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Human Molecular Genetics Advance Access published online on July 22, 2003
Human Molecular Genetics, doi:10.1093/hmg/ddg246
© 2003 by Oxford University Press
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©2003 Oxford University Press

Article

Functional Analysis of Human Promoter Polymorphisms

Bastiaan Hoogendoorn 1*, Sharon L Coleman 1, Carol A Guy 1, Kaye Smith 1, Tim Bowen 1, Paul R Buckland 1, and Michael C O'Donovan 1

1 Department of Psychological Medicine, University of Wales College of Medicine, Heath Park, Cardiff, CF14 4XN, UK

* To whom correspondence should be addressed. E-mail: hoogendoornb{at}cf.ac.uk.


  Abstract

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, we have found SNPs in approximately 35% of genes. We 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. Our findings suggest that around a third of promoter variants may alter gene expression to a functionally relevant extent.

Key Words: luciferase, promoter, functional SNP, transcriptional activation


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