Polymorphisms in gene regulatory regions and their role in the physiopathology of complex disease in the post-genomic era;Polimorfismos reguladores y su participación en la patogenia de enfermedades complejas en la era posgenómica

Salud Publica de Mexico

Volumn 51, Issue SUPPL.3, 2009, Pages

  Hernández Romano, Jesús ^a   Martínez Barnetche, Jesús ^b   Valverde Garduño, Verónica ^b  

^a Univ Autdnoma del Estado de Morelos   (Mexico)

^b INSTITUTO NACIONAL DE SALUD PÚBLICA   (Mexico)

Author keywords

Alleles; Gene expression regulation; Genetic polymorphism; Genetic variation; Genetics, disease; Transcription

Indexed keywords

GENERAL ASPECTS OF DISEASE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOMICS; HUMAN; REVIEW;

DISEASE; GENETIC VARIATION; GENOMICS; HUMANS; POLYMORPHISM, GENETIC;

EID: 77957007406     PISSN: 00363634     EISSN: 16067916     Source Type: Journal    
DOI: 10.1590/S0036-36342009000900011     Document Type: Article

References (59)

1. Botstein D, Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 2003;33(Suppl):228-237.
2. Frodsham AJ, Hill AV. Genetics of infectious diseases. Hum Mol Genet 2004;13:R187-194.
3. International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1299-1320.
4. Cooper GM, Sidow A. Genomic regulatory regions: insights from comparative sequence analysis. Curr Opin Genet Dev 2003;13:604-610.
5. Drake JA, Bird C, Nemesh J, Thomas DJ, Newton-Cheh C, Reymond A, et al. Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet 2006;38:223-227.
6. King MC, Wilson AC. Evolution at two levels in humans and chimpanzees. Science 1975;188:107-116.
7. Sandberg R, Yasuda R, Pankratz DG, Carter TA, Del Rio JA, Wodicka L, et al. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc Natl Acad Sci U S A 2000;97:11038-11043.
8. Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet 2001;29:389-395.
9. Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, McCusker JH, et al. Dissecting the architecture of a quantitative trait locus in yeast. Nature 2002;416:326-330.
10. Glazier AM, Nadeau JH, Aitman TJ. Finding genes that underlie complex traits. Science 2002;298:2345-2349.
11. Carlson CS, Eberle MA, Kruglyak L, Nickerson DA. Mapping complex disease loci in whole-genome association studies. Nature 2004;429:446-452.
12. Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 2005;6:95-108.
13. Woychik NA, Hampsey M. The RNA polymerase II machinery: structure illuminates function. Cell 2002;108:453-463.
14. Kadonaga JT. Regulation of DNA polymerase II transcription by sequence-specific DNA binding factors. Cell 2004;116:247-257.
15. Levine M, Tjian R. Transcription regulation and animal diversity. Nature 2003;424:147-151.
16. Khorasanizadeh S. The nucleosome: from genomic organization to genomic regulation. Cell 2004;116:259-272.
17. Leung TH, Hoffmann A, Baltimore D. One nucleotide in a kB site can determine cofactor specificity for NF-kB dimmers. Cell 2004;118:453-464.
18. Buckland PR. The importance and identification of regulatory polymorphisms and their mechanisms of action. Biochim Biophys Act 2006;1762:17-28.
19. Pastinen T, Ge B, Hudson TJ. Influence of human genome polymorphism on gene expression. Hum Mol Genet 2006;15:R9-16.
20. Yan H, Yuan W, Velculescu VE, Vogelstein B, Kinzler KW. Allelic variation in human gene expression. Science 2002;297:1143.
21. Bennett ST, Lucassen AM, Gough SC, Powell EE, Undlien DE, Pritchard LE, et al. Susceptibility to human type 1 diabetes at IDDM2 is determined by tandem repeat variation at the insulin gene minisatellite locus. Nat Genet 1995;9:284-292.
22. Pastinen T, Sladek R, Gurd S, Sammak A, Ge B, Lepage P, et al. A survey of genetic and epigenetic variation affecting human gene expression. Physiol Genomics 2003;16:184-193.
23. Krawczak M, Ball EV, Fenton I, Stenson PD, Abeysinghe S, Thomas N, et al. Human gene mutation database-a biomedical information and research resource. Hum Mutat 2000;15:45-51.
24. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29:308-311.
25. Brookes AJ, Lehvaslaiho H, Siegfried M, Boehm JG, Yuan YP, Sarkar CM, et al. HGBASE: a database of SNPs and other variations in and around human genes. Nucleic Acids Res 2000;28:356-360.
26. Cheung KH, Osier MV, Kidd JR, Pakstis AJ, Miller PL, Kidd KK. ALFRED: an allele frequency database for diverse populations and DNA polymorphisms. Nuc Acid Res 2000;28:361-363.
27. McKusick VA. Mendelian inheritance in man. A catalog of human genes and genetic disorders. 12th ed. Baltimore: Johns Hopkins University Press, 1998.
28. Ponomarenko JV, Merkulova TI, Vasiliev GV, Levashova ZB, Orlova GV, Lavryushev SV, et al. rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations. Nucleic Acids Res 2001;29:312-316.
29. Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004; 5:276-287.
30. Tomso DJ, Inga A, Menendez D, Pittman GS, Campbell MR, Storici F, et al. Functionally distinct polymorphic sequences in the human genome that are targets for p53 transactivation. Proc Natl Acad Sci U S A 2005;102:6431-6436.
31. Mottagui-Tabar S, Faghihi MA, Mizuno Y, Engstrom PG, Lenhard B, Wasserman WW, et al. Identification of functional SNPs in the 5-prime flanking sequences of human genes. BMC Genomics 2005;6:18.
32. Lin W, Yang HH, Lee MP. Allelic variation in gene expression identified through computational analysis of the dbEST database. Genomics 2005;86:518-527.
33. Ge B, Gurd S, Gaudin T, Dore C, Lepage P, Harmsen E, et al. Survey of allelic expression using EST mining. Genome Res 2005;15:1584-1591.
34. Lo HS, Wang Z, Hu Y, Yang HH, Gere S, Buetow KH, et al. Allelic variation in gene expression is common in the human genome. Genome Res 2003;13:1855-1862.
35. Pant PV, Tao H, Beilharz EJ, Ballinger DG, Cox DR, Frazer KA. Analysis of allelic differential expression in human white blood cells. Genome Res 2006;16:331-339.
36. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, Morley M, et al. Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 2003;33:422-425.
37. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, et al. Genetic analysis of genome-wide variation in human gene expression. Nature 2004;430:743-747.
38. Monks SA, Leonardson A, Zhu H, CundiffP, Pietrusiak P, Edwards S, et al. Genetic inheritance of gene expression in human cell lines. Am J Hum Genet 2004;75:1094-1105.
39. Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science1996;273:1516-1517.
40. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, Burdick JT. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005;437:1365-1369.
41. Arbini AA, Pollak ES, Bayleran JK, High KA, Bauer KA. Severe factor VII deficiency due to a mutation disrupting a hepatocyte nuclear factor 4 binding site in the factorVII promoter. Blood 1997;89:176-182
42. Buckland PR, Hoogendoorn B, Coleman SL, Guy CA, Smith SK, O'Donovan MC. Strong bias in the location of functional promoter polymorphisms. Hum Mutat 2005;26:214-223.
43. Knight JC, Keating BJ, Rockett KA, Kwiatkowski DP. In vivo characterization of regulatory polymorphisms by allele-specific quantification of RNA polymerase loading. Nat Genet 2003;33:469-475.
44. Liu X, Campbell MR, Pittman GS, Faulkner EC, Watson MA, Bell DA. Expression-based discovery of variation in the human glutathione S-transferase M3 promoter and functional analysis in a glioma cell line using allele specific chromatin immunoprecipitation. Cancer Res 2005;65:99-104.
45. Jansen RC, Nap JP. Genetical genomics: the added value from segregation. Trends Genet 2001;17:388-391.
46. de Koning DJ, Haley CS. Genetical genomics in humans and model organisms. Trends Genet 2005;21:377-381.
47. Gibson G, Weir B. The quantitative genetics of transcription. Trends Genet 2005;21:616-623.
48. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA et al. Genome Wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Gen 2008;9:356-369.
49. Ioannidis JPA, Thomas G, Daly MJ. Validating, augmenting and refining genome-wide association signals. Nat Rev Gen 2009;10:318-329.
50. Knight JC. Regulatory polymorphisms underlying complex disease traits. J Mol Med 2005; 83:97-109.
51. Pastinen T, Ge B, Gurd S, Gaudin T, Dore C, LemireM, et al. Mapping common regulatory variants to human haplotypes. Hum Mol Genet 2005;14:3963-3971.
52. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, et al. An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 2005;37:710-717.
53. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, et al. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 2005;37:243-253.
54. Tournamille C, Colin Y, Cartron JP, Le Van Kim C. Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat Genet 1995;10:224-228.
55. De Gobbi M, Viprakasit V, Hughes JR, Fisher C, Buckle VJ, Ayyub H, et al. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 2006;312:1215-1217.
56. Knight JC, Keating BJ, Kwiatkowski DP. Allele-specific repression of lymphotoxin-alpha by activated B cell factor-1. Nat Genet 2004;36:394-399.
57. Gonsky R, Deem RL, Bream JH, Young HA, Targan SR. An IFNG SNP with an estrogen-like response element selectively enhances promoter expression in peripheral but not lamina propria T cells. Genes Immun 2006;1-10.
58. Bream JH, Young HA, Rice N, Martin MP, Smith MW, Carrington M, et al. CCR5 promoter alleles and specific DNA binding factors. Science 1999;284:223
59. Hacking D, Knight JC, Rockett K, Brown H, Frampton J, Kwiatkowski DP, et al. Increased in vivo transcription of an IL-8 haplotype associated with respiratory syncytial virus disease-susceptibility. Genes Immun 2004;5:274-282.