Positive and negative regulation of a transfected chimeric tyrosine aminotransferase gene: effect of copy number

Intestinal expression of the calbindin-D9K gene in transgenic mice. Requirement for a Cdx2-binding site in a distal activator region

The calbindin-D9K gene encodes a vitamin D-induced calcium-binding protein that is expressed as a marker of small intestine differentiation. We have shown that 4580 base pairs of its 5' DNA regulatory region can target reporter transgene expression in the intestine and cause this transgene to respond like the endogenous gene to vitamin D active metabolite and that the homeoprotein Cdx2 is bound to the TATA box in the intestine. We now show that the 4580 base pairs construct confers a differentiated pattern of reporter transgene expression in the intestine and that cooperation between the proximal promoter and a distal element located in an opened chromatin structure is responsible for the intestinal expression and vitamin D responsiveness of the transgene. Gel shift and footprinting assays using duodenal nuclear extracts indicate that this distal element contains a Cdx2-binding site. Finally, a mutation in this distal Cdx2-binding site dramatically decreases intestinal expression in transgenic mice. This report, using an in vivo approach, demonstrates the crucial role of Cdx2 for the transcription of an intestinal gene.

Tissue specificity of a glucocorticoid-dependent enhancer in transgenic mice

The glucocorticoid-responsive units (GRUs) of the rat tyrosine aminotransferase were associated with the regulatory sequences of a cellular gene expressed ubiquitously--that coding for the largest subunit of RNA polymerase II. In transient expression assays, glucocorticoid responsiveness of the hybrid regulatory regions depends on the spatial relationship and number of regulatory elements. Two parameters affect the ratio of induction by glucocorticoids: the basal level of the hybrid promoter that is affected by the RNA polymerase II regulatory sequences and the glucocorticoid-induced level that depends on the distance between the GRUs and the TATA box. A fully active glucocorticoid-responsive hybrid gene was used to generate transgenic mice. Results show that a composite regulatory pattern is obtained: ubiquitous basal expression characteristic of the RNA polymerase II gene and liver-specific glucocorticoid activation characteristic of the tyrosine aminotransferase GRUs. This result demonstrates that the activity of the tyrosine aminotransferase GRUs is cell-type-specific not only in cultured cells but also in the whole animal.

Hepatocyte nuclear factor 3 determines the amplitude of the glucocorticoid response of the rat tyrosine aminotransferase gene

Hepatocyte nuclear factor 3 (HNF3) recognizes two apparently distinct classes of sequence. However, a detailed mutational analysis of a representative binding site of each class reveals that these sequences display common features. We propose a unified consensus sequence for HNF3-binding sites. The basis of the sequence specificity of the interaction of HNF3 with DNA is analyzed in light of the recently determined structure of an HNF3-DNA complex (Clark et al., Nature 364, 412-420, 1993). Particularly, our study reveals that the DNA site used for this structural analysis is too short to account for all HNF3-DNA interactions. The better knowledge of the sequence determinant recognized by HNF3 has allowed us to analyze its function in the glucocorticoid response of the rat tyrosine aminotransferase (TAT) gene. This response is mediated through a complex array of neighboring and overlapping transcription factor binding sites. Selective inactivation of the HNF3-binding sites in this glucocorticoid response unit (GRU) allows us to demonstrate unambiguously that they play a major role in the amplitude of the glucocorticoid response. Furthermore, HNF3 beta overexpression results in a stimulation of the glucocorticoid response that is dependent on the integrity of its binding sites. We also show that the relative level of HNF3 determines the extent of the contribution of one of the glucocorticoid receptor binding sites. Our results indicate that HNF3 accounts for most of the liver-specific activity of this GRU.

The inductive effect of a human DNA sequence (HALF1) on the differentiation of a variant rat hepatoma cell (C2) is restricted to episomal forms of the molecule

HALF1, a 4.3 kb human DNA sequence, was originally identified as a double-stranded, closed-circular DNA molecule in revertants from a dedifferentiated rat hepatoma cell (C2) transfected with human liver DNA. Here we report its specific properties in inducing the transition to the hepatic phenotype. (i) In vitro recircularized HALF1 induces reversion after a minimum time lag of 7 days post-transfection. (ii) After induction, the presence of HALF1 is not required for maintaining the induced hepatic state. (iii) HALF1 is detected as a sequence integrated in high molecular mass DNA of human liver. (iv) HALF1 monomer or dimer plasmid constructs do not induce reversion when integrated into the genome of transfectants. (v) Short ubiquitous RNA transcripts (approximately 400 bases) are detected with specific HALF1 probes. These results indicate that the reversion process is linked to the presence of HALF1 extrachromosomal molecules.

Expression from the tyrosine aminotransferase promoter (nt -350 to +1) is liver-specific and dependent on the binding of both liver-enriched and ubiquitous trans-acting factors

The rat tyrosine aminotransferase(TAT) gene promoter (nucleotides -350 to +1; TAT0.35) was able to sustain liver-specific expression both ex vivo in transient transfection (TAT-expressing H411EC3 hepatoma cells vs. TAT non-expressing CCL1.2 fibroblasts) and in in vitro transcription (rat liver vs. spleen crude nuclear extracts). In either case, the index of tissue specificity (6.2 and 6.7 in ex vivo and in vitro experiments, respectively) was close to that obtained with 10 Kb of TAT gene 5'-flanking sequences in transient transfection. Using computer-assisted search of homologies, DNase I footprinting, gel retardation and methylation interference assays, we showed that TAT0.35 sequences spanning nt -156 to -175 and nt -268 to -281 interacted with the liver enriched NF-1Liver (a member of the NF1 gene family) and HNF1 respectively, whereas those encompassing nt -57 to -85 and nt -283 to -288 interacted with the ubiquitous NF-Y and with ubiquitous 'CCAAT'-box binding factor(s), respectively. Competition studies in in vitro transcription carried out with wild type and mutated oligonucleotides, demonstrated that NF-Y cis-elements were crucial for basal TAT promoter activity, both in liver and spleen whereas NF1Liver and HNF1 were only efficient in the liver (supported approximately 60% and 30% of basal TAT0.35 activity respectively). Altogether, these results support the conclusion that TAT0.35 was able to sustain at least part of the liver specificity of TAT gene expression.

Differential expression of tyrosine aminotransferase by glucocorticoids and insulin

The differential response of the tyrosine aminotransferase (TAT) gene to glucocorticoids and insulin in HTC cells and cell clones derived from Reuber H35 cells (FaO and Fu5.5) have been analyzed by nuclear run-on assay. It has been previously shown that clones of cells from HTC and Reuber H35 cell lines, exhibit different sensitivities for the induction of TAT mRNA and enzyme activity. The purpose of the present study was to determine whether this difference in TAT expression between hepatocytes and hepatoma cell lines occurs at the level of TAT gene transcription or mRNA stability. A study of the TAT mRNA accumulation in all cell types showed that TAT mRNA in the Reuber H35 cell clones and hepatocytes was synthesized at a higher rate than in HTC cells. However, dexamethasone induction of alpha 1 AGP mRNA and glutamine synthetase was comparable to glucocorticoid bound receptors. In addition, cycloheximide decreased the rate at which induced levels of TAT mRNA were degraded. We also show that a heterologous fusion gene constructed from 3.0 kilobases (kb) 5' to the transcription initiation site of the rat TAT gene and the bacterial chloramphenicol acetyltransferase gene (CAT) responds similarly to dexamethasone in Fu5.5 and HTC cells as determined by transient transfection assay; and insulin inhibits dexamethasone mediated transcription in Reuber H35 cells and primary adult hepatocytes. These data indicate that DNA sequences involved in the differential response of the TAT gene to hormone treatments between HTC and Reuber H35 cell lines are not located in the first 3.0 kb fragment.

Cloning of a human DNA sequence that restores expression of hepatic functions in a dedifferentiated rat hepatoma cell

In a study of the regulation of gene expression in liver cells, a strain of dedifferentiated cells (C2) derived from the rat hepatoma line H4IIEC3 was transfected with DNA from human liver. After growth of these C2 variants in a glucose-free medium, revertants were selected which were characterized by the expression of a complete set of liver functions. A 4.3 kb human DNA sequence was detected with an Alu sequence probe in cells of four independent revertant clones and was shown to be an extrachromosomal, covalently closed duplex DNA. This molecule, called HALF1 for reversion inducing sequence, was cloned and transfected into C2 cells. Analyses of the transfectants indicated a correlation between the introduction of this cloned genomic human DNA sequence and the recovery of hepatic traits.

Cell-type specific activity of two glucocorticoid responsive units of rat tyrosine aminotransferase gene is associated with multiple binding sites for C/EBP and a novel liver-specific nuclear factor

The structures of two remote glucocorticoid responsive units (GRUs) that cooperatively interact to promote cell-type specific glucocorticoid induction of rat tyrosine aminotransferase gene expression have been analyzed. DNAase I footprinting and gel mobility shift analyses reveal a complex array of contiguous and overlapping sites for cell type-specific DNA binding proteins. Apart from the glucocorticoid receptor, two liver-specific nuclear factors possess multiple binding sites in each of these GRUs: C/EBP and a newly identified liver-specific factor: HNF5. C/EBP possesses four binding sites in each GRU; a DNA-binding protein with similar binding specificity has been identified in fibroblasts; this protein could be related to AP-3. HNF5 possesses two binding sites in one GRU and four in the other. There are also HNF5 binding sites in numerous regulatory regions of other liver-specific genes. The interaction of HNF5 with DNA gives a characteristic DNAase I footprint with hypersensitive sites in the middle of the recognition sequence. Some of the C/EBP and HNF5 binding sites overlap in a conserved arrangement.

Chromatin structure of hormono-dependent promoters

Transient transfections of mutated MMTV LTRs, driving the luciferase reporter gene, have shown the presence of at least one cis-acting element cooperating with the GREs. Studies of the chromatin structure of two glucocorticoid-regulated promoters, the mouse mammary tumor virus (MMTV) long terminal repeat (LTR), a retroviral promoter, and the rat tyrosine aminotransferase (TAT) promoter, demonstrate that both DNAs are organized into precisely positioned nucleosomes. Hormonal activation of transcription is accompanied by structural changes of one (MMTV LTR) or two (TAT promoter) nucleosomes associated with the hormone-response elements (HREs). These changes can be visualized by the appearance of DNasel hypersensitive sites. Association of the hormone-receptor complex with the nucleus is necessary to induce the DNasel hypersensitive site and to maintain transcription, but is not necessary to maintain DNasel hypersensitivity. Anti-hormones, even when able to promote a strong binding of the receptor to the nucleus, are unable to induce the chromatin structural change. Using cell lines containing approx. 200 copies of a MMTV LTR/Hv-ras chimeric construct, we have demonstrated a strong, hormono-independent nuclear matrix interaction of sequences located just upstream and downstream of the ras coding sequences.

Glucocorticoids locally disrupt an array of positioned nucleosomes on the rat tyrosine aminotransferase promoter in hepatoma cells

Transcriptional activation by steroid hormones is often associated with the appearance of a DNase I hypersensitive site resulting from a local alteration of the nucleoprotein structure of the promoter. For the mouse mammary tumor virus long terminal repeat, a viral promoter under glucocorticoid control, a model has been proposed: the appearance of the hormonodependent DNase I hypersensitive site reflects the displacement of a single precisely positioned nucleosome associated with the glucocorticoid responsive elements. To determine if such a mechanism is of general relevance in transcriptional activation by steroid hormones, we have investigated the nucleosomal organization of the rat tyrosine aminotransferase promoter over a 1-kilobase region that contains the glucocorticoid regulatory target. This region displays a hormonodependent DNase I hypersensitive site. In the absence of hormone, micrococcal nuclease digestion of nuclei demonstrates the presence of positioned nucleosomes, with cutting sites centered around positions -3080, -2900, -2700, -2800, -2255, and -2040. Treatment of the cells with dexamethasone induces a disruption of the chromatin structure over a relatively short stretch of DNA (approximately positions -2400 to -2650) that overlaps two nucleosomes. These observations suggest a strong similarity in the role of chromatin structure in glucocorticoid-dependent transcriptional activation of mouse mammary tumor virus and tyrosine aminotransferase promoters.

Two remote glucocorticoid responsive units interact cooperatively to promote glucocorticoid induction of rat tyrosine aminotransferase gene expression

Tyrosine aminotransferase (TAT) gene transcription is specifically activated by glucocorticoid hormones in liver cells. This regulation involves a glucocorticoid responsive region located 2,500 bases upstream from the transcription start site of the rate gene. By transient transfection of TAT-CAT fusion genes into a rat hepatoma cell line expressing the TAT gene we found that this region promotes only 30% of the glucocorticoid stimulation. We have identified a new cis-acting region far upstream (-5,400) from the transcription start site that is essential to achieve the physiological level of glucocorticoid stimulation of endogenous TAT gene expression. This region corresponds to a tissue-specific DNAse I hypersensitive site which is constitutive despite the fact it possesses a glucocorticoid receptor binding site. It is by itself almost inactive on a promoter but it cooperatively enhances the action of the proximal glucocorticoid responsive region. Its activity requires both the glucocorticoid receptor binding site and its flanking sequences.