Functional analysis of human promoter polymorphisms

• Published in: Human molecular genetics Vol. 12; no. 18; pp. 2249 - 2254
• Main Authors: Hoogendoorn, Bastiaan, Coleman, Sharon L., Guy, Carol A., Smith, Kaye, Bowen, Tim, Buckland, Paul R., O'Donovan, Michael C.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15-09-2003; Oxford Publishing Limited (England)
• Subjects: 5' Flanking Region; 5' Untranslated Regions; Base Sequence; Biological and medical sciences; Cell Line; Chromatography, High Pressure Liquid; Chromosomes; Classical genetics, quantitative genetics, hybrids; Databases, Factual; Fundamental and applied biological sciences. Psychology; Gene Expression; Gene Expression Regulation; Genes, Reporter; Genetic Variation; Genetic Vectors; Genetics of eukaryotes. Biological and molecular evolution; Haplotypes; Human; Humans; Luciferases - genetics; Molecular and cellular biology; Plasmids; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Promoter Regions, Genetic; Sequence Alignment; Transcription, Genetic; Transfection; Human; Genetics; Analysis; Polymorphism
• ISSN: 0964-6906; 1460-2083; 1460-2083
• DOI: 10.1093/hmg/ddg246

The potential importance of gene regulation in disease susceptibility and other inherited phenotypes has been underlined by the observation that the human genome contains fewer protein coding genes than expected. Promoter sequences are potential sources of polymorphism affecting gene expression, although to date there are no large-scale systematic studies that have determined how frequently such variants occur. We have used denaturing high performance liquid chromatography to screen the first 500 bp of the 5′ flanking region of 170 opportunistically selected genes identified from the Eukaryotic Promoter Database (EPD) for common polymorphisms. Using a screening set of 16 chromosomes, single-nucleotide polymorphisms were found in ∼35% of genes. It was attempted to clone each of these promoters into a T-vector constructed from the reporter gene vector pGL3. The relative ability of each promoter haplotype to promote transcription of the luciferase gene was tested in each of three human cell lines (HEK293, JEG and TE671) using a co-transfected SEAP-CMV plasmid as a control. The findings suggest that around a third of promoter variants may alter gene expression to a functionally relevant extent.