Tissue-specific differences in the expression of the human ADH2 alcohol dehydrogenase gene and in binding of factors to cis-acting elements in its promoter

Variation in the ADH1B proximal promoter affects expression

The primary pathway of metabolism of dietary alcohol is via its oxidation in liver by alcohol dehydrogenases (ADH). Differences in the ADH enzyme activity or levels of enzyme present could affect the risk for alcoholism. Regulatory variations have been shown to affect the promoter activity and thereby affect the risk for alcoholism. In this study the functional effects of the two SNPs (rs1159918 and rs1229982) in the proximal promoter region of ADH1B that were associated with alcoholism were explored. We examined the effects of five naturally occurring haplotypes on the promoter activity. We observed that a C to A change at rs1229982 increased promoter activity 1.4-fold.

GATA-2 and HNF-3beta regulate the human alcohol dehydrogenase 1A (ADH1A) gene

In this paper, we have identified several distal cis-acting elements that contribute to the regulation and tissue- specificity of ADH1A, which encodes an alcohol dehydrogenase (ADH) that metabolizes ethanol. A negative element from bp -1873 to -1558, relative to the translational start site, decreased transcriptional activity to 52% in H4IIE-C3 cells and 70% in CV-1 cells. A positive element from bp -2459 to -2173 increased transcriptional activity twofold in H4IIE-C3 cells and 1.7-fold in CV-1 cells. Gel mobility shift and supershift assays demonstrated that GATA-2 bound a region within this positive element. A tissue-specific regulatory element from bp -6380 to -5403 increased transcription twofold in H4IIE-C3 cells while decreasing transcription to 86% in CV-1 cells. Within this tissue-specific fragment, the region from bp -5668 to -5403 increased transcription 1.7-fold in H4IIE-C3 cells and 1.3-fold in CV-1 cells. Hepatocyte nuclear factor-3beta (HNF- 3beta) bound a region of the tissue-specific element in CV-1 cells, but not in H4IIE-C3 cells. Positive regulation of the ADH1A gene may be influenced by GATA-2 binding, while differences in HNF-3beta binding in cells/tissues may contribute to tissue specificity.

A retroviral repetitive element confers tissue-specificity to the human alcohol dehydrogenase 1C (ADH1C) gene

The human ADH1A, ADH1B, and ADH1C genes encode alcohol dehydrogenases (ADHs) that metabolize ethanol. They evolved by recent tandem duplications and have similar proximal cis-acting elements, but differ in tissue-specificity. We hypothesized that distal cis-acting elements confer tissue-specificity. In this article, we identify multiple cis-acting elements in the ADH1C upstream region. Negative elements in the fragments from bp -1,078 to -622 and from bp -3,957 to -2,651 decreased transcription activity to 41 and 14%, respectively. A tissue-specific regulatory element in the region between bp -1,503 and -1,053 stimulated transcription sixfold in H4IIE-C3 hepatoma cells but reduced transcription to 23% in HeLa cells. This regulatory element was mapped to a repetitive sequence that is similar to the U3 repeat within the long terminal repeat of human endogenous retrovirus ERV9. The 30-fold difference in expression between two cell lines demonstrates that this upstream U3 element, which inserted after the duplications that created the three class I ADH genes, plays an important role in regulating tissue-specificity of ADH1C. The ubiquitous Nuclear factor-Y (NF-Y) and an H4IIE-C3/liver-specific factor bound to the subrepeat sequence. This result suggested that tissue specificity might result from combinatorial regulation by these two transcription factors.

Tissue-specific regulatory elements in the human alcohol dehydrogenase 6 gene

The human alcohol dehydrogenase gene ADH6 is expressed at the highest levels in fetal and adult liver. We have mapped cis-acting elements that affect its expression. The sequence from bp -34 to -62 (site C) that includes the TATA box was strongly bound by nuclear proteins from liver, hepatoma cells, and fibroblasts. A truncation that removed the upstream part of site C but left the TATA homology intact dramatically reduced transcription; altering 5 bp in this region had much less effect. Part of site C can be bound by C/EBPalpha, but cotransfection with C/EBPalpha or C/EBPbeta did not stimulate transcription. The proximal region did not display tissue specificity, so we cloned the upstream region to search for additional regulatory sequences. The region between -1.6 and -2.3 kb stimulated transcription in hepatoma cells and inhibited it in fibroblasts. We identified two sites in this region that affect transcription independently of their orientation. Site 1 was a negative regulatory element in fibroblasts but had no effect in hepatoma cells. Site 2 was a positive regulatory element in hepatoma cells but had no effect in fibroblasts. This combination of positive and negative regulatory elements can play a significant role in the tissue-specific expression of ADH6.

Regulation of the mammalian alcohol dehydrogenase genes

This review focuses on the regulation of the mammalian medium-chain alcohol dehydrogenase (ADH) genes. This family of genes encodes enzymes involved in the reversible oxidation of alcohols to aldehydes. Interest in these enzymes is increased because of their role in the metabolism of beverage alcohol as well as retinol, and their influence on the risk for alcoholism. There are six known classes ADH genes that evolved from a common ancestor. ADH genes differ in their patterns of expression: most are expressed in overlapping tissue-specific patterns, but class III ADH genes are expressed ubiquitously. All have proximal promoters with multiple cis-acting elements. These elements, and the transcription factors that can interact with them, are being defined. Subtle differences in sequence can affect affinity for these factors, and thereby influence the expression of the genes. This provides an interesting system in which to examine the evolution of tissue specificity. Among transcription factors that are important in multiple members of this gene family are the C/EBPs, Sp1,USF, and AP1, HNF-1, CTF/NF-1, glucocorticoid, and retinoic acid receptors, and several as-yet unidentified negative elements, are important in at least one of the genes. There is evidence that cis-acting elements located far from the proximal promoter are necessary for proper expression. Three of the genes have upstream AUGs in the 5' nontranslated regions of their mRNA, unusual for mammalian genes. The upstream AUGs have been shown to significantly affect expression of the human ADH5 gene.

Regulation of human alcohol dehydrogenase gene ADH7: importance of an AP-1 site

The structure and function of the human alcohol dehydrogenase 7 (ADH7) promoter were analyzed. A promoter fragment extending to bp -232 functioned well in H4IIE-C3, CV-1, and HeLa cells, whereas the region extending further upstream to bp -799 had no significant effect on activity. We identified cis-acting elements in the proximal 232 bp and examined their effect on promoter activity. Mutation of site A, where c-Jun bound, caused a drastic decrease in the promoter activity in H4IIE-C3 and CV-1 cells, suggesting that AP-1 plays an important role in the regulation of ADH7. Mutation of site B also caused a large drop in promoter activity in both cell lines; C/EBPalpha can bind to this site, but because the site affects activity approximately equally in CV-1 cells that lack C/EBPalpha and in H4IIE-C3 cells that contain low levels, other proteins are likely to play the major roles in vivo. Mutation of site C, where C/EBP bound and c-Jun bound weakly, had different effects in the two cell lines: in H4IIE-C3 cells, the site C mutation did not significantly increase promoter activity, whereas in CV-1 cells, which lack C/EBPalpha, it led to a doubling of activity. Surprisingly, cotransfection of the wild-type promoter with C/EBPa or C/EBPbeta led to a decrease in promoter activity, which might in part explain the lack of activity of ADH7 in adult liver.

Function of cis-acting elements in human alcohol dehydrogenase 4 (ADH4) promoter and role of C/EBP proteins in gene expression

The ADH4 gene, which encodes human pi-alcohol dehydrogenase, is expressed in a tissue-specific manner, with the highest level in liver and lower levels in the gastrointestinal tract. We examined the location and function of the cis-acting elements that regulate ADH4 transcription. Liver contains proteins that bound to seven sites in the proximal promoter (from bp -387 to bp +17). Proteins from other tissues bound to subsets of these sites and to two additional sites, one of which is a negative cis-acting element. Members of two important transcription factor families, C/EBP and AP-1, bound to several sites in this promoter. The proximal ADH4 promoter functioned in a hepatoma cell line (H4IIE-C3) and a kidney cell line (CV-1). Coexpression of members of the C/EBP family strongly enhanced promoter activity, which can in part explain the high level of expression of ADH4 in liver. At one site that can be bound by both C/EBP and c-Jun, a mutation that abolished binding by C/EBP but not by c-Jun decreased promoter activity in both cell lines. This mutation had a stronger effect in the context of a longer promoter, suggesting interaction among cis-acting elements.

Transcriptional regulation of the rat poly(ADP-ribose) polymerase gene by Sp1

Expression of the gene encoding poly(ADP-ribose) polymerase (PARP), although ubiquitous, nevertheless varies substantially between tissues. We have recently shown that Sp1 binds five distinct target sequences (US-1 and F1-F4) in the rat PARP (rPARP) gene promoter. Here we used deletion analyses and site-directed mutagenesis to address the regulatory function played by these Sp1 sites on the basal transcriptional activity directed by the rPARP promoter. Transfection experiments revealed that the most proximal Sp1 site is insufficient by itself to direct any promoter activity. In addition, a weak negative regulatory element was identified between positions -101 and -60. The rPARP promoter directed high levels of chloramphenicol acetyltransferase activity in Jurkat T-lymphoblastoid and Ltk- fibroblast cells but only moderate levels in pituitary GH4C1 and liver HTC cells, correlating with the amounts of PARP detected in these cells by western blot analysis. However, the reduced promoter efficiency in HTC and GH4C1 cells did not result from the lack of Sp1 activity in these cells but suggested that yet uncharacterized regulatory proteins might turn off PARP gene expression by binding negative regulatory elements from the rPARP promoter. Similarly, site-directed mutagenesis on the three most proximal Sp1 elements suggested the influence exerted by Sp1 on the rPARP promoter activity to vary substantially between cell types. It also provided evidence for a basal rPARP promoter activity driven through the recognition of unidentified cis-acting elements by transcription factors other than Sp1.

Gene expression in a young multigene family: tissue-specific differences in the expression of the human alcohol dehydrogenase genes ADH1, ADH2, and ADH3

Three human alcohol dehydrogenase genes, ADH1, ADH2, and ADH3, were formed by tandem duplications and have diverged in their tissue-specific and developmental expression. Their proximal promoters remain 80-84% identical in sequence, approximately the same degree of identity as at synonymous sites in the coding regions of these three genes. To understand the evolution of tissue specificity, gene expression must be studied in many different cells and tissues. A systematic comparison of their promoters reveals the effects of subtle sequence differences on the binding of nuclear proteins to their cis-acting elements. There are differences in the affinity with which some proteins are bound to altered sites including C/EBP sites, USF/MLTF sites, and the G3T site (which binds Sp1). There are also differences in the sites that are occupied, e.g. CTF/NFI-related sites. These sequence differences are reflected in differences in gene expression in three cell lines. In H4IIE-C3 hepatoma cells, the ADH1 promoter was more active than the ADH2 promoter, and the ADH3 promoter was nearly nonfunctional. In HeLa cells, both ADH1 and ADH2 promoters directed expression; again the ADH3 promoter was extremely weak. None of the three promoters had much activity in CV-1 cells. Coexpression of C/EBP alpha greatly stimulated expression of the ADH1 promoter in HeLa cells and in CV-1 cells, but only weakly stimulated expression in H4IIE-C3 cells. The stimulation of the ADH1 promoter by C/EBP alpha was comparable to that of ADH2, despite the weaker binding to the C/EBP sites that flank the TATA box in ADH1. The ADH3 promoter was not greatly stimulated by C/EBP alpha, despite good binding of C/EBP alpha. These results demonstrate that small differences in the cis-acting elements affect affinity of binding by transcription factors and the pattern of gene expression.