERASES; PLASMIDS; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; TRANSCRIPTION, GENETIC; TRANSFECTION; VARIATION (GENETICS);

CUCUMBER MOSAIC VIRUS; EUKARYOTA;

EID: 0042359360     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddg246     Document Type: Article

References (28)

1. Peltonen, L. and McKusick, V.A. (2001) Genomics and medicine. Dissecting human disease in the postgenomic era. Science, 291, 1224-1229.
2. MacKay, T (2002) Quantitative trait loci in Drosophila. Nat. Rev. Genet., 2, 11-20.
3. Toma, D.P., White, K.P., Hirsch, J. and Greenspan, R.J. (2002) Identification of genes involved in Drosophila melanogaster geotaxis, a complex behavioral trait. Nat. Genet., 31, 349-353.
4. International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
5. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H,O., Yandell, M., Evans, C.A., Holt, R.A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
6. Yan, H., Yuan, W., Velculescu, V.E., Vogelstein, B. and Kinzler, K.W. (2002) Allelic variation in human gene expression. Science, 297, 1143.
7. Praz, V., Périer, R.C., Bonnard, C. and Bucher, P. (2002) The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucl. Acids Res., 30, 322-324.
8. Périer, R.C., Praz, V., Junier, T., Bonnard, C. and Bucher, P. (2000) The Eukaryotic Promoter Database (EPD). Nucl. Acids Res., 28, 302-303.
9. Oefner, P.J. and Underhill, P.A. (1998) DNA mutation detection using denaturing high-performance liquid chromatography (DHPLC). Curr. Protoc. Hum. Genet., 19 (suppl.), 7.10.1-7.10.12.
10. Collins, D.W. and Jukes, T.H. (1994) Rates of transition and transversion in coding sequences since the human-rodent divergence. Genomics, 20, 386-396.
11. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C.R., Lim, E.P., Kalyanaraman, N. et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet., 22, 231-238.
12. Cooper, D.N. and Youssoufian, H. (1988) The CpG dinucleotide and human genetic disease. Hum. Genet., 78, 151-155.
13. Sachidanandam, R., Weissman, D., Schmidt, S.C., Kakol, J.M., Stein, L.D., Marth, G., Sherry, S., Mullikin, J.C., Mortimore, B.J., Willey, D.L. et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928-933.
14. Coleman, S.L., Hoogendoorn, B., Guy, C., Smith, S.K., O'Donovan, M.C. and Buckland, P.R. (2002) A streamlined approach to functional analysis of promoter polymorphisms. Bio Techniques, 33, 412-418.
15. Kubo, E., Fatma, N., Sharma, P., Shinohara, T., Chylack, L.T. Jr., Akagi, Y. and Singh, D.P. (2002) Transactivation of involucrin, a marker of differentiation in keratinocytes, by lens epithelium-derived growth factor (LEDGF). J. Mol. Biol., 320, 1053-1063.
16. Tillotson, L.G. (1999) A novel zinc finger gene, encodes proteins that bind to the CACC element of the gastrin promoter. J. Biol. Chem., 274, 8123-8128.
17. + exchanger gene expression. Role of a novel poly(dA.dT) element in regulation of the NHE1 promoter. J. Biol. Chem., 271, 20444-20449.
18. Liu, R. and States, D.J. (2002) Consensus promoter identification in human genome utilizing expressed sequence markers and gene modeling. Genome Res., 12, 462-469.
19. Quandt, K., Frech, K., Karas, H., Wingender, E. and Werner, T. (1995) MatInd and MatInspector - New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucl. Acids Res., 23, 4878-4884.
20. Lander, E.S. (1996) The new genomics: global views of biology. Science, 274, 536-539.
21. Reich, D.E. and Lander, E.S. (2001) On the allelic spectrum of human disease. Trends Genet., 17, 502-510.
22. Pritchard, J.K. (2001) Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet., 69, 124-137.
23. Wright, A.F. and Hastie, N.D. (2001) Complex genetic diseases: controversy over the Croesus code. Genome Biol., 2, 2007.1-2007.8.
24. Kruglyak, L. and Nickerson, D.A. (2001) Variation is the spice of life. Nat. Genet., 27, 234-236.
25. Cowles, C.R., Hirschhorn, J.N., Altshuler, D. and Lander, E.S. (2002) Detection of regulatory variation in mouse genes. Nat. Genet., 32, 432-437.
26. Rozen, S. and Skaletsky, H.J. (1998) Primer3. Code available at www.genome.wi.mit.edu/genomeftware/other/primer3.html
27. Burke, T.W. and Kadonaga, J.T. (1997) The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev., 11, 3020-3031.
28. Jones, A.C., Austin, J., Hansen, N., Hoogendoorn, B., Oeftner, P.J., Cheadle, J.P. and O'Donovan, M.C. (1999) Optimal temperature selection for mutation detection by denaturing HPLC and comparison to single-stranded conformation polymorphism and heteroduplex analysis. Clin. Chem., 45, 1133-1140.