Control of eukaryotic messenger RNA synthesis by sequence-specific DNA-binding proteins

A novel plant cysteine protease has a dual function as a regulator of 1-aminocyclopropane-1-carboxylic Acid synthase gene expression

The hormone ethylene influences plant growth, development, and some defense responses. The fungal elicitor Ethylene-Inducing Xylanase (EIX) elicits ethylene biosynthesis in tomato (Lycopersicon esculentum) and tobacco (Nicotiana tabacum) leaves by induction of 1-aminocyclopropane-1-caboxylic acid synthase (Acs) gene expression. A minimal promoter element in the LeAcs2 gene required for EIX responsiveness was defined by deletion analysis in transgenic tomato plants. The sequence between -715 and -675 of the tomato Acs2 gene was found to be essential for induction by EIX. A Cys protease (LeCp) was isolated that specifically binds to this cis element in vitro. Ectopic expression of LeCp in tomato leaves induced the expression of Acs2. Moreover, chromatin immunoprecipitation showed that LeCp binds in vivo to the Acs promoter. We propose a mechanism for the dual function of the LeCp protein. The protease acts enzymatically in the cytoplasm. Then, upon signaling, a small ubiquitin-related modifier protein binds to it, enabling entrance into the nucleus, where it acts as a transcription factor. Thus, LeCp can be considered a dual-function protein, having enzymatic activity and, upon elicitor signaling, exhibiting transcriptional factor activity that induces LeAcs2 expression.

Molecular cloning and characterization of gene for Golgi-localized syntaphilin-related protein on human chromosome 8q23

Loci for several human genetic diseases including glaucoma have been mapped to q23 region on chromosome 8. We carried out homology search analysis of the genomic sequence of a bacterial artificial chromosome (BAC) clone, KB1590E11, on 8q23 region, and mapped a previously described cDNA, KIAA1472, to this BAC clone. In this study, we determined the complete genomic structure of the KIAA1472 gene and its expression in various tissues and cell lines. Four mRNA species (types 1a, 1b, 1c, and 2) were produced from this gene by use of alternative transcription start sites and alternative-splicing events. These mRNAs were expressed in various tissues, except for type 1a, which was found only in the brain. Further, type 1 mRNA could be translated into two protein isoforms with different N-terminal sequences; and type 2 mRNA, into another type of isoform. All three of these KIAA1472 gene products were localized in Golgi apparatus and contained a C-terminal hydrophobic segment characteristic of a transmembrane domain, thus indicating them to be Golgi membrane-bound proteins. Furthermore, these proteins were homologous to syntaphilin, a molecule involved in guiding vesicular transport. These results indicate that KIAA1472 gene products may play an important role in vesicular traffic in various tissues including the brain.

Characterization of adrenomedullin in non-human primates

Adrenomedullin (AM) is a 52 amino acid peptide involved in the pathophysiology of several human diseases. Here we show the gene structure, organ distribution, and regulated expression of AM in monkey. The monkey AM (mAM) gene is located on the short arm of chromosome 9 and it codes for a 185 amino acid preprohormone, which contains two amidated peptides identical to the human AM and proadrenomedullin N-terminal 20 peptide. The promoter region of the mAM gene contains a variety of transcription factor binding motifs. mAM is widely expressed throughout many organs as shown by real-time PCR and immunohistochemical techniques, and we have found similar levels of circulating plasma AM in monkeys and humans. A significant upregulation of the mAM mRNA was observed in monkey cells exposed to low oxygen tension conditions, TGF-beta1, all-trans-retinoic acid, and dexamethasone. Our collective data show a high degree of homology between mAM and hAM, which renders the monkey an attractive animal model for future pharmacological and pre-clinical studies targeting AM.

Cloning, expression, and pore-forming properties of mature and precursor forms of pleurotolysin, a sphingomyelin-specific two-component cytolysin from the edible mushroom Pleurotus ostreatus

Pleurotolysin, a sphingomyelin-specific cytolysin consisting of A (17 kDa) and B (59 kDa) components from the basidiomycete Pleurotus ostreatus, assembles into a transmembrane pore complex. Here, we cloned complementary and genomic DNAs encoding pleurotolysin, and studied pore-forming properties of recombinant proteins. The genomic regions encoding pleurotolysin A and B contained two and eight introns, respectively, and putative promoter sequences. The complementary DNA (cDNA) for pleurotolysin A encoded 138 amino acid residues, and the predicted product was identical with natural pleurotolysin A, except for the presence of the first methionine. Recombinant pleurotolysin A lacking the first methionine was purified as a 17-kDa protein with sphingomyelin-binding activity. The cDNA for pleurotolysin B encoded a precursor consisting of 523 amino acid residues, of which N-terminal 48 amino acid residues were absent in natural pleurotolysin B. Mature and precursor forms of pleurotolysin B were expressed as insoluble 59- and 63-kDa proteins, respectively, which were unfolded with 8 M urea and refolded by 100-fold dilution with 10 mM Tris-HCl buffer, pH 8.5. Although neither recombinant pleurotolysin A nor B alone was hemolytically active at higher concentrations of up to 100 mg/ml, they cooperatively assembled into a membrane pore complex on human erythrocytes and lysed the cell as efficiently as the natural proteins at nanomolar concentrations. In contrast, the precursor of pleurotolysin B was much less hemolytically active than mature pleurotolysin B in the presence of pleurotolysin A.

Clustering of DNA sequences in human promoters

We have determined the distribution of each of the 65,536 DNA sequences that are eight bases long (8-mer) in a set of 13,010 human genomic promoter sequences aligned relative to the putative transcription start site (TSS). A limited number of 8-mers have peaks in their distribution (cluster), and most cluster within 100 bp of the TSS. The 156 DNA sequences exhibiting the greatest statistically significant clustering near the TSS can be placed into nine groups of related sequences. Each group is defined by a consensus sequence, and seven of these consensus sequences are known binding sites for the transcription factors (TFs) SP1, NF-Y, ETS, CREB, TBP, USF, and NRF-1. One sequence, which we named Clus1, is not a known TF binding site. The ninth sequence group is composed of the strand-specific Kozak sequence that clusters downstream of the TSS. An examination of the co-occurrence of these TF consensus sequences indicates a positive correlation for most of them except for sequences bound by TBP (the TATA box). Human mRNA expression data from 29 tissues indicate that the ETS, NRF-1, and Clus1 sequences that cluster are predominantly found in the promoters of housekeeping genes (e.g., ribosomal genes). In contrast, TATA is more abundant in the promoters of tissue-specific genes. This analysis identified eight DNA sequences in 5082 promoters that we suggest are important for regulating gene expression.

Characterization of functional elements in the neurofibromatosis (NF1) proximal promoter region

An essential requirement to understand how genes contribute to genetic disease is the thorough knowledge of the transcriptional regulation of gene expression. Here, we have characterized transcription factor binding sites within the type 1 neurofibromatosis (NF1) proximal regulatory region, and addressed the molecular mechanisms that regulate NF1 transcription. Overlapping regions of the NF1 proximal promoter have been cloned and characterized for use in luciferase reporter assays. These assays have identified a 500 bp region displaying activities up to 80-fold higher than control reporter levels. Mutations at putative CRE and SP1-binding sites immediately 5' to the transcription start site have dramatic effects that lead to a 70-90% decrease in reporter activity in all cell lines tested. Gelshift assays confirm binding of CREB and SP1/KLF family members to their putative recognition sequences, and provide the first evidence identifying functional sites likely involved in regulating NF1 transcription. These assays have also revealed a putative repressor region within the NF1 promoter region corresponding to CCCTC-rich sequences between the transcription and translation start sites. This work provides new information concerning the transcriptional regulation of the NF1 gene, and is the most thorough attempt to date to map functionally relevant regions within the NF1 proximal promoter region.

Regulation of the human MSH6 gene by the Sp1 transcription factor and alteration of promoter activity and expression by polymorphisms

Defects in human DNA mismatch repair have been reported to underlie a variety of hereditary and sporadic cancer cases. We characterized the structure of the MSH6 promoter region to examine the mechanisms of transcriptional regulation of the MSH6 gene. The 5'-flanking region of the MSH6 gene was found to contain seven functional Sp1 transcription factor binding sites that each bind Sp1 and Sp3 and contribute to promoter activity. Transcription did not appear to require a TATA box and resulted in multiple start sites, including two major start sites and at least nine minor start sites. Three common polymorphisms were identified in the promoter region (-557 T-->G, -448 G-->A, and -159 C-->T): the latter two were always associated, and each of these functionally inactivated a different Sp1 site. The polymorphic allele -448 A -159 T was demonstrated to be a common Caucasian polymorphism found in 16% of Caucasians and resulted in a five-Sp1-site promoter that had 50% less promoter activity and was more sensitive to inactivation by DNA methylation than the more common seven Sp1 site promoter allele, which was only partially inactivated by DNA methylation. In cell lines, this five-Sp1-site polymorphism resulted in reduced MSH6 expression at both the mRNA and protein level. An additional 2% of Caucasians contained another polymorphism, -210 C-->T, which inactivated a single Sp1 site that also contributes to promoter activity.

The use of amplified flanking region-PCR in the isolation of laccase promoter sequences from the edible fungus Pleurotus sajor-caju

AIMS

To determine the regulation of laccase isozyme gene transcription in Pleurotus sajor-caju in response to different aromatic inducers and physiological parameters.

METHODS AND RESULTS

The promoter regions for each of four different laccase isozymes were cloned from P. sajor-caju, using amplified flanking region-PCR (AFR-PCR). Sequences stretching 724, 214, 840 and 1740 bp upstream from the predicted start codons for lac1, lac2, lac3 and lac4, respectively, were cloned in each case and analysed for the presence of putative transcriptional response elements. A number of putative response elements including metal response elements, xenobiotic response elements and antioxidant response elements appear to be present. In addition putative consensus sequences such as those for the binding of AP1, AP2, creA and NIT2 transcription factors, which are involved in nitrogen and carbon regulation in different fungi, are also present in the promoter regions of some of the isozymes.

CONCLUSIONS

These elements may be involved in the transcriptional regulation of laccase gene expression in P. sajor-caju.

SIGNIFICANCE AND IMPACT OF THE STUDY

The presence of a number of putative transcriptional response elements in the promoter regions of different isozyme genes indicates a potential role for these sites in regulating laccase gene transcription in P. sajor-caju. In addition this work demonstrates the potential usefulness of AFR-PCR as a technique to clone fungal DNA sequences located upstream from known sequences.

N-myc oncogene expression in neuroblastoma is driven by Sp1 and Sp3

Regulation of N-myc oncogene expression is an important determinant of the biological behavior of neuroblastoma. The N-myc promoter contains several potential binding sites for transcription factors of the Sp1 family. Mutation of a CT-box motif contained within a 26 bp region required for N-myc downregulation by retinoic acid decreased basal transcriptional activity and altered DNA-protein interactions of the promoter, while mutations flanking this motif did neither. On super-shift, this region was shown to recruit Sp1 and Sp3 transcription factor proteins, while a functionally significant CT-box mutation resulted in their replacement by NF-1 transcription factor. Lysates from Drosophila S2 cells expressing exogenous Sp1, Sp3, and NF-1 proteins were able to partially mimic gel shift complexes seen with neuroblastoma nuclear extract and either wild type or mutant probes. Transient transfections of S2 cells showed that both individually and together, Sp1 and Sp3 were able to trans-activate a wild type CT-box-driven luciferase reporter construct in a dose-dependent manner. Transfection of the wild type but not mutant CT-box oligonucleotide was able to decrease endogenous N-myc expression in neuroblastoma cells. Together these results suggest that the CT-box element serves a critically functional role, and in the basal state, allows for N-myc trans-activation by Sp1 and Sp3. Moreover when mutated, the CT-box may still function as a binding motif for alternate transcription factors such as NF-1 that can allow persistent N-myc expression.

The regulation of catalase gene expression in mouse muscle cells is dependent on the CCAAT-binding factor NF-Y

Catalase is an antioxidant enzyme whose expression is transcriptionally regulated and tissue-specific. The level of expression determines, in part, the susceptibility of a cell to oxidative stress. Skeletal muscle is a tissue that experiences high levels of oxidative stress during normal metabolic activity, so the expression of antioxidant enzymes is critical to preventing cellular damage. To study the transcriptional regulation of the catalase gene in mouse muscle cells, the 5'-flanking region of the mouse catalase gene was isolated from genomic DNA. The transcriptional activity of the 5'-flanking region was investigated in transiently transfected murine myoblasts using a promoter-less luciferase reporter vector and site-directed mutagenesis. Strikingly, we found that nearly all of the transcriptional activity was restricted to the final 191 bp of the greater than 2.5 kb of the 5'-flanking region examined. Of the potential consensus binding sites for transcriptional regulators within this 191-bp region, we identified two CCAAT boxes and no other consensus sites that were important for the transcriptional activity of this promoter. Gel shift and super shift assays indicated that the transcription factor NF-Y bound to both CCAAT boxes. Furthermore, co-transfection of reporter constructs with NF-Y expression vectors into Drosophila SL2 cells demonstrated NF-Y-mediated transcriptional activation of the catalase gene. Interestingly, there were no nearby sites that appeared to interact with either NF-Y binding sites, and thus it appears that NF-Y acts as a bona fide transcription factor for catalase gene expression in mouse muscle cells. These data provide the first examination of the regulation of the mouse catalase gene and indicate unique aspects of its regulation that may pertain to the tissue-specific patterns of expression.

SLURP-2, a novel member of the human Ly-6 superfamily that is up-regulated in psoriasis vulgaris

By microarray assay we identified ESTs (expressed sequence tags) whose expression was predominantly increased in the affected skin of patients with psoriasis vulgaris. Among them, a full-length cDNA sequence corresponding to one of those ESTs (AI829641) was isolated by screening of cultured human keratinocyte cDNA libraries. This cDNA encodes a novel member of the Ly-6/uPAR superfamily, designated SLURP-2 (secreted Ly-6/uPAR related protein 2). SLURP-2 has an open reading frame of 97 amino acids containing 10 conserved cysteine residues. SLURP-2 has a single functional copy within the LY6 superfamily gene cluster at chromosome 8q24.3. RT-PCR (reverse transcriptase-polymerase chain reaction) expression analysis revealed that SLURP-2 was expressed in multiple tissues, mainly in the epithelial cells including the skin and keratinocytes, but not in spleen or bone marrow. Comparison of the expression of this gene among the psoriatic lesional and nonlesional skin of patients and the normal skin of healthy individuals detected by quantitative real-time RT-PCR analysis disclosed that SLURP-2 was up-regulated threefold in psoriatic lesional skin. These findings suggest that SLURP-2 may be involved in the pathophysiology of psoriasis through its role in keratinocyte hyperproliferation and/or T cell differentiation/activation.

Structural characterization of the human carboxypeptidase D gene and its promoter

Human carboxypeptidase D (CPD) is a 180-kDa type I membrane protein with three tandem active site domains. CPD is a B-type (or kininase I-type) carboxypeptidase that cleaves C-terminal basic residues from proteins and peptides, such as Arg9 from bradykinin. The human carboxypeptidase D (CPD) gene was found to encompass approximately 88.3 kb of genomic sequence, containing 21 exons ranging in size from 65 to 1813 bp, and 21 introns ranging in size from 112 bp to 35.6 kb. Although CPD and CPM belong to the same metallocarboxypeptidase subfamily, their intron/exon structures differ significantly. Multiple transcription start sites were found in the CPD gene within a GC-rich sequence lacking the typical TATA box, but containing three GC boxes. Luciferase reporter assays with various size constructs containing the promoter region upstream of the start sites showed that it was active in three different cell lines, especially in the human hepatoma cell line HepG2 and the human monocytic cell line THP-1, which have high constitutive expression of CPD.

Purification of proteins specifically binding human endogenous retrovirus K long terminal repeat by affinity elution chromatography

A novel affinity elution procedure for purification of DNA-binding proteins was developed and employed to purify to near homogeneity the proteins recognizing a 21 base pair sequence within the long terminal repeat of human endogenous retroviruses K. The approach involves loading the initial protein mixture on a heparin-agarose column and elution of protein(s) of interest with a solution of double-stranded oligonucleotide containing binding sites of the protein(s). The affinity elution has several advantages over conventional DNA-affinity chromatography: (i) it is easier and faster, permitting to isolate proteins in a 1 day-one stage procedure; (ii) yield of a target protein is severalfold higher than that in DNA-affinity chromatography; (iii) it is not necessary to prepare a special affinity support for each factor to be isolated. Theaffinity elution could be a useful alternative to conventional DNA-affinity chromatography.

A approximately 35 kDa polypeptide from insect cells binds to yeast ACS like elements in the presence of ATP

BACKGROUND

The S. cerevisiae origin recognition complex binds to the ARS consensus sequence in an ATP dependent fashion. Recently, the yeast Cdc6 has been reported to have DNA binding activity. Conservation of replication proteins among different species strongly supports their functional similarity. Here we report the results of an investigation into the DNA binding activity of human Cdc6 protein. Cdc6 was expressed and purified from baculovirus infected Sf9 (Spodoptera frugiperda) insect cells as GST fusion protein (GST-Cdc6) and its DNA binding activity was tested.

RESULTS

Partially purified fractions containing GSTCdc6 or GST showed an ACS binding activity in an ATP dependent manner. However, further purification revealed the presence of a putative 35 kDa insect cell protein (p35) which was found responsible for the DNA binding activity. A close match to the 9/11 bases of the ARS consensus sequence was sufficient for p35 binding activity. A DNA fragment from the human c-myc origin region containing yeast ACS like elements also showed p35 binding activity.

CONCLUSIONS

We have identified a Spodoptera frugiperda protein with ATP dependent DNA binding activity to ACS like elements. ACS like elements have been reported to be essential for ORC binding and replication initiation in yeast but their role in higher eukaryotes still remains elusive. Like the ARS consensus sequence elements of yeast, ACS like elements found in c-myc and lamin beta 2 origin regions may play similar roles in replication and indicate a conserved role for this DNA motif among eukaryotes.

POZ domain transcription factor, FBI-1, represses transcription of ADH5/FDH by interacting with the zinc finger and interfering with DNA binding activity of Sp1

The POZ domain is a protein-protein interaction motif that is found in many transcription factors, which are important for development, oncogenesis, apoptosis, and transcription repression. We cloned the POZ domain transcription factor, FBI-1, that recognizes the cis-element (bp -38 to -22) located just upstream of the core Sp1 binding sites (bp -22 to +22) of the ADH5/FDH minimal promoter (bp -38 to +61) in vitro and in vivo, as revealed by electrophoretic mobility shift assay and chromatin immunoprecipitation assay. The ADH5/FDH minimal promoter is potently repressed by the FBI-1. Glutathione S-transferase fusion protein pull-down showed that the POZ domains of FBI-1, Plzf, and Bcl-6 directly interact with the zinc finger DNA binding domain of Sp1. DNase I footprinting assays showed that the interaction prevents binding of Sp1 to the GC boxes of the ADH5/FDH promoter. Gal4-POZ domain fusions targeted proximal to the GC boxes repress transcription of the Gal4 upstream activator sequence-Sp1-adenovirus major late promoter. Our data suggest that POZ domain represses transcription by interacting with Sp1 zinc fingers and by interfering with the DNA binding activity of Sp1.

A role for C/EBP delta in human surfactant protein A (SP-A) gene expression

C/EBP delta, a member of the leucine zipper transcription factor family, is expressed at higher levels in the lung than in any other tissue. We detected C/EBP delta mRNA and protein in NCI-H441 cells, a cell line derived from a human adenocarcinoma that produces surfactant protein A (SP-A). NCI-H441 cells were exposed to phosphorothioate-substituted antisense oligonucleotides directed against C/EBP delta. After exposure to the oligonucleotides, cells were harvested, total RNA prepared, and levels of mRNA for C/EBP delta, SP-A and a control, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were quantified from Northern blots. An oligonucleotide that overlapped the translational start was effective in reducing C/EBP delta mRNA. Oligonucleotides that corresponded to regions upstream and downstream from the translational start were not as effective. The loss of C/EBP delta was accompanied by a decrease in the level of SP-A mRNA. The overlapping oligonucleotide was tested more extensively. After 72 h, antisense oligonucleotide at 3 and 5 microM reduced the level of C/EBP delta mRNA and protein by 50% or more as compared with sense and scrambled controls. The SP-A mRNA level was reduced even more, by about 75%. GAPDH mRNA was not affected. We conclude that C/EBP delta plays a role in the regulation of SP-A gene expression.

Functional promoter variants of highly conserved inducible hsp70 genes significantly affect stress response

Promoter variants differing in potential cis-acting elements and showing impaired binding of corresponding transcription factors are described in the inducible porcine hsp70.2 gene (GC box; initiator-like region, InR) and in its bovine homologue (AP2 site), respectively. Interestingly, all these promoter variants are stable established in the analysed populations in spite of significant negative effects on transcriptional activity and indications of not neutral behaviour in response to breeding selection. Moreover, in pigs they are likely to be evolutionary fixed as suggested by their presence in recent breeds and in wild boars as well. Compensation of the effect of the observed 'down'-mutations by further yet unknown gene variants is assumed.

The mechanism of sex-specific splicing at the doublesex gene is different between Drosophila melanogaster and Bombyx mori

We have previously reported that Bmdsx, a homologue of the sex-determining gene, doublesex (dsx), was found to be sex-specifically expressed in various tissues at larval, pupal, and adult stages in the silkworm, Bombyx mori, and was alternatively spliced to yield male- and female-specific mRNAs. To reveal sex-specific differences in splicing patterns of Bmdsx pre-mRNA, the genomic sequence was determined and compared with male- and female-specific Bmdsx cDNA sequences. The open reading frame (ORF) consisted of five exons. Exons 3 and 4 were specifically incorporated into the female type of Bmdsx mRNA. On the other hand, exon 2 was spliced to exon 5 to produce the male type mRNA of Bmdsx. As in the case of Drosophila dsx, the OD2 domain was separated by a female-specific intron into sex-independent and sex-dependent regions. Sex-specific splicing occurred in equivalent positions in the Drosophila dsx gene. However, unlike Drosophila dsx, the female-specific introns showed no weak 3' splice sites, and the TRA/TRA-2 binding site related sequences were not found in the female-specific exon, nor even in any other regions of the Bmdsx gene. Moreover, an in vitro splicing reaction consisting of HeLa cell nuclear extracts showed that the female-type of Bmdsx mRNA represented the default splicing. These findings suggest that the structural features of the sex-specific splicing patterns of Bmdsx pre-mRNA are similar to those of Drosophila dsx but the regulation of sex-specific alternative splicing of Bmdsx pre-mRNA is different.

Cloning and characterization of the pseudonajatoxin b precursor

An Australian common brown snake, Pseudonaja textilis, is known to contain highly lethal neurotoxins. Among them, a long-chain alpha-neurotoxin, pseudonajatoxin b, has been identified. In this report, while presenting evidence for the presence of at least four such long-chain alpha-neurotoxins in the venom of P. textilis, we describe the characteristics of both the mRNA and the gene responsible for the synthesis of these neurotoxins. A precursor toxin synthesized from the gene has been identified as being capable of producing the isoforms possibly by post-translational modifications at its C-terminal end. Recombinant toxins corresponding to the precursor and its product have been found to possess similar binding affinities for muscular acetylcholine receptors (IC(50)=3x10(-8) M) and a lethality, LD(50), of 0.15 microg/g in mice.

Organizations and promoter analyses of the human and the mouse genes for PACT, the protein-activator of the interferon-induced protein kinase, PKR

PACT is an activator of the protein kinase, PKR. Here we report the isolation and the characterization of the mouse Pact gene. It contains eight exons ranging in size from 79 to 630 bp spanning a region of 18 kb with the largest and smallest introns being 3700 and 500, respectively. The human PACT gene, as analyzed from sequence available in the GenBank database, has a very similar organization. The 5' flanking regions of both mouse and human PACT genes are devoid of TATA boxes but are rich in GC boxes. Although there are putative binding sites of numerous transcription factors on both promoters, their organizations and identities are different. For examining promoter activities, about 2 kb of DNA 5' to the transcription start sites of both genes was cloned upstream of a reporter luciferase gene. Transient transfection assays demonstrated that both promoters are strong. Deletion analyses revealed that most of the positive cis-elements lie within 400 bp upstream of the transcription start sites of both mouse and human PACT genes.

Sp1 and krüppel-like factor family of transcription factors in cell growth regulation and cancer

The Sp/KLF family contains at least twenty identified members which include Sp1-4 and numerous krüppel-like factors. Members of the family bind with varying affinities to sequences designated as 'Sp1 sites' (e.g., GC-boxes, CACCC-boxes, and basic transcription elements). Family members have different transcriptional properties and can modulate each other's activity by a variety of mechanisms. Since cells can express multiple family members, Sp/KLF factors are likely to make up a transcriptional network through which gene expression can be fine-tuned. 'Sp1 site'-dependent transcription can be growth-regulated, and the activity, expression, and/or post-translational modification of multiple family members is altered with cell growth. Furthermore, Sp/KLF factors are involved in many growth-related signal transduction pathways and their overexpression can have positive or negative effects on proliferation. In addition to growth control, Sp/KLF factors have been implicated in apoptosis and angiogenesis; thus, the family is involved in several aspects of tumorigenesis. Consistent with a role in cancer, Sp/KLF factors interact with oncogenes and tumor suppressors, they can be oncogenic themselves, and altered expression of family members has been detected in tumors. Effects of changes in Sp/KLF factors are context-dependent and can appear contradictory. Since these factors act within a network, this diversity of effects may arise from differences in the expression profile of family members in various cells. Thus, it is likely that the properties of the overall network of Sp/KLF factors play a determining role in regulation of cell growth and tumor progression.

DNA replication efficiency depends on transcription factor-binding sites

Naturally arising variants of simian virus 40 (SV40), generated by serial passage of the virus at high multiplicities of infection, provide important insight into the role of transcription factor-binding sites in enhancing DNA replication. Although the variants that arise from numerous recombination events are the result of selective pressure to replicate more efficiently than the other variants in the infection, there is no transcription pressure. Therefore, it is interesting that a minimum of two viral Sp1 transcription factor-binding sites are retained and that host AP-1 and NF-1 transcription factor-binding sites are incorporated into the 100-bp regulatory region that maximizes DNA replication in these variants. We cotransfected COS-1 cells (that provide viral large T antigen for DNA replication) to examine the effect of transcription factor-binding sites on the replication of plasmid constructs that contain the SV40 origin of replication (ori). The level of relative replication efficiency (RRE) depends on the number and type of transcription factor-binding sites. Replication increases as the number of transcription factor-binding sites increases within the regulatory region of the variants; AP-1 sites are more effective than NF-1 transcription factor-binding sites. Competition between constructs in transfections magnifies the difference in their RREs. The results indicate that transcription factor-binding sites play an important role in enhancing DNA replication.

Structure and expression of the murine phosphatidylserine synthase-1 gene

In mammalian cells, phosphatidylserine is synthesized by two different enzymes, phosphatidylserine synthase (PSS)-1 and -2, via a base exchange reaction in which the head group of a phospholipid (phosphatidylcholine or phosphatidylethanolamine) is replaced by l-serine. Since the amino acid sequences of PSS1 and PSS2 are only approximately 30% identical, it is likely that they are encoded by different genes. We have screened a murine liver genomic DNA library, included in bacterial artificial chromosomes, with full-length murine PSS1 cDNA and isolated a clone containing the majority of the PSS1 gene. This gene spans approximately 35 kilobases and contains 13 exons and 12 introns. The sizes of the exons range from 44 to 1035 base pairs. The gene was localized to chromosome 13 in region B-C1. According to reverse transcriptase-mediated polymerase chain reaction, PSS1 and PSS2 mRNAs were expressed in all murine tissues examined. The mRNA encoding PSS1 was most abundant in kidney, brain, and liver, whereas PSS2 mRNA was most highly expressed in testis. In general agreement with the levels of mRNA expression, the choline exchange activity (contributed by PSS1, but not PSS2) was highest in brain, whereas serine and ethanolamine exchange activities were highest in testis and kidney. The transcriptional initiation site for PSS1 was identified 111 base pairs upstream of the ATG specifying the start of translation. The putative 5'-proximal promoter region of the gene contained no TATA or CAAT box, but did have a high GC content. Isolation of the murine PSS1 gene is a step toward generation of genetically modified mouse models that will help to understand the functions of PSS1 and PSS2 in animal biology.

Transgenic zebrafish as sentinels for aquatic pollution

Using the golden mutant zebrafish having a decrease in interfering pigmentation, we are developing transgenic lines in which DNA motifs that respond to selected environmental pollutants are capable of activating a reporter gene that can be easily assayed. We have begun with three response elements that recognize three important classes of foreign chemicals. Aromatic hydrocarbon response elements (AHREs) respond to numerous polycyclic hydrocarbons and halogenated coplanar molecules such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; dioxin) and polychlorinated biphenyls. Electrophile response elements (EPREs) respond to quinones and numerous other potent electrophilic oxidants. Metal response elements (MREs) respond to heavy metal cations such as mercury, copper, nickel, cadmium, and zinc. Soon, we will include estrogen response elements (EREs) to detect the effects of environmental endocrine disruptors, and retinoic acid response elements (RARE, RXRE) to detect the effects of retinoids in the environment. Each of these substances is known to be bioconcentrated in fish to varying degrees; for example, 10(-17) M TCDD in a body of water becomes concentrated to approximately 10(-12) M TCDD in a fish, where it would act upon the AHRE motif and turn on the luciferase (LUC) reporter gene. The living fish as a sentinel will not only be assayed intact in the luminometer, but--upon several days or weeks of depuration--would be usable again. To date, we have established that zebrafish transcription factors are able to recognize both mammalian and trout AHRE, EPRE, and MRE sequences in a dose-dependent and chemical-class-specific manner, and that expression of both the LUC and jellyfish green fluorescent protein (GFP) reporter genes is easily detected in zebrafish cell cultures and in the intact live zebrafish. Variations in sensitivity of this model system can be achieved by increasing the copy number of response elements and perhaps by altering the sequence of each core consensus response element and flanking regions. This transgenic technology should allow for a simple, exquisitely sensitive, and inexpensive assay for monitoring aquatic pollution. We have already initiated studies using sentinel zebrafish to monitor a public drinking water source.

Kinetic analysis of Sp1-mediated transcriptional activation of the human DNA polymerase beta promoter

In the present studies, we have examined the effect of Sp1 on the activation of the human DNA polymerase beta (beta-pol), a TATA-less promoter. A HeLa cell nuclear extract (NE) based in vitro runoff transcription system of core beta-pol promoter human DNA (pbetaP8) three-step kinetic model of transcription initiation were used to describe the kinetic effect of Sp1. The results showed that distal Sp1-binding sites in the core beta-pol promoter are important for transcriptional activation of the pbetaP8 promoter. A detailed kinetic analysis showed that Sp1 stimulates the activity of the pbetaP8 promoter through distal Sp1-binding sites by increasing the amount of recruitment, instead of stimulating the apparent rate of RPc assembly (k1). There was no significant effect of Sp1 on the apparent rate of open complex (RPo) formation (k2) or on the apparent rate of promoter clearance (k3) of the pbetaP8 promoter. These studies define the kinetic mechanisms by which Sp1 may regulate the rate of transcript formation of the pbetaP8 promoter, and these results may have implications for Sp1 regulation of TATA-less promoters.

Coding sequence, genomic organization and expression of a folate binding protein gene in the rat

The complementary DNA (cDNA) and the gene encoding the folate binding protein alpha isoform (FBPalpha) have been reported for the human and mouse protein. However, there is no information about this gene in the rat, an animal that could be a model to study expression of this protein in vivo when folate metabolism is modified. Accordingly, the cloning and characterization of this gene in the rat have been the subject of this research. The gene has seven exons and six introns and is approximately 10kb in size. The organization and nucleotide sequence of the coding exons are similar to those of the corresponding human and mouse genes, which are the only other mammalian FBP genes cloned. However, the amino acid sequence of the rat FBPalpha is less homologous, having 48% identity with the published sequences for all the mammalian FBP isoforms. A finding not previously reported is the expression of two FBPalpha transcripts in the kidney that differ in the length of the 5' untranslated sequences, as determined by rapid amplification of cDNA end-polymerase chain reaction amplification (RACE-PCR). The brain expresses a single transcript intermediate in size between the two transcripts expressed in the kidney. The kidney transcripts are encoded by the same gene and appear to be regulated either from two independent promoters or from a single promoter in association with alternative RNA splicing.

Regulation of CD34 transcription by Sp1 requires sites upstream and downstream of the transcription start site

CD34 is a cell surface glycoprotein expressed on hematopoietic stem and progenitor cells, but not on fully differentiated cells in the peripheral blood. To better understand the molecular regulation of early hematopoiesis, we are elucidating the mechanisms of CD34 transcriptional regulation. By deletion analysis we identify a 39-bp element in the proximal region of murine CD34 promoter that is critical for promoter activity. Electromobility shift assays indicate that nuclear proteins of hematopoietic cells bind to this domain; however, the presence of this binding activity does not correlate directly with CD34 expression.Using methylation interference, the DNA binding site for this activity was localized to four guanine residues within the GGGGTCGG sequence from -48 to -54 bp. When the four contact guanines were mutated, both protein binding and promoter activity were abolished. Although this sequence does not contain a standard consensus for Sp1, this transcription factor binds specifically to the 39-bp region and stimulates promoter activity in both hematopoietic cells and in Sp1 null Drosophila S2 cells. In addition, Ku binds to this domain in a sequence-specific manner. Activation of the CD34 promoter by Sp1 requires the presence of a binding domain at -48 bp as well as the 5' untranslated region, which also binds Sp1.A functional interaction between regulatory regions upstream and downstream of the transcription start site is required for CD34 gene expression.

The transcription factor EGR-1 directly transactivates the fibronectin gene and enhances attachment of human glioblastoma cell line U251

EGR-1, a transcription factor with important functions in the regulation of growth and differentiation, is highly expressed in brain. Previous studies have shown that EGR-1 suppresses the transformed phenotype. However, the expression and role of EGR-1 in human glioblastoma cells are not yet determined. In this study, we found that the basal expression of the EGR-1 protein is undetectable, but is inducible in four human glioblastoma cell lines. To determine EGR-1 functions, we re-expressed EGR-1 in human glioblastoma U251 cells and found that the secretion of transforming growth factor-beta1 (TGF-beta1), plasminogen activator inhibitor-1 (PAI-1), and fibronectin (FN) was greatly enhanced. Addition of anti-TGF-beta antibodies completely inhibited the secretion of PAI-1, but had little effect on secretion of FN, indicating that PAI-1 is under the control of EGR-1-induced TGF-beta1. An examination of the promoter of the FN gene revealed two EGR-1-binding sites between positions -75 and -52 and positions -4 and +14 that specifically bound EGR-1 in gel mobility shift experiments. Utilizing wild-type and mutant FN promoter/luciferase reporter genes, we demonstrated that EGR-1 positively regulated the activity of the FN gene. In addition, cell adhesion and migration were greatly increased in the EGR-1-expressing cells, and adhesion was reversed by addition of RGD-containing peptides. These results suggest that EGR-1 may regulate cell interaction with the extracellular matrix by coordinated induction of TGF-beta1, FN, and PAI-1 in human glioblastoma cells.

Inducible expression of basic transcription element-binding protein 2 in proliferating smooth muscle cells at the vascular anastomotic stricture

OBJECTIVE

The proliferation of vascular smooth muscle cells surrounding a suture line is an important factor in the development of anastomotic stricture that is frequently seen after coronary artery bypass grafting. The aim of this study was to investigate the time course of intimal thickening and to examine the expression of the molecular marker of smooth muscle cell activation surrounding the suture line.

METHODS

Longitudinal aortotomy was performed in the abdominal aorta of rats. The rats were put to death 1, 2, 4, and 8 weeks after aortotomy, and the percentage of the lumen occluded by intimal thickening was calculated. All tissues were stained with antibodies against basic transcription element- binding protein 2, human cyclin-dependent kinase (cdk4), and Sp1 for immunohistochemistry. Basic transcription element-binding protein 2 is a transcription factor that is involved in phenotypic modulation of vascular smooth muscle cells. Cdk4 represents a marker for G(1) phase of the cell cycle. Sp1 is a transcription factor known to be expressed in a variety of tissues. Basic transcription element-binding protein 2 messenger RNA expression was confirmed by means of reverse transcriptase-polymerase chain reaction.

RESULTS

We noted significant thickening of the intimal layer 1 week after aortotomy. Immunohistochemistry demonstrated that smooth muscle cells in the neointima were strongly positive for basic transcription element-binding protein 2 and human cyclin-dependent kinase 4, which peaked 2 weeks after aortotomy. Basic transcription element-binding protein 2 expression was closely associated with human cyclin-dependent kinase 4 expression in the neointima, although Sp1 was not. Basic transcription element-binding protein 2 messenger RNA levels were significantly up-regulated early after aortotomy.

CONCLUSION

The experimental rat aortotomy model is useful to investigate the proliferation of vascular smooth muscle cells around the suture line. Moreover, our results suggest the possible role of basic transcription element-binding protein 2 in the development of vascular anastomotic strictures.

Enhancement of the basal-level activity of HIV-1 long terminal repeat by HIV-1 nucleocapsid protein

Two HIV-1 proteins, Tat and NCp7 (NC), have zinc finger-like structures. NC is a virion protein and has been shown to accumulate in the nucleus 8 h postinfection. Since transcription factors with zinc fingers assist the transcriptional activity of both RNA polymerases II and III, we examined the effect of NC on HIV-1 LTR-directed gene expression. The HIV-1 NC binds to the HIV-1 LTR and results in a mobility shift in polyacrylamide gel electrophoresis. Competition assays with cold probes revealed that the binding of NC and formation of a DNA-protein complex could be prevented by the addition of excess unlabeled LTR self-probe, but not the HIV-1 V3 envelope gene. The DNase I footprint analysis showed that NC binds to six regions within HIV-1 LTR, four of which are near the transcription start site. The NC alone enhances LTR basal-level activity in RNA runoff experiments. When the general transcription factors (GTFs) were added in the assay, NC enhances NF-kappaB, Sp1, and TFIIB-induced HIV-1 LTR-directed RNA transcription. RNA transcription directed by the adenovirus major late promoter, however, is not significantly affected by NC in the cell-free system. Transient transfection of human T lymphocytes with the plasmids containing HIV-1 nc or gag showed enhancement of LTR-CAT activity. Moreover, transfection of HIV-1 provirus containing mutations in NC zinc-finger domains dramatically decreases the enhancement activity in human T cells, in which HIV-1 LTR is stably integrated into the cellular genome. These observations show that NC binds to HIV-1 LTR and cooperatively enhances GTFs and NF-kappaB induced HIV-1 LTR basal-level activity. NC may play the role of a nucleation protein, which binds to LTR and enhances basal-level transcription by recruiting cellular transcription factors to the HIV-1 promoter in competition with cellular promoters.

Genomic structure and novel variants of myo-inositol monophosphatase 2 (IMPA2)

Recently, we cloned the human myo-inositol monophosphatase 2 (IMPA2) cDNA and established its map location to chromosome 18p11.2, a region previously implicated in bipolar disorder. Because the myo-inositol monophosphatase enzyme has been shown to be inhibited by lithium, an effective therapeutic agent for bipolar disorder, IMPA2 is a plausible positional and functional candidate gene. To permit comprehensive screening for variants we characterized the genomic structure and isolated the potential promoter of IMPA2. The gene was found to encode eight exons spanning;27 kb. The proximal 1-kb 5' flanking region did not contain an obvious TATA box but multiple potential binding sites for Sp1 and consensus motifs for AP2 and other transcription factors were evident. Sequencing of the coding region and splice junctions in unrelated bipolar disorder patients detected novel variants. A missense mutation in exon 2, His76Tyr, was found in one patient. His76 is evolutionarily conserved and replacement with Tyr introduces a potential site for phosphorylation. The other polymorphisms included an RsaI polymorphism, IVS1-15G>A, and a T --> C silent mutation in the third nucleotide of codon 53 in exon 2. By Fisher's exact test the silent mutation showed a trend for association (P = 0.051) with bipolar disorder suggesting that further scrutiny of this gene is warranted.

Insulin and insulin-like growth factor-1 receptors in an evoluted fish, the turbot: cDNA cloning and mRNA expression

The insulin receptor (IR) and the structurally related insulin-like growth factor type 1 receptor (IGF-1R) belong to the tyrosine kinase (TK) receptor family. In this study, we have carried out the molecular characterization of both receptors from turbot (Psetta maxima), an evoluted teleost flatfish. The cDNA encoding the precursors of IGF-1R and the nearly entire IR (only the first 16 amino acids of the alpha subunit are missing when compared to the published human sequence) were cloned from an embryonic cDNA library. The deduced polypeptides contain all the topological features characterizing the insulin/IGF-1 receptor family. They are highly conserved compared to their mammalian counterparts, particularly within domains involved in the catalytic activity and in the transduction pathways. Nevertheless, some differences in the primary sequences, especially in the carboxy-terminal domain of the precursors, may affect the functions fulfilled by these receptors. As in mammals, the long IGF-1R 5'-untranslated sequence contains open reading frames and potential Sp1 binding sites. Northern blot analyses have revealed a major IR transcript of 11 kb, which is approximately the size of IGF-1R transcript (Eliès, G., Groigno, L., Wolff, J., Boeuf, G., Boujard, D., 1996. Characterization of the insulin-like growth factor type 1 receptor messenger in two teleost species. Mol. Cell. Endocrinol. 124, 131-140.). If IR and IGF-1R transcripts are detected by RT-PCR at all developmental stages and in all tissues examined, in situ hybridization studies have shown that these mRNA can be visualized as ubiquitous signals only in young larvae, whereas IGF-1R and IR expression appears weaker during later development and in adult tissues.

USP25, a novel gene encoding a deubiquitinating enzyme, is located in the gene-poor region 21q11.2

We have identified a new gene, USP25, spanning over 150 kb at 21q11. 2, one of the lowest gene-density regions of the human genome. USP25 is made up of 25 exons and encodes a 1087-aa protein. Database comparisons reveal high homology with members of the ubiquitin protease family (UBP). Basal expression was observed in all human tissues tested, and two main transcripts were identified. The homologous murine gene has also been characterized. In situ hybridization in mouse embryonic brains showed a clear correlation of expression with proliferative neuroepithelial cells and postmitotic neurons. Moreover, high expression was observed in adult mouse testis. UBPs belong to a complex family of deubiquitinating enzymes that specifically cleave ubiquitin conjugates on a great variety of substrates. These enzymes have an essential role in protein degradation via the 26S proteasome and thus regulate many cellular pathways. An increase in USP25 gene dosage in Down syndrome patients could seriously disturb the balance between ubiquitinated and deubiquitinated substrates.

Structure and sequence of the mouse V1a and V1b vasopressin receptor genes

The structural organization and 5'-flanking region of the mouse V1a and V1b vasopressin receptor genes were determined. The mouse V1a receptor gene was located within an 8-kb XbaI fragment, and the mouse V1b receptor gene was located within a 14-kb EcoRV fragment. Both genes were comprised of two coding exons that were separated by a 2.3-kb and a 8.0-kb intron, respectively, located before the respective seventh transmembrane domain of the receptor sequence. The availability of these genes would allow us to study the functional role of V1a and V1b receptors by disrupting the gene in mice.

Three conserved transcriptional repressor domains are a defining feature of the TIEG subfamily of Sp1-like zinc finger proteins

Sp1-like transcription factors are characterized by three highly homologous C-terminal zinc finger motifs that bind GC-rich sequences. These proteins behave as either activators or repressors and have begun to be classified into different subfamilies based upon the presence of conserved motifs outside the zinc finger domain. This classification predicts that different Sp1-like subfamilies share certain functional properties. TIEG1 and TIEG2 constitute a new subfamily of transforming growth factor-beta-inducible Sp1-like proteins whose zinc finger motifs also bind GC-rich sequences. However, regions outside of the DNA-binding domain that differ in structure from other Sp1-like family members remain poorly characterized. Here, we have used extensive mutagenesis and GAL4-based transcriptional assays to identify three repression domains within TIEG1 and TIEG2 that we call R1, R2, and R3. R1 is 10 amino acids, R2 is 12 amino acids, and R3 is approximately 80 amino acids long. None of these domains share homology with previously described transcriptional regulatory motifs, but they share strong sequence homology and are functionally conserved between TIEG1 and TIEG2. Together, these data demonstrate that TIEG proteins are capable of repressing transcription, define domains critical for this function, and further support the idea that different subfamilies of Sp1-like proteins have evolved to mediate distinct transcriptional functions.

Organization and chromosomal localization of the human endothelial protein C receptor gene

Endothelial protein C receptor (EPCR), present on endothelial cells of relatively large veins and arteries, plays a role in the enhancement of protein C activation by the thrombin-thrombomodulin complex. In the present study, we determined the organization and the complete nucleotide sequence of the human EPCR gene using polymerase chain reaction-direct sequencing method. The transcription initiation site of the EPCR gene was also determined by the cap site hunting method, using a cap site cDNA prepared from human placenta. The human EPCR gene spanned approx. 6 kb and was composed of four exons and three introns. All exon-intron boundaries agreed with the GT-AG rule. The 5'-flanking region (300 bp) of the EPCR gene contained a putative AP1-binding site, two Sp1-binding sites and two AP2-binding sites, but not definite TATAA or CCAAT sequences. Fluorescence in situ hybridization analysis showed that the EPCR gene is located in chromosome 20q11.2.

The promoter of human tissue factor pathway inhibitor gene: identification of potential regulatory elements

Tissue factor pathway inhibitor is the major potent physiologic inhibitor of tissue factor-induced coagulation. Several potential binding sites for transcription factors have been described in the 750 bp of the 5' flanking region of the human tissue factor pathway inhibitor gene reported earlier. To identify elements that regulate the expression of tissue factor pathway inhibitor in endothelial, hepatocyte, and monocyte cells, the sequence of an additional 770 bp of tissue factor pathway inhibitor was determined. Comparison of this new sequence as well as that reported earlier with consensus sequences for transcription factor binding sites provided matches for GATA-2, SP1, and c-Myc sequences. Moreover, plasmids containing deletion mutants of the 5' tissue factor pathway inhibitor promoter region and the luciferase reporter gene were transfected into HepG2, ECV304, and THP1 cells. Three negative regulatory elements were localized between -548 to -390, - 390 to -75, and -1158 to -796 relative to the transcriptional start, respectively, in HepG2, ECV304 and THP-1 cells.

Mouse very low-density lipoprotein receptor (VLDLR): gene structure, tissue-specific expression and dietary and developmental regulation

The very low density lipoprotein receptor (VLDLR) is a multifunctional apolipoprotein (apo) E receptor that shares a common structural feature as well as some ligand specificity to apo E with members of the low density lipoprotein receptor gene family. We have isolated and characterized the mouse VLDLR gene. The mouse VLDLR gene contains 19 exons spanning approximately 50 kb. The exon-intron organization of the gene is completely conserved between mouse and human. Since the 5'-flanking region of the mouse VLDLR gene contains two copies of a sterol regulatory element-1 like sequence (SRE-1), we next studied regulation of the VLDLR mRNA expression in heart, skeletal muscle and adipose tissue in C57BL/6, LDLR-/-, apo E-/- and LDLR-/-apo E-/- mice fed normal chow or atherogenic diet. The VLDLR mRNA expression was down-regulated 3-fold by feeding atherogenic diet in heart and skeletal muscle only in LDLR-/- mice. In contrast, VLDLR mRNA expression was up-regulated by atherogenic diet in adipose tissue in all animal models except double knockout mice. These results suggest that SRE-1 may be functional and VLDLR plays a role in cholesterol homeostasis in heart and skeletal muscle when LDLR is absent and that apo E is required for this modulation. Developmental regulation of the VLDLR mRNA expression was also tissue-specific. VLDLR mRNA expression in heart displayed significant up and down regulation during development. Maximal level was detected on post-natal day 3. However, the VLDLR mRNA levels in skeletal muscle remained relatively constant except a slight dip on post-natal day 7. In kidney and brain, VLDLR mRNA also peaked on post-natal day 3 but remained relatively constant thereafter. In liver, VLDLR mRNA expression was very low; it was barely detectable at day 19 of gestation and was decreased further thereafter. In adipose tissue, the VLDLR mRNA level showed an increase on post-natal day 13, went down again during weaning and then continued to increase afterwards. This developmental pattern as well as dietary regulation in adipose tissue supports the notion that VLDLR plays a role in lipid accumulation in this tissue. Although the primary role of VLDLR in heart, muscle and adipose tissue is likely in lipid metabolism, developmental pattern of this receptor in other tissues suggests that VLDLR has functions that are unrelated to lipid metabolism.

Molecular mechanism for cooperation between Sp1 and steroidogenic factor-1 (SF-1) to regulate bovine CYP11A gene expression

Bovine cholesterol side-chain cleavage cytochrome P450 (P450scc; product of the CYP11A gene) gene expression is regulated by gonadotropins via cAMP in the ovary, and by ACTH via cAMP in adrenal cortical cells. Previously, we characterized response elements located at -57/-32 and at -111/-101 bp in the 5'-flanking region of the bovine CYP11A gene required for cAMP-stimulated transcription in both mouse Y-1 adrenal tumor cells and bovine ovarian cells in primary culture, which bind SF-1 (or Ad4-BP) and Sp1, respectively. The role of these transcription factors in CYP11A transcription was further confirmed by deletion and mutation analyses. In addition, results obtained employing a double mutation of the Sp1- and SF-1-binding sites and a mammalian two-hybrid system indicate that Sp1 and SF-1 function cooperatively in the transactivation of the bovine CYP11A promoter in both bovine luteal cells and Y-1 cells. Here we report that SF-1 and Sp1 are able to associate with one another in vitro and in vivo. The NH2-terminal region of SF-1, especially the DNA-binding domain, is the binding site for Sp1. In addition, as CBP is a common coactivator required for the transcriptional activity of numerous transcription factors including nuclear receptors, we investigated whether CBP functions as a cofactor for the regulation of bovine CYP11A promoter activity. We show here that CBP enhanced the PKA-induced CYP11A promoter activity, while a double mutation of both Sp1 and SF-1 sites within the CYP11A promoter region abolished CBP-induced activity. Furthermore, CBP stimulated Sp1-dependent transactivation, and a CBP/Sp1 complex in vivo was demonstrated by a co-immunoprecipitation assay. Also, CBP potentiated the transcriptional activity of GAL4-SF-1 in the presence of PKA. Thus, the cooperation between SF-1 and Sp1, required for the regulation of bovine CYP11A gene expression, is mediated by a direct protein-protein interaction and/or the common coactivator CBP.

Genomic organization, expression, and analysis of the troponin C gene pat-10 of Caenorhabditis elegans

We have cloned and characterized the troponin C gene, pat-10 of the nematode Caenorhabditis elegans. At the amino acid level nematode troponin C is most similar to troponin C of Drosophila (45% identity) and cardiac troponin C of vertebrates. Expression studies demonstrate that this troponin is expressed in body wall muscle throughout the life of the animal. Later, vulval muscles and anal muscles also express this troponin C isoform. The structural gene for this troponin is pat-10 and mutations in this gene lead to animals that arrest as twofold paralyzed embryos late in development. We have sequenced two of the mutations in pat-10 and both had identical two mutations in the gene; one changes D64 to N and the other changes W153 to a termination site. The missense alteration affects a calcium-binding site and eliminates calcium binding, whereas the second mutation eliminates binding to troponin I. These combined biochemical and in vivo studies of mutant animals demonstrate that this troponin is essential for proper muscle function during development.

Characterization of the human glycogenin-1 gene: identification of a muscle-specific regulatory domain

The de-novo synthesis of glycogen is now known to involve a novel class of self-glucosylating protein primers. In mammalian skeletal muscle, glycogenin-1 is the protein responsible for this initiation step. Northern blot analysis revealed that glycogenin-1 gene transcription is differentially regulated in the C2C12 mouse muscle cell line. To define the regulatory elements that control expression of the glycogenin-1 gene, we have cloned and characterized the genomic structure of the human glycogenin-1 gene and its promoter region. This gene consists of seven exons and six introns, and spans over 13kb. Transcription of human glycogenin-1 is initiated at two major sites, 80 and 86bp upstream from the initiation of translation codon. Nucleotide sequence analysis of 2.1kb of the 5'-flanking region revealed the proximal promoter contains both a TATA box and two putative Sp1 binding sites located in a CpG island. There are numerous binding sites for developmental and cell-type-specific transcription factors, including AP-1, AP-2, GATA, and several potential Oct 1 binding domains. There are also nine consensus E-boxes that bind the basic helix-loop-helix family of muscle-specific transcription factors. The transcriptional activity of the glycogenin-1 gene was investigated by transient transfection of the 5'-flanking region in HepG2 cells and C2C12 myoblasts and myotubes. These results permitted the definition of a minimal 232bp promoter fragment that is responsible for basal level transcription in a cell-type-independent manner. Furthermore, we have identified a regulatory region located between -2076 and -1736 of the 5'-flanking region of the human glycogenin-1 gene that allows myotube-specific expression in C2C12 cells.

Differential metal response and regulation of human heavy metal-inducible genes

A number of heavy metal-inducible genes have been reported, but their ranges of response to various metal species are not well known. It is also unclear if these genes are regulated through common mechanisms. To answer these questions, we compared induction kinetics of human metal-inducible genes including the MT-IIA (coding for a metallothionein isoform), hsp70 (coding for the 70-kDa heat-shock protein), and c-fos genes in HeLa cells exposed to Zn, Cd, Ag, Hg, Cu(II), Co, or Ni ions. Transcripts from these three genes were increased after exposure to wide ranges of metals, but each gene was unique in its induction kinetics. Generally, induction was observed at lower metal concentrations in the order of MT-IIA, hsp70, and c-fos. These genes also showed differential responses in time course: more rapid induction was observed in the order of c-fos, hsp70, and MT-IIA after exposure to Zn or Cd. Since the metal-responsive element (MRE) and heat shock element (HSE) of the MT-IIA and hsp70 genes, respectively, are thought to be the cis-acting DNA elements that mediate metal response, we compared the properties of proteins that specifically bind to these elements. MRE-binding activity was detected only in the extract from cells exposed to Zn. By contrast, HSE-binding activity was detected in extracts from cells treated with Zn, Cd, Ag, and Cu. The former was also activated by Zn in vitro, while the latter was not. Each of these DNA-binding activities showed no affinity to the recognition sequence of the other. These results demonstrate that the human metal-inducible genes have broad ranges of response to a variety of heavy metals, but suggest that they are probably regulated through independent mechanisms.

Regulation of the murine NMDA-receptor-subunit NR2C promoter by Sp1 and fushi tarazu factor1 (FTZ-F1) homologues

We have cloned the 5'-region of the murine N-methyl-d-aspartate (NMDA) receptor channel subunit NR2C (GluRepsilon3) gene and characterized the cis- and trans-activating regulatory elements responsible for its tissue specific activity. By using a native epsilon3-promoter/lacZ-construct & various 5'-deletion constructs, we compared beta-galactosidase expression in non-neuronal NIH3T3 cells and in neuronal epsilon3-gene-expressing HT-4 cells and show that large parts of the epsilon3 promoter are responsible for the repression of the epsilon3 gene in non-neuronal cells. Deletion of exon 1 sequences led to an enhancement of epsilon3 transcription, suggesting a role of the 5'-untranslated region in epsilon3 gene regulation. Sequence analysis of the promoter region revealed potential binding sites for the transcription factor Sp1, the murine fushi tarazu factor1 (FTZ-F1) homologues, embryonic LTR binding proteins (ELP1,2,3) and steroidogenic factor (SF-1), as well as for the chicken ovalbumin upstream promoter transcription-factor (COUP-TF). Electrophoretic mobility shift assays confirmed specific binding of Sp1, SF-1 and COUP-TFI. Whereas point mutation studies indicate that, in neuronal HT-4 cells, Sp1 is apparently not critically involved in basal epsilon3 gene transcription, SF1 is a positive regulator. This was evident from a selective enhancement of epsilon3-promoter-driven reporter gene expression upon cotransfection of an SF1-expression vector, which was reverted by deletion and point mutation of the SF1 binding site.

Genomic cloning and promoter analysis of the mouse 105-kDa heat shock protein (HSP105) gene

The 105-kDa heat shock protein (HSP105) is a member of the high-molecular-mass heat shock protein family. We have isolated and characterized the mouse HSP105 gene including about 1.2 kb of the 5'-flanking region. The mouse HSP105 gene spans about 22 kb, consisting of 18 exons separated by 17 introns. Southern blotting analysis revealed the existence of a single copy of HSP105. Primer extension analysis revealed that the transcription initiation site was located 165 bp upstream of the ATG translation initiation codon. The 5'-promoter region of the HSP105 gene contained a TATA box, a CAAT box, an inverted CAAT box, and two GC boxes. Two heat shock element (HSE) sequences were found as four nGAAn repeats at nt -64 and nt -128. Promoter analysis using deletion derivatives revealed that a minimal region which contained the two consensus HSE sequences was active in response to heat shock and also for constitutive expression of the gene.

Decrease with age in methylcytosines in the promoter region of receptor for advanced glycated end products (RAGE) gene in autopsy human cortex

Changes with age in the methylation status of cytosines in the promoter region of the receptor for advanced glycated end products (RAGE) in autopsy human cortex were investigated, using the bisulfite method, polymerase chain reaction (PCR), and direct sequencing of PCR products. The total number of methylcytosines significantly decreased with age. While the number of methylated cytosines at CpG dinucleotides was stable throughout adult life, that at sites other than CpG dinucleotides significantly decreased with age in cases >/=70 years old. Of 13 transcription factor binding sites, cytosines in CpG doublets in NF-IL6 and SP-1 binding sites were methylated in all cases, suggesting that these sites are repressed throughout adulthood. In contrast, the number of methylcytosines in AP-2 or SP-1 binding sites located at CpC, CpA, or CTG was significantly lower or at least tended to be lower in cases >/=70 years than <70 years old. These reductions in the number of methylcytosines at transcription factor binding sites may increase expression of RAGE, which may in turn play a role in aging of the brain.

Mutations in the promoter reveal a cause for the reduced expression of the human manganese superoxide dismutase gene in cancer cells

Manganese superoxide dismutase (MnSOD) has been shown to play an important role in preventing the development of cancer. MnSOD activity is reduced in many transformed cells and tumor tissues. We previously showed that the reduced level of MnSOD activity in cancer cells was not due to a defect in the primary structure of MnSOD protein, but rather was due to defects in gene expression. To elucidate the cause for the reduced expression of human MnSOD in cancer, we investigated the nucleotide sequence in the regulatory region of the MnSOD gene in a normal human cell line and various human tumor cell lines. A DNA fragment spanning 3.4 kb 5' flanking region of the MnSOD gene isolated from a normal human genomic DNA library was used to determine the DNA sequence of MnSOD promoter. PCR primers were used for amplification of the 3.4 kb 5' flanking region of the human MnSOD gene in cancer cells. Sequence analysis identified three heterozygous mutations in the proximal region of the promoter in five human tumor cell lines. These mutations, clustered around the GC-rich region of the human MnSOD promoter, change the binding pattern of AP-2 and lead to a reduction in transcription activity using a luciferase reporter assay system. These results suggest that the reduced level of MnSOD expression in some tumor cells is, at least in part, due to a defect in the DNA sequence of the promoter region.