title: Identification of functional SNPs in the 5-prime flanking sequences of human genes.
abstract: BACKGROUND
  Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach.
  
  
  RESULTS
  Sequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines.
  
  
  CONCLUSIONS
  We propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types.
authors.affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177 Stockholm, Sweden. salim.mottagui-tabar@cgb.ki.se
authors.forename: Salim
authors.initials: S
authors.lastname: Mottagui-Tabar
authors.forename: Mohammad A
authors.initials: MA
authors.lastname: Faghihi
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Mizuno
authors.forename: Pär G
authors.initials: PG
authors.lastname: Engström
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
authors.forename: Claes
authors.initials: C
authors.lastname: Wahlestedt
mesh_terms: D000465:Algorithms; D000483:Alleles; D000818:Animals; D001665:Binding Sites; D002460:Cell Line; D002874:Chromosome Mapping; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D008156:Luciferases / Q000378:metabolism; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry; D010641:Phenotype; D010957:Plasmids / Q000378:metabolism; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D009841:Oligonucleotides; D014157:Transcription Factors; D008156:Luciferases
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Bioinformatics. 2000 Jan;16(1):16-23
references.pmid: 10812473
references.citation: Bioinformatics. 2002 Aug;18(8):1135-6
references.pmid: 12176838
references.citation: Nucleic Acids Res. 2002 Sep 1;30(17):3894-900
references.pmid: 12202775
references.citation: Nature. 2002 Dec 5;420(6915):563-73
references.pmid: 12466851
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):51-4
references.pmid: 12519945
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):118-21
references.pmid: 12519962
references.citation: Genome Res. 2003 Jan;13(1):103-7
references.pmid: 12529312
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D91-4
references.pmid: 14681366
references.citation: J Biol. 2003;2(2):13
references.pmid: 12760745
references.citation: Mol Cell Biol. 1996 Jan;16(1):437-41
references.pmid: 8524326
references.citation: J Mol Biol. 1997 Feb 21;266(2):231-45
references.pmid: 9047360
references.citation: Curr Opin Struct Biol. 1997 Jun;7(3):399-406
references.pmid: 9204283
references.citation: Methods Biochem Anal. 1998;39:231-45
references.pmid: 9707933
references.citation: Pac Symp Biocomput. 2000;:467-78
references.pmid: 10902194
references.citation: Curr Med Chem. 2000 Sep;7(9):861-88
references.pmid: 10911020
references.citation: Nucleic Acids Res. 2001 Jan 1;29(1):308-11
references.pmid: 11125122
references.citation: Nat Rev Genet. 2001 Feb;2(2):100-9
references.pmid: 11253049
references.citation: Hum Mol Genet. 2001 Mar 15;10(6):591-7
references.pmid: 11230178
references.citation: J Mol Biol. 2001 Mar 23;307(2):683-706
references.pmid: 11254390
references.citation: Annu Rev Pharmacol Toxicol. 2001;41:593-624
references.pmid: 11264470
references.citation: Trends Genet. 2001 Jul;17(7):373-6
references.pmid: 11418197
references.citation: Genome Res. 2001 Sep;11(9):1559-66
references.pmid: 11544200
references.citation: Arterioscler Thromb Vasc Biol. 2001 Nov;21(11):1834-9
references.pmid: 11701474
references.citation: Genome Res. 2001 Dec;11(12):2151-7
references.pmid: 11731507
references.citation: AAPS PharmSci. 2001;3(3):E22
references.pmid: 11741273
references.citation: Nat Genet. 1999 Jul;22(3):231-8
references.pmid: 10391209
references.citation: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D447-53
references.pmid: 15608235
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):356-60
references.pmid: 10592273
references.citation: Science. 2000 Mar 24;287(5461):2204-15
references.pmid: 10731134
references.citation: Science. 2000 Apr 7;288(5463):136-40
references.pmid: 10753117
references.citation: Trends Genet. 2000 May;16(5):198-200
references.pmid: 10782110
references.citation: FEBS Lett. 2002 Apr 10;516(1-3):253-6
references.pmid: 11959142