A critical assessment of the factors affecting reporter gene assays for promoter SNP function: A reassessment of -308 TNF polymorphism function using a novel integrated reporter system

European Journal of Human Genetics

Volumn 17, Issue 11, 2009, Pages 1454-1462

  Karimi, Mahdad ^a   Goldie, Lauren C ^a   Cruickshank, Mark N ^a   Moses, Eric K ^b   Abraham, Lawrence J ^a  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b SOUTHWEST FOUNDATION FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR NECROSIS FACTOR;

ALLELE; ARTICLE; CONTROLLED STUDY; DNA CONFORMATION; DNA TRANSFECTION; FUNCTIONAL ASSESSMENT; GENE CONSTRUCT; GENETIC ANALYSIS; GENETIC VARIABILITY; HOST CELL; HUMAN; HUMAN CELL; LEUKEMIA CELL LINE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; REPORTER GENE ASSAY; SINGLE NUCLEOTIDE POLYMORPHISM;

3' UNTRANSLATED REGIONS; CELL CYCLE; CELL LINE; CELL PROLIFERATION; GENE EXPRESSION; GENES, REPORTER; GENETIC TECHNIQUES; GENETIC VECTORS; HUMANS; NUCLEIC ACID CONFORMATION; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; PROMOTER REGIONS, GENETIC; REPRODUCIBILITY OF RESULTS; TRANSFECTION; TUMOR NECROSIS FACTOR-ALPHA;

EID: 70350366111     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.80     Document Type: Article

References (33)

1. Kraft P, Cox DG: Study designs for genome-wide association studies. Adv Genet 2008; 60: 465-504.
2. Wray NR, Goddard ME, Visscher PM: Prediction of individual genetic risk to disease from genome-wide association studies. Genome Res 2007; 17: 1520-1528.
3. Blangero J, Goring HH, Kent Jr JW et al: Quantitative trait nucleotide analysis using Bayesian model selection. Hum Biol 2005; 77: 541-559.
4. Goring HH, Curran JE, Johnson MP et al: Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet 2007; 39: 1208-1216.
5. Buckland PR: The importance and identification of regulatory polymorphisms and their mechanisms of action. Biochim Biophys Acta 2006; 1762: 17-28.
6. Chorley BN, Wang X, Campbell MR, Pittman GS, Noureddine MA, Bell DA: Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: Current and developing technologies. Mutat Res 2008; 659: 147-157.
7. Knight JC: Functional implications of genetic variation in non-coding DNA for disease susceptibility and gene regulation. Clin Sci 2003; 104: 493-501.
8. Butash KA, Natarajan P, Young A, Fox DK: Reexamination of the effect of endotoxin on cell proliferation and transfection efficiency. Biotechniques 2000; 29: 610-614.
9. Bergeron D, Barbeau B, Leger C, Rassart E: Experimental bias in the evaluation of the cellular transient expression in DNA co-transfection experiments. Cell Mol Biol Res 1995; 41: 155-159.
10. Carey M, Smale ST: Transcriptional Regulation in Eukaryotes: Concepts, Strategies, and Techniques. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2000.
11. Mercola M, Goverman J, Mirell C, Calame K: Immunoglobulin heavy-chain enhancer requires one or more tissue-specific factors. Science 1985; 227: 266-270.
12. Smith CL, Hager GL: Transcriptional regulation of mammalian genes in vivo. A tale of two templates. J Biol Chem 1997; 272: 27493-27496.
13. Agarwal ML, Agarwal A, Taylor WR, Chernova O, Sharma Y, Stark GR: A p53-dependent S-phase checkpoint helps to protect cells from DNA damage in response to starvation for pyrimidine nucleotides. Proc Natl Acad Sci USA 1998; 95: 14775-14780.
14. Braun N MU, Ernst BP, Metzner R, Bitsch A, Weber F, Rieckmann P: Gene polymorphism at position -308 of the tumor-necrosis-factor-alpha (TNF-alpha) in multiple sclerosis and it's influence on the regulation of TNF-alpha production. Neurosci Lett 1996; 215: 75-78.
15. Kroeger KM, Carville KS, Abraham LJ: The -308 tumor necrosis factor-alpha promoter polymorphism effects transcription. Mol Immunol 1997; 34: 391-399.
16. Wilson AG, Symons JA, McDowell TL, McDevitt HO, Duff GW: Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc Natl Acad Sci USA 1997; 94: 3195-3199.
17. Wu WS, McClain KL: DNA polymorphisms and mutations of the tumor necrosis factor-alpha (TNF-alpha) promoter in Langerhans cell histiocytosis (LCH). J Interferon Cytokine Res 1997; 17: 631-635.
18. Brinkman BM ZD, Kaijzel EL, Breedveld FC, Verweij CL: Relevance of the tumor necrosis factor alpha (TNF alpha) -308 promoter polymorphism in TNF alpha gene regulation. J Inflamm 1995; 46: 32-41.
19. Stuber F, Udalova IA, Book M et al: -308 tumor necrosis factor (TNF) polymorphism is not associated with survival in severe sepsis and is unrelated to lipopolysaccharide inducibility of the human TNF promoter. J Inflamm 1995; 46: 42-50.
20. Uglialoro AM, Turbay D, Pesavento PA et al: Identification of three new single nucleotide polymorphisms in the human tumor necrosis factor-alpha gene promoter. Tissue Antigens 1998; 52: 359-367.
21. Bayley JP, de Rooij H, van den Elsen PJ, Huizinga TW, Verweij CL: Functional analysis of linker-scan mutants spanning the -376, -308, -244, and -238 polymorphic sites of the TNF-alpha promoter. Cytokine 2001; 14: 316-323.
22. Abraham LJ, Kroeger KM: Impact of the -308 TNF promoter polymorphism on the transcriptional regulation of the TNF gene: Relevance to disease. J Leukoc Biol 1999; 66: 562-566.
23. Kroeger KM, Steer JH, Joyce DA, Abraham LJ: Effects of stimulus and cell type on the expression of the -308 tumour necrosis factor promoter polymorphism. Cytokine 2000; 12: 110-119.
24. Karimi M, Goldie LC, Ulgiati D, Abraham LJ: Integration site-specific transcriptional reporter gene analysis using Flp recombinase targeted cell lines. Biotechniques 2007; 42: 217-224.
25. Schmid I, Uittenbogaart CH, Giorgi JV: A gentle fixation and permeabilization method for combined cell surface and intra-cellular staining with improved precision in DNA quantification. Cytometry 1991; 12: 279-285.
26. Yan C, Wang H, Aggarwal B, Boyd DD: A novel homologous recombination system to study 92 kDa type IV collagenase transcription demonstrates that the NF-kappaB motif drives the transition from a repressed to an activated state of gene expression. FASEB J 2004; 18: 540-541.
27. Bray NJ, Buckland PR, Owen MJ, O'Donovan MC: Cis-acting variation in the expression of a high proportion of genes in human brain. Hum Genet 2003; 113: 149-153.
28. Knight JC, Keating BJ, Rockett KA, Kwiatkowski DP: In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading [see comment]. Nat Genet 2003; 33: 469-475.
29. Cirulli ET, Goldstein DB: In vitro assays fail to predict in vivo effects of regulatory polymorphisms. Hum Mol Genet 2007; 16: 1931-1939.
30. Bayley JP, Ottenhoff TH, Verweij CL: Is there a future for TNF promoter polymorphisms? Genes Immun 2004; 5: 315-329.
31. Fernando MM, Stevens CR, Walsh EC et al: Defining the role of the MHC in autoimmunity: A review and pooled analysis. PLoS Genet 2008; 4: E1000024.
32. Awdeh ZL, Raum D, Yunis EJ, Alper CA: Extended HLA/complement allele haplotypes: Evidence for T/t-like complex in man. Proc Natl Acad SciUSA 1983; 80: 259-263.
33. Christiansen FT, Witt CS, Ciccone E et al: Human natural killer (NK) alloreactivity its association with the major histo-compatibility complex: Ancestral haplotypes encode particular NK-defined haplotypes. J Exp Med 1993; 178: 1033-1039.