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Single-Nucleotide Polymorphisms Interact to Affect ADH7 Transcription

Authors

  • Sowmya Jairam,

    1. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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  • Howard J. Edenberg

    Corresponding author
    1. Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
    2. Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
    • Reprint requests: Howard J. Edenberg, PhD, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS4063, Indianapolis, IN 46202 Tel.: 317-274-2353; Fax: 317-274-4686; E-mail: edenberg@iu.edu

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Abstract

Background

The class IV alcohol dehydrogenase (ADH7, μ-ADH, σ-ADH) is important in the metabolism of ethanol and retinol. ADH7 is the only ADH not expressed in liver, instead being expressed mainly in the upper gastrointestinal tract. Genome-wide studies have identified significant associations between single-nucleotide polymorphisms in ADH7 and alcoholism and cancer, but the causative variants have not been identified.

Methods

In vitro studies of gene expression by transient transfection into cell lines that express endogenous ADH7 (CP-A cells) and that do not (HepG2 cells).

Results

We have identified transcriptional regulatory elements of ADH7 and observed differences in the effects of variants on gene expression in CP-A cells and HepG2 cells. Two haplotypes of the proximal promoter that differ in a single nucleotide at rs2851028, A7P-G and A7P-A, have different transcriptional activities. There is an interaction between variants farther upstream and these proximal variants: Upstream regulatory sequences generally showed a greater increase or smaller reduction in activity when combined with the A7P-A promoter than with the A7P-G promoter. A sequence located 12.5-kb upstream (7P10) can function as an enhancer. In CP-A cells, both haplotypes of 7P10 increased A7P-A activity by 2.5-fold while having only 1.2-fold effect on A7P-G. In HepG2 cells, the 7P10-TTT haplotype had no effect on the A7P-A promoter but decreased A7P-G promoter activity by 50%, whereas the CTT haplotype increased A7P-A activity by 50%, but had no effect on A7P-G.

Conclusions

These complex interactions indicate that the effects of variants in the ADH7 regulatory elements depend on both sequence and cellular context and should be considered in interpretation of the association of variants with alcoholism and cancer.

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