Identification of functional cis-acting elements within the rat liver S14 promoter

Characterization of the mouse CP27 promoter and NF-Y mediated gene regulation

The cp27 gene is a highly conserved and unique gene with important roles related to craniofacial organogenesis. The present study is a first analysis of the CP27 promoter and its regulation. Here, we have cloned the promoter of the mouse cp27 gene, examined its transcriptional activity, and identified transcription factor binding sites in the proximal promoter region. Two major transcription start sites were mapped adjacent to exon 1. Promoter function analysis of the 5' flanking region by progressive 5' deletion mutations localized transcription repression elements between -1993bp and -969bp and several positive elements between -968bp and the preferred transcription start site. EMSA and functional studies indicated two function-cooperative CCAAT boxes and identified the NF-Y transcription factor as the CCAAT activator controlling transactivation of the CP27 promoter. In addition, this study demonstrated that for its effective binding and function, NF-Y required not only the minimal DNA segment length identified by deletion studies, but also a defined nucleotide sequence in the distal 3' flanking region of the CP27 proximal promoter CCAAT box. These results provide a basis for our understanding of the specific regulation of the cp27 gene in the NF-Y-mediated gene transcription network.

Dependence of rat spot14 promoter activity on NF-Y binding to the inverted CCAAT-element at -100

Electrophoretic mobility shift assay (EMSA) and in vitro transcription/translation show that NF-Y binds to the inverted CCAAT-element in the promoter of the rodent spot14 gene. The NF-Y-binding sequence has been shown to be responsible for basal activity in H4IIE. Given the similar role found for the inverted CCAAT-element in the promoter of the FAS gene, NF-Y may have an important function in the control of lipogenesis.

Sterol response element-binding protein 1c (SREBP1c) is involved in the polyunsaturated fatty acid suppression of hepatic S14 gene transcription

Polyunsaturated fatty acids (PUFA) suppress hepatic lipogenic gene transcription through a peroxisome proliferator activated receptor alpha (PPARalpha)- and cyclooxygenase-independent mechanism. Recently, the sterol response element-binding protein 1 (SREBP1) was implicated in the nutrient control of lipogenic gene expression. In this report, we have assessed the role SREBP1 plays in the PUFA control of three hepatic genes, fatty acid synthase, L-pyruvate kinase (LPK), and the S14 protein (S14). PUFA suppressed both the hepatic mRNA(SREBP1) through a PPARalpha-independent mechanism as well as SREBP1c nuclear content (nSREBP1c, 65 kDa). Co-transfection of primary hepatocytes revealed a differential sensitivity of the fatty acid synthase, S14, and LPK promoters to nSREBP1c overexpression. Of the three promoters examined, LPK was the least sensitive to overexpressed nSREBP1c. Promoter deletion and gel shift analyses of the S14 promoter localized a functional SREBP1c cis-regulatory element to an E-box-like sequence ((-139)TCGCCTGAT(-131)) within the S14 PUFA response region. Although overexpression of nSREBP1c significantly reduced PUFA inhibition of S14CAT, overexpression of other factors that induced S14CAT activity, such as steroid receptor co-activator 1 or retinoid X receptor alpha, had no effect on S14CAT PUFA sensitivity. These results suggest that PUFA regulates hepatic nSREBP1c, a factor that functionally interacts with the S14 PUFA response region. PUFA regulation of nSREBP1c may account for the PUFA-mediated suppression of hepatic S14 gene transcription.

Cell-specific regulation of transcription of the malic enzyme gene: characterization of cis-acting elements that modulate nuclear T3 receptor activity

Stimulation of malic enzyme transcription by triiodothyronine (T3) is robust (> 60-fold) in chick embryo hepatocytes, weak (5-fold) in chick embryo fibroblasts that stably overexpress the nuclear T3 receptor-alpha, and still weaker (1-fold) in chick embryo fibroblasts which contain nuclear T3 receptor levels that are similar to those of chick embryo hepatocytes. Using DNase I hypersensitivity, functional transfection, and in vitro DNA-binding analyses, four cis-acting elements were identified in the malic enzyme 5'-flanking DNA that conferred differences in nuclear T3 receptor activity between chick embryo hepatocytes and chick embryo fibroblasts. These cell-specific regulatory elements are located at -3895/-3890, -3761/-3744, -3703/-3686, and -3474/-2715 bp and overlap with DNase I hypersensitive sites that are observed in chromatin of chick embryo hepatocytes. Each element enhances T3 responsiveness of the malic enzyme promoter in chick embryo hepatocytes but has no effect on T3 responsiveness in chick embryo fibroblasts. Three of the cell-specific regulatory elements flank a previously identified DNA fragment (-3889 to -3769 bp; Hodnett et al., Arch. Biochem. Biophys. 334, 309-324, 1996) that contains one major and four minor T3 response elements. The cell-specific regulatory element at -3703/-3686 bp binds to the liver-enriched factor, CCAAT/enhancer-binding protein-alpha, whereas cell-specific regulatory elements at -3895/-3890 and -3761/-3744 bp bind proteins of unknown identity. While the cell-specific regulatory element at -3761/-3744 bp contains sequences that resemble binding sites for CCAAT/enhancer-binding protein, activator protein-1, cyclic AMP response element binding protein, and NF-1, none of these proteins appear to bind to this DNA fragment. These data suggest that cell-specific differences in T3 responsiveness of the malic enzyme gene are mediated in large part by nonreceptor proteins that augment the transcriptional activity of the nuclear T3 receptor in hepatocytes.

The CCAAT box binding factor, NF-Y, is required for thyroid hormone regulation of rat liver S14 gene transcription

Triiodothyronine (T3) activates rat liver S14 gene transcription through T3 receptors (TRbeta) binding distal thyroid hormone response elements located between -2.8 and -2.5 kilobase pairs upstream from the transcription start site. Previous studies suggested that proximal promoter elements located between -220 to -80 base pairs upstream from the 5' end of the S14 gene were involved in hormone activation of the S14 gene. This report identifies an inverted CCAAT box (or Y box) at -104ATTGG-100 as a core cis-regulatory element. Gel shift studies using rat liver nuclear proteins show that at least three CCAAT-binding factors interact with this region as follows: NF-Y and c/EBP-related proteins formed major complexes, whereas NF-1/CTF forms a minor complex in gel shift assay. Mutation of the Y box indicated that loss of NF-Y binding, but not c/EBP or NF-1, correlated closely with a decline in basal activity and a loss of T3-mediated transactivation. Substitution of the S14 Y box in reporter genes with elements binding only NF-Y elevated basal activity and T3-mediated transactivation, whereas substitution with elements binding c/EBP-related proteins or SP1 displayed low basal activity and T3-mediated transactivation. These studies indicate that NF-Y and TRbeta functionally interact to confer T3 control to the S14 gene.

Mechanisms by which carbohydrates regulate expression of genes for glycolytic and lipogenic enzymes

Regulation of gene expression by nutrients is an important mechanism in the adaptation of mammals to their nutritional environment. This is especially true for enzymes involved in the storage of energy, such as the lipogenic and glycolytic enzymes in liver and adipose tissue. Transcription of the genes for lipogenic and glycolytic enzymes is stimulated by glucose in adipose tissue, liver, and pancreatic beta-cells. Several lines of evidence suggest that glucose must be metabolized to glucose-6-phosphate to stimulate gene transcription. In adipose tissue, insulin increases the expression of lipogenic enzymes indirectly by stimulating glucose uptake. In the liver, insulin also acts indirectly by stimulating the expression of glucokinase and, hence, by increasing glucose metabolism. Glucose response elements have been characterized for the L-pyruvate kinase and S14 genes. They have in common the presence of a sequence 5'-CACGTG-3', which binds a transcription factor called USF (upstream stimulatory factor). Another glucose response element, which uses a transcription factor named Sp1, has been characterized in the gene for the acetyl-coenzyme A carboxylase. The mechanisms linking glucose-6-phosphate to the glucose-responsive transcription complex are largely unknown.

Peroxisome proliferator-activated receptor alpha inhibits hepatic S14 gene transcription. Evidence against the peroxisome proliferator-activated receptor alpha as the mediator of polyunsaturated fatty acid regulation of s14 gene transcription

The peroxisome proliferator-activated receptor (PPARalpha) has been implicated in fatty acid regulation of gene transcription. Lipogenic gene transcription is inhibited by polyunsaturated fatty acids (PUFA). We have used the PUFA-sensitive rat liver S14 gene as a model to examine the role PPARalpha plays in fatty acid regulation of hepatic lipogenic gene transcription. Both PPARalpha and the potent peroxisome proliferator, WY14643, inhibit S14CAT activity in transfected primary hepatocytes. WY14643 and PPARalpha target the S14 T3 regulatory region (TRR, -2.8 to -2.5 kilobases), a region containing 3 T3 response elements (TRE). Transfer of the TRR to the thymidine kinase (TK) promoter conferred negative control to the TKCAT gene following WY14643 and PPARalpha treatment. Gel shift analysis showed that PPARalpha, either alone or with RXRalpha, did not bind the S14TRR. However, PPARalpha interfered with TRbeta/RXRalpha binding to a TRE (DR+4). Functional studies showed that co-transfected RXRalpha, but not T3 receptor beta1 (TRbeta1), abrogated the inhibitory effect of PPARalpha on S14 gene transcription. These results suggest that WY14643 and PPARalpha functionally interfere with T3 regulation of S14 gene transcription by inhibiting TRbeta1/RXR binding to S14 TREs. Previous studies had established that the cis-regulatory targets of PUFA control were located within the proximal promoter region of the S14 gene, i.e. between -220 and -80 bp. Finding that the cis-regulatory elements for WY14643/PPARalpha and PUFA are functionally and spatially distinct argues against PPARalpha as the mediator of PUFA suppression of S14 gene transcription.

Regulation of lipogenic enzyme expression by glucose in liver and adipose tissue: a review of the potential cellular and molecular mechanisms

Regulation of gene expression by nutrients is an important part of the mechanisms allowing mammals to adapt to their nutritional environment. This is especially true for enzymes involved in the storage of energy such as the lipogenic and glycolytic enzymes in the liver and adipose tissue. We review in the present paper the cellular and molecular mechanisms involved in the regulation of glycolytic and lipogenic enzyme gene expression by glucose. In vivo and in vitro experiments have demonstrated that FAS and ACC gene expression is upregulated by glucose in adipose tissue, FAS, ACC and L-PK expression in the liver and ACC and L-PK expression in a pancreatic beta-cell line. This regulation involves the stimulation of their transcription. In order for glucose to act as a gene inducer, it must be metabolized. In adipose tissue, insulin increases indirectly the expression of FAS and ACC by stimulating glucose metabolism through its well-known effect on glucose transport. In the liver, the action of insulin is also indirect by allowing the expression of glucokinase and hence by increasing glucose metabolism. In the liver, fructose has a potentiating effect on the stimulation of gene expression by glucose through its stimulatory effect on glucokinase activity. Several evidences suggest that glucose-6-phosphate is the signal metabolite: (i) the effect of glucose is mimicked by 2-deoxyglucose (a glucose analogue whose metabolism stops after its phosphorylation by hexokinase) in adipose tissue and beta-cell line but not in the liver in which 2-deoxyglucose-6-phosphate does not accumulate, (ii) intracellular glucose-6-phosphate concentration varies in parallel with ACC, FAS and L-PK mRNA concentrations in liver, adipose tissue and beta-cell line, (iii) in vivo, the kinetics of hexose-phosphate fits with the time-related pattern of gene induction. Glucose response elements have been characterized on three genes, L-PK, S14 (a gene which codes for a protein of unknown function but which is directly related to lipogenesis) and FAS. These glucose response elements have all in common the presence of a sequence 5'-CACGTG-3' which binds a transcription factor of the basic domain, helix-loop-helix, leucine zipper family called USF/MLTF, although the organization of the overall glucose response element probably differs from one gene to another. The mechanisms linking glucose-6-phosphate to the glucose responsive transcription complex are presently largely unknown.

DNase I hypersensitivity sites and nuclear protein binding on the fatty acid synthase gene: identification of an element with properties similar to known glucose-responsive elements

We have shown previously that fatty acid synthase (FAS) gene expression is positively regulated by glucose in rat adipose tissue and liver. In the present study, we have identified in the first intron of the gene a sequence closely related to known glucose-responsive elements such as in the L-pyruvate kinase and S14 genes, including a putative upstream stimulatory factor/major late transcription factor (USF/MLTF) binding site (E-box) (+ 292 nt to + 297 nt). Location of this sequence corresponds to a site of hypersensitivity to DNase I which is present in the liver but not in the spleen. Moreover, using this information from a preliminary report of the present work, others have shown that a + 283 nt to + 303 nt sequence of the FAS gene can confer glucose responsiveness to a heterologous promoter. The protein binding to this region has been investigated in vitro by a combination of DNase I footprinting and gel-retardation experiments with synthetic oligonucleotides and known nuclear proteins. DNase I footprinting experiments using a + 161 nt to + 405 nt fragment of the FAS gene demonstrate that a region from + 290 nt to + 316 nt is protected by nuclear extracts from liver and spleen. This region binds two ubiquitous nuclear factors, USF/MLTF and the CAAT-binding transcription factor/nuclear factor 1 (CTF/NF1). Binding of these factors is similar in nuclear extracts from liver which does or does not express the FAS gene as observed for glucose-responsive elements in the L-pyruvate kinase and S14 genes. This suggests a posttranslational modification of a factor of the complex after glucose stimulation.

Effects of fatty acids on hepatic gene expression

Polyunsaturated fatty acids (PUFA) have dramatic effects on hepatic lipid metabolism by regulating the transcription of specific genes encoding enzymes involved in glycolysis and lipogenesis. The S14 gene, a putative lipogenic protein, has been used as a model to define the molecular basis of PUFA action on hepatic gene expression. We have shown that PUFA-regulated hepatic transcription factors target cis-regulatory elements located between -220 and -80 bp upstream from the 5' end of the S14 gene. Peroxisomal proliferators (PP) also have dramatic effects on hepatic lipid metabolism through effects on gene expression. The mechanism of PP action is mediated, at least in part, through nuclear receptors, i.e. PP activated receptor (PPAR). We found that the potent PP, i.e. WY14,643, suppressed mRNAS14 and the activity of an S14CAT fusion gene in cultured primary hepatocytes. Preliminary mapping studies showed that WY14,643 cis-regulatory elements were located either within the S14 proximal promoter (-290 and +19), the S14 TRE (-2900 to -2500) or both regions. Gel shift analysis showed that PPAR did not bind S14 promoter elements. These studies suggest that PUFA- and PP-regulated factors may share common cis-acting elements within the S14 promoter. However, if PUFA control of S14 gene transcription is mediated by PPAR, this mechanism does not involve direct interaction of PPAR with the S14 proximal promoter.

Polyunsaturated fatty acids inhibit S14 gene transcription in rat liver and cultured hepatocytes

Polyunsaturated fatty acids (PUFAs) have been shown to have significant effects on hepatic lipogenic gene expression. The S14 gene has been used as a model to examine the effects of PUFAs on hepatic lipogenic gene expression. In vivo studies showed that feeding rats a high carbohydrate diet containing menhaden oil rapidly (within hours) and significantly (> or = 50%) attenuates hepatic S14 gene transcription and S14 mRNA abundance. The suppressive effect of menhaden oil was both gene and tissue specific. The effect of PUFAs on expression of the S14 mRNA and a transfected S14 fusion gene (i.e., S14CAT4.3) was examined in cultured hepatocytes in the presence of triiodothyronine (T3), insulin, dexamethasone, and albumin under serum-free conditions. Whereas T3 stimulated both S14 mRNA (> 40-fold) and S14CAT4.3 (> 100-fold), eicosapentaenoic acid (C20:5 omega 3) significantly attenuated (> or = 80%) both S14 mRNA and S14CAT activity in a dose-dependent fashion. The effects of C20:5 on hepatocyte gene expression were both gene and fatty acid specific. Deletion analysis of transfected S14CAT fusion genes indicated that the S14 thyroid hormone response element (at -2.5 to -2.9 kb) was not sensitive to C20:5 control. The cis-linked PUFA response elements were localized to a region within the S14 proximal promoter (at -80 to -220 bp). This region also contains cis-acting elements that potentiate T3 activation of S14 gene transcription. These studies suggest that C20:5 (or its metabolites) regulates factors within the S14 proximal promoter region that are important for T3 activation of S14 gene transcription.

Localization of an adipocyte-specific retinoic acid response domain controlling S14 gene transcription

S14 gene transcription is induced by retinoic acid (RA) in cultured adipocytes, but not preadipocytes. Transfection of 3T3-L1 cells with S14-CAT fusion genes showed that adipocyte-specific RA responsive cis-acting elements are located between -1588 and -1381 bp upstream from the 5' end of the S14 gene. This region has enhancer-like properties. In contrast, an artificial RA response element conferred RA control to a CAT gene in both preadipocyte and adipocyte phenotypes indicating that the RA regulatory network is functional in both phenotypes. These studies show that RA receptors interact with adipocyte-specific transcription factors to control S14 gene expression.

Tissue specificity of S14 and fatty acid synthase in vitro transcription

Hepatic nuclear extracts support in vitro transcription from S14 and fatty acid synthase (FAS) promoters. Renal nuclear extracts support in vitro transcription from S14 promoter constructs at rates comparable to hepatic nuclear extracts, but lack the apparent positive and negative control observed with liver. In contrast, renal nuclear extracts do not support in vitro transcription from the FAS promoter. NF-1 or a related protein in both hepatic and renal extracts contributes to in vitro transcriptional activity from the S14 promoter, but not the FAS promoter. These studies indicate that different mechanisms regulate tissue-specific expression of S14 and FAS.