Interaction of a liver-specific factor with an enhancer 4.8 kilobases upstream of the phosphoenolpyruvate carboxykinase gene

Identification of a transthyretin enhancer site that selectively binds the hepatocyte nuclear factor-3 beta isoform

The upstream proximal region of the transthyretin (TTR) promoter and a distal enhancer are sufficient to drive liver-specific expression of the TTR gene, as demonstrated by experiments in transgenic mice. Previous analyses have characterized the binding of a number of liver-enriched transcription factors of the TTR promoter including hepatocyte nuclear factors one (HNF-1), HNF-4, and three distinct HNF-3 proteins (alpha, beta, and gamma), which are members of the winged helix (fork head) family. The TTR enhancer was shown to bind members of the CCAAT/enhancer binding protein (C/EBP) family at two distinct sites (TTR-2 and TTR-3), and an oligonucleotide containing the activation protein one (AP-1) binding sequence competed for recognition to a third enhancer site (TTR-1). In this study, we have carried out a detailed analysis of the transcription factors that recognize the TTR enhancer elements (TTR-1, TTR-2, and TTR-3 oligonucleotide sequences). Analysis of the TTR-1 site demonstrates that the putative AP-1 site in the TTR enhancer binds a ubiquitously expressed factor that is distinct from the AP-1 family of proteins. Next we demonstrate, via gel shift analysis, that the TTR-3 site is recognized by the C/EBP family in liver nuclear extracts. We also show that whereas the TTR-2 enhancer site is capable of binding recombinant C/EBP proteins, it does not bind C/EBP proteins from liver nuclear extracts. The TTR-2 site does, however, contain a variant HNF-3 recognition sequence that exclusively binds the HNF-3 beta isoform. Mutation of this HNF-3 beta-specific recognition sequence caused reductions in TTR enhancer activity. We had previously observed a 95% decrease in HNF-3 alpha expression and a 20% reduction in HNF-3 beta expression in acute phase livers, which correlated with a 60% decrease in TTR gene transcription. We propose that the HNF-3 beta-specific binding site in the TTR enhancer may play a role in maintaining TTR gene expression during the acute phase response in spite of the dramatic reduction in HNF-3 alpha protein levels.

Pathophysiologic role of hepatocyte nuclear factor 6

Hepatocyte nuclear factor 6 (HNF6) is one of liver-enriched transcription factors. HNF6 utilizes the bipartite onecut-homeodomain sequence to localize the HNF6 protein to the nuclear compartment and binds to specific DNA sequences of numerous target gene promoters. HNF6 regulates an intricate network and mediates complex biological processes that are best known in the liver and pancreas. The function of HNF6 is correlated to cell proliferation, cell cycle regulation, cell differentiation and organogenesis, cell migration and cell-matrix adhesion, glucose metabolism, bile homeostasis, inflammation and so on. HNF6 controls the transcription of its target genes in different ways. The details of the regulatory pathways and their mechanisms are still under investigation. Future study will explore HNF6 novel functions associated with apoptosis, oncogenesis, and modulation of the inflammatory response. This review highlights recent progression pertaining to the pathophysiologic role of HNF6 and summarizes the potential mechanisms in preclinical animal models. HNF6-mediated pathways represent attractive therapeutic targets for the treatment of the relative diseases such as cholestasis.

The Fox genes in the liver: from organogenesis to functional integration

Formation and function of the liver are highly controlled, essential processes. Multiple signaling pathways and transcriptional regulatory networks cooperate in this complex system. The evolutionarily conserved FOX, for Forkhead bOX, class of transcriptional regulators is critical to many aspects of liver development and function. The FOX proteins are small, mostly monomeric DNA binding factors containing the so-called winged helix DNA binding motif that distinguishes them from other classes of transcription factors. We discuss the biochemical and genetic roles of Foxa, Foxl1, Foxm1, and Foxo, as these have been shown to regulate many processes throughout the life of the organ, controlling both formation and function of the liver.

Role of hepatocyte nuclear factor 3γ in the expression of human CYP2C genes

Hepatocyte nuclear factor 3 gamma (HNF-3 gamma) is an important transcription factor for the maintenance of specific liver functions. However, its relevance in the expression of human cytochrome P450 (CYP) genes has not yet been explored. Several HNF3 putative binding sites can be identified in human CYP2C 5'-flanking regions. Gene reporter experiments with proximal promoters revealed that HNF-3 gamma transactivated CYP2C8, CYP2C9, and CYP2C19 (25-, 4-, and 4-fold, respectively), but it did not transactivate CYP2C18. However, overexpression of HNF-3 gamma in hepatoma cells by means of a recombinant adenovirus induced CYP2C9, CYP2C18, and CYP2C19 mRNA (4.5-, 20-, and 50-fold, respectively) but did not activate endogenous CYP2C8. The lack of effect of HNF-3 gamma on endogenous CYP2C8 could be reversed by treating cells with the deacetylase inhibitor, trichostatin A, suggesting the existence of chromatin condensation around functional HNF3 elements in this gene. We conclude that HNF3 gamma is an important transcription factor for the hepatic-specific expression of human CYP2C genes. Our results also evidence that efficient transfection tools, such as adenoviral vectors, may be decisive for assessing the role of transcription factor on chromatin organized genes.

Trefoil factors: initiators of mucosal healing

Maintaining the integrity of the gastrointestinal tract, despite the continual presence of microbial flora and injurious agents, is essential. Epithelial continuity depends on a family of small, yet abundant, secreted proteins--the trefoil factors (TFFs). TFFs protect mucous epithelia from a range of insults and contribute to mucosal repair, although the signalling events that mediate these responses are only partially understood.

Repression and activation of transcription of phosphoenolpyruvate carboxykinase gene during liver development

Transcriptional activation of the hepatic phosphoenolpyruvate carboxykinase (PEPCK) gene at birth is critical since PEPCK appearance initiates hepatic gluconeogenesis. A delayed appearance results in hypoglycemia, while a premature appearance results in neonatal diabetes, both are incompatible with sustaining life. Experiments using transgenic mice and transfected hepatoma cells suggest that both repression and activation underlie the correct onset of hepatic PEPCK gene transcription. In transgenic mice, transgenes driven by the proximal PEPCK promoter are prematurely expressed in the fetal liver and over-expressed in the neonatal liver, indicating that sequences upstream of the proximal promoter restrain perinatal expression. In Hepa1c1c7 cells, which mimic the fetal liver, the proximal PEPCK promoter (597 bp) exhibited a 3. 5-10-fold higher activity than longer promoters. Repression of the longer promoter (2000 bp) was diminished upon deletion of the sequence spanning positions(-840) to(- 1116) which contains a PPAR/RXR recognition element. The intact 2000 bp PEPCK promoter could be markedly activated by co-transfecting the transcription factor HNF-1 together with C/EBP. It could be repressed by co-transfection with RXRalpha and adding PPARalpha relieved this inhibition.

Characterization of a kidney-specific pattern of chromatin structure in the rat phosphoenolpyruvate carboxykinase gene

The kidney-specific chromatin structure of the phosphoenolpyruvate carboxykinase (PEPCK) gene was examined and compared to that of the liver. Kidney nuclear extracts were found to lack a liver-enriched factor, pepA, that binds to HSS A, a distal enhancer of the PEPCK gene that may be involved in opening the chromatin domain of the PEPCK gene in the liver. To begin the characterization of the kidney-specific chromatin structure of the PEPCK gene, nuclease hypersensitive sites (HSS) were mapped by indirect end-labeling analysis in proximal tubules from control rats, proximal tubules from acidotic rats which express induced levels of PEPCK, and NRK52E cells, a rat kidney epithelial cell line which does not express the PEPCK gene. A subset of HSS, at -400/+1 over the proximal promoter and at +1900 within the coding region, correlate with kidney-specific PEPCK expression. Two other HSS, at -3.1 kb and +6.2 kb, are detected in kidney cells regardless of PEPCK expression. The HSS at -4800, -1240, and +4650, previously identified in PEPCK-expressing liver cells, were not observed in the kidney. As in the liver, the pattern of hypersensitivity in the kidney does not change by altering the rate of transcription.

Adipose expression of the phosphoenolpyruvate carboxykinase promoter requires peroxisome proliferator-activated receptor gamma and 9-cis-retinoic acid receptor binding to an adipocyte-specific enhancer in vivo

A putative adipocyte-specific enhancer has been mapped to approximately 1 kilobase pair upstream of the cytosolic phosphoenolpyruvate carboxykinase (PEPCK) gene. In the present study, we used transgenic mice to identify and characterize the 413-base pair (bp) region between -1242 and -828 bp as a bona fide adipocyte-specific enhancer in vivo. This enhancer functioned most efficiently in the context of the PEPCK promoter. The nuclear receptors peroxisome proliferator-activated receptor gamma (PPARgamma) and 9-cis-retinoic acid receptor (RXR) are required for enhancer function in vivo because: 1) a 3-bp mutation in the PPARgamma-/RXR-binding element centered at -992 bp, PCK2, completely abolished transgene expression in adipose tissue; and 2) electrophoretic mobility supershift experiments with specific antibodies indicated that PPARgamma and RXR are the only factors in adipocyte nuclear extracts which bind PCK2. In contrast, a second PPARgamma/RXR-binding element centered at -446 bp, PCK1, is not involved in adipocyte specificity because inactivation of this site did not affect transgene expression. Moreover, electrophoretic mobility shift experiments indicated that, unlike PCK2, PCK1 is not selective for PPARgamma/RXR binding. To characterize the enhancer further, the rat and human PEPCK 5'-flanking DNA sequences were compared by computer and found to have significant similarities in the enhancer region. This high level of conservation suggests that additional transcription factors are probably involved in enhancer function. A putative human PCK2 element was identified by this sequence comparison. The human and rat PCK2 elements bound PPARgamma/RXR with the same affinities. This work provides the first in vivo evidence that the binding of PPARgamma to its target sequences is absolutely required for adipocyte-specific gene expression.

Variable expression of hepatic glucokinase in mice is due to a regulational locus that cosegregates with the glucokinase gene

The Gk activity locus affects expression of hepatic glucokinase (GK) in mice. Analysis of microsatellites within the mouse GK gene locus revealed two major haplotypes in 19 of 22 inbred strains predictive of either high or low hepatic GK gene expression. C3H/HeJ mice, a high-activity strain, and two other wild-derived strains contain less common haplotypes. No coding sequence differences were found in hepatic GK-coding sequences from representative high and low Gk activity strains, thereby excluding kinetic abnormalities as the basis for hepatic GK activity differences. Screening of approximately 10 kb of potential regulatory DNA, including all eight known and three of four newly identified DNase I-hypersensitive sites, by restriction enzyme fingerprinting-single-strand conformation analysis revealed a tetranucleotide microsatellite, the length of which was also predictive of the Gk activity phenotype. This tetranucleotide repeat is located in the first intron of the hepatic transcription unit and lies close to a newly identified liver-specific DNase I-hypersensitive site. These results indicate that the Gk activity alleles are a regulational locus associated with the GK gene locus.

Characterization of a specific region in the hepatitis B virus enhancer I for the efficient expression of X gene in the hepatic cell

Hepatitis B virus (HBV) enhancer I has been shown to consist of several cis-acting sequences for the HBV gene expression efficiently in certain types of cells. Transcriptional regulation of HBV X gene mediated by enhancer I might be one of the mechanisms by which HBV obtains hepatotropism. By mutagenesis analysis of enhancer I function in the enhancer I/X gene promoter complex, we characterized a specific transcriptional regulatory region (designated as a LSR element, nt 989-1030) of enhancer I for the X gene promoter by means of the transient transfection technique using hepatic and nonhepatic cells. Based on the analysis of protein factors interacting with the LSR element, liver-enriched transcriptional factors, HNF3 and HNF4 or retinoid X receptor alpha (RXR alpha), are probably implicated in the activity of enhancer I for the efficient expression of X gene through their interaction with the LSR element in the hepatic cell. Furthermore, the isolated LSR element was demonstrated to function alone as a specific cis-acting element and to be able to activate transcription from the X gene promoter efficiently in the hepatic cell in an orientation-independent manner.

The hepatocyte nuclear factor 3beta stimulates the transcription of the human insulin-like growth factor I gene in a direct and indirect manner

Promoter 1 (P1) of the human insulin-like growth factor I (IGF-I) gene is most active in adult liver. In this study we show that HNF-3beta, a member of the winged helix protein family of liver-enriched transcription factors, has a strong stimulatory effect on the activity of P1. Transient transfection experiments in combination with bandshift and DNase I footprinting analysis revealed the presence of two HNF-3 binding sites in the proximal promoter region of P1. Both binding sites, which are well conserved in evolution, are required for maximal transactivation. Studies employing HNF-3 mutant constructs indicated that IGF-I expression is also regulated indirectly by HNF-3beta as a consequence of enhanced expression of HNF-1alpha. This liver-enriched transcription factor has previously been shown to transactivate P1. Thus, HNF-3beta regulates the expression of the human IGF-I gene via two distinct mechanisms.

Five years on the wings of fork head

Since its discovery five years ago the conserved family of fork head/HNF-3-related transcription factors has gained increasing importance for the analysis of gene regulatory mechanisms during embryonic development and in differentiated cells. Different members of this family, which is defined by a conserved 110 amino acid residues encompassing DNA binding domain of winged helix structure, serve as regulatory keys in embryogenesis, in tumorigenesis or in the maintenance of differentiated cell states. The purpose of this review is to summarize the accumulating amount of data on structure, expression and function of fork head/HNF-3-related transcription factors.

The hepatocyte nuclear factor-3/forkhead transcription regulatory family in development, inflammation, and neoplasia

HNF-3/FKH genes are a large family of transcriptional activators. They are expressed in specific developmental and tissue patterns. Indeed, several of them are known to be essential for normal development (e.g. Dfkh and slp-1,2). Mutation within one of these genes produces mutant fruitfly embryos that are unable to survive. This family shares conserved DNA binding and transcriptional activation domains. The DNA binding domain has been crystallized, and its structure determined. Although it has resemblance to helices of homeodomains and H5 histones, it represents a new DNA binding motif, which has been called the 'winged helix,' because it contains additional interactive peptide regions called termed wings. Subtle amino acid variations in a region adjacent to the DNA recognition helix influence the recognition specificity of each HNF-3/FKH protein and therefore confer selectivity in promoter regulation. Members of this family are important in regulating the inflammatory response of the liver (the three HNF-3 genes). In addition, several members may be important in blood cell development (H3 and 5-3). Finally, two of these genes have been found to produce neoplasia (qin and FKHR). As investigation progresses, the mechanism by which these genes regulate development, inflammation and neoplasia will become more clear.

Transient inhibition of angiotensinogen production in transgenic mice bearing an antisense angiotensinogen gene

Angiotensinogen is the precursor of the biologically active hormone angiotensin II. Enzyme kinetic parameters suggest that concentrations of plasma angiotensinogen are rate limiting in the renin reaction. It is therefore assumed that a decrease in angiotensinogen synthesis in vivo would result in a decrease in angiotensin II plasma levels and then of blood pressure. To test this hypothesis, we generated a transgenic mouse line that carries an inducible antisense angiotensinogen gene. Transient inhibition of angiotensinogen synthesis could be demonstrated in these transgenic animals. However, the amounts of liver angiotensinogen message and plasma angiotensinogen concentrations were rapidly back to levels observed in control animals.

DNA recognition site analysis of Xenopus winged helix proteins

DNA binding proteins of the winged helix family contain a conserved 110 amino acid region, the fork head/HNF-3 domain. Three members of the recently described XFD (Xenopus fork head domain related) multigene family in the frog Xenopus laevis that contain this DNA-binding domain have been studied. We determined the in vitro DNA recognition sequences by means of two independent methods: PCR supported site selection with degenerated deoxyoligonucleotides and affinity chromatography of genomic Xenopus DNA fragments. In contrast to a remarkable sequence divergence within their protein sequence of the fork head domains, all three proteins share a similar 7 bp DNA target motif. The protein-DNA interaction has been studied by means of DMS interference and hydroxyl radical footprinting. A region of 18 bp encompassing the 7 bp target motif is sufficient to confer binding and specificity. The specificity of binding could be attributed on the DNA level to residues located 5' to the 7 bp core region, and on the protein level most likely to a region within the first half of the fork head domain. The possible role of specific nucleotides within the target site in binding the protein is discussed in the context of the current crystal structure of the complex of this domain with DNA.

Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5

The three-dimensional structure of an HNF-3/fork head DNA-recognition motif complexed with DNA has been determined by X-ray crystallography at 2.5 A resolution. This alpha/beta protein binds B-DNA as a monomer, through interactions with the DNA backbone and through both direct and water-mediated major and minor groove base contacts, inducing a 13 degrees bend. The transcription factor fold is very similar to the structure of histone H5. In its amino-terminal half, three alpha-helices adopt a compact structure that presents the third helix to the major groove. The remainder of the protein includes a twisted, antiparallel beta-structure and random coil that interacts with the minor groove.

Multiple elements regulate phosphoenolpyruvate carboxykinase gene expression in hepatoma hybrid cells

The phosphoenolpyruvate carboxykinase (PEPCK) gene is highly expressed in cultured rat hepatoma cells, but extinguished in hepatoma x fibroblast hybrids. Extinction of PEPCK gene expression in hybrids is a polygenic process that involves several fibroblast loci, only one of which (tissue-specific extinguisher-1, TSE1) has been characterized to date. To identify sequence elements of the PEPCK gene that are involved both in TSE1-mediated extinction and in TSE1-independent processes, we assayed expression of chimeric PEPCK transgenes in transiently and stably transfected hybrid cells. We report that TSE1 responsiveness mapped to the PEPCK CRE (cAMP response element), as shown previously for the tyrosine aminotransferase gene. This was expected from the recent identification of the TSE1 gene product as a regulatory subunit of protein kinase A. However, none of the transgenes we assayed were responsive to TSE1-independent extinction mechanisms, suggesting that these controls require DNA sequences and/or chromatin structures that were not present in the transfected reporters. The implications of these findings are discussed.

Non-random distribution and co-localization of purine/pyrimidine-encoded information and transcriptional regulatory domains

In order to detect sequence-based information predictive for the location of eukaryotic transcriptional regulatory domains, the frequencies and distributions of the 36 possible purine/pyrimidine reverse complement hexamer pairs was determined for test sets of real and random sequences. The distribution of one of the hexamer pairs (RRYYRR/YYRRYY, referred to as M1) was further examined in a larger set of sequences (> 32 genes, 230 kb). Predominant clusters of M1 and the locations of eukaryotic transcriptional regulatory domains were found to be associated and non-randomly distributed along the DNA consistent with a periodicity of approximately 1.2 kb. In the context of higher ordered chromatin this would align promoters, enhancers and the predominant clusters of M1 longitudinally along one face of a 30 nm fiber. Using only information about the distribution of the M1 motif, 50-70% of a sequence could be eliminated as being unlikely to contain transcriptional regulatory domains with an 87% recovery of the regulatory domains present.

Transcriptional regulation of liver-specific gene expression

Liver-specific gene expression is regulated by four families of transcriptional activatory proteins that are not liver-specific, but are still restricted to a subset of tissues. The current opinion is that liver-specificity is a consequence of the combinatorial action of these factors, which could represent 'functional compartments' coexisting in the hepatocyte.

Regulation of phosphoenolpyruvate carboxykinase (GTP) gene transcription

Transcription of the gene for phosphoenolpyruvate carboxykinase is regulated by several hormones which control the level of glucose synthesis in vertebrate animals. A 490 bp segment located at the 5' end of the structural gene contains the necessary regulatory elements to account for the pattern of transcriptional regulation characteristic of the phosphoenolpyruvate carboxykinase gene. Multiple cis binding sites within the promoter and nuclear binding proteins have been identified and shown to play a role in the regulation of gene transcription. The interaction of these transcription factors with each other and with the phosphoenolpyruvate carboxykinase promoter is central to the regulated expression of this gene. The key role of cAMP and insulin in controlling the level of gene transcription will be discussed and related to the function of transcription factors currently known to regulate the tissue specific expression of the phosphoenolpyruvate carboxykinase gene.

Genomic organization of the rat aromatic L-amino acid decarboxylase (AADC) locus: partial analysis reveals divergence from the Drosophila dopa decarboxylase (DDC) gene structure

Aromatic L-amino acid decarboxylase (AADC) is responsible for the conversion of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan to dopamine and serotonin, respectively, which are important neurotransmitters. We characterized genomic clones derived from the rat AADC locus by Southern blot and nucleotide sequencing analyses to explore the exonal organization of the gene. Our results suggest that the rat AADC gene is relatively large, containing at least 12 exons and spanning at least 40 kb in the rat genome. In this study, nine exons corresponding to 71% of the published cDNA sequence were identified, the smallest of which was as short as 20 base pairs (bp). In the Drosophila dopa decarboxylase (DDC) gene, the sequences homologous to these nine exons are all present in the fourth exon. This implies that either multiple intron sequences have been added to the vertebrate AADC gene or alternatively, deleted from the invertebrate gene after the divergence of vertebrates and invertebrates during evolution.

Cell-specific accumulation of maize phosphoenolpyruvate carboxylase is correlated with demethylation at a specific site greater than 3 kb upstream of the gene

Development of the C4 photosynthetic pathway relies upon the cell-specific accumulation of photosynthetic enzymes. Although the molecular basis of this cell-specific gene expression is not known, regulation appears to be exerted at the level of transcript accumulation. We have investigated the relationship between gene expression patterns and DNA methylation for genes of two of the C4 photosynthetic enzymes, ribulose bisphosphate carboxylase (RuBPCase) and phosphoenolpyruvate carboxylase (PEPCase). We found no correlation between methylation state and gene expression for either the large subunit or a small subunit gene of RuBPCase. In contrast, demethylation of a specific site 5' to the PEPCase gene was correlated with the light-induced, cell-specific accumulation of PEPCase mRNA. This differentially methylated site is positioned at great distance (greater than 3 kb) from the start of transcription. This observation is made more interesting by the fact that the immediate 5' region of the gene, and some of the coding region, represents an unmethylated CpG island. Such islands are normally associated with constitutively expressed genes.