Transcription initiation from the dihydrofolate reductase promoter is positioned by HIP1 binding at the initiation site

Context is key: Understanding the regulation, functional control, and activities of the p53 tumour suppressor

The p53 tumour suppressor is considered one of the most critical genes in cancer biology. By upregulating apoptosis, cell cycle arrest, and DNA damage repair in normal cells, p53 prevents the propagation of cells with tumorigenic potential; therefore, mutations in p53 are associated with carcinogenic transformation and can be accompanied by the accumulation of a novel gain-of-function oncogenic protein, mutant p53. Although p53 is most often understood to utilize context-dependent post-translational modifications to achieve regulation of its many target genes, recent research has also sought to define other mechanisms of regulating p53 gene expression prior to translation and to understand how this alternative regulation of p53 may influence target gene expression and cellular outcome. This review attempts to summarize what is known about p53 regulation at the transcriptional, post-transcriptional, and post-translational levels while paying special attention to the ways in which context may influence p53 regulation and subsequent regulation of its target genes.

Upstream stimulatory factor 2 activates the mammalian F1F0 ATP synthase alpha-subunit gene through an initiator element

The F1F0 ATP synthase is the central enzyme complex of the mitochondrial oxidative phosphorylation system synthesizing ATP from ADP and Pi. Our laboratory has been studying the transcriptional regulation of the nuclear gene that encodes the alpha-subunit of the mammalian mitochondrial ATP synthase complex (ATPA). We have previously identified an initiator element in the core promoter that plays an important role in expression of this gene. In this article, we demonstrate that ectopic expression of the transcription factor, upstream stimulatory factor 2 (USF2), transactivates the ATPA gene through this initiator element. Importantly, cotransfection of a dominant-negative USF2 mutant significantly reduces both the basal activity and the level of activation of the ATPA initiator by coexpressed USF2 demonstrating the role of endogenous USF2 proteins in this activation. We also identify several nucleotides in the ATPA initiator element that are important for both basal activity and USF2-dependent transactivation. We have also previously determined that the binding of the multifunctional regulatory protein, YY1, to this initiator element can positively regulate the ATPA gene. Here, we show that expression of YY1 together with USF2 results in a decreased level of activation of the ATPA initiator relative to expression of USF2 alone, suggesting competition between these two regulatory proteins.

Sp1 activation of RNA polymerase II transcription complexes involves a heat-labile DNA-binding component

We have identified a component of the eukaryotic RNA polymerase II transcriptional machinery that is more heat-labile than TFIID. DHFR transcriptional activity was severely reduced in 40 degrees C heat-treated extracts in which TFIID was fully active. This heat-labile activity was required for the transcription of both TATA box and non-TATA box promoters that are activated by the transcription factor Sp1. Gel mobility shifts indicated that Sp1 DNA binding activity was heat-labile, and the addition of purified Sp1 to 40 degrees C heat-treated extracts fully restored DHFR transcriptional activity. In contrast, the addition of Sp1 to 47 degrees C heat-treated extract did not result in transcriptional activity from the DHFR promoter. We conclude that reduction in Sp1 DNA binding activity is partially responsible for the heat-sensitive loss of DHFR transcriptional activity, but that a second essential activity is also inactivated by 47 degrees C heat-treatment. The discovery of this heat-labile component of Sp1 activation has two important implications in the analysis of transcriptional regulation. First, it demonstrates that heat-treated extracts are not appropriate for examination of the involvement of TFIID in the transcription of Sp1-activated promoters. Second, it explains the previously reported low-temperature optima for transcription from the DHFR promoter and demonstrates that transcriptional studies of Sp1-activated promoters should not be performed at 30 degrees C.

Temporal and spatial control of gene expression in horticultural crops

Biotechnology provides plant breeders an additional tool to improve various traits desired by growers and consumers of horticultural crops. It also provides genetic solutions to major problems affecting horticultural crops and can be a means for rapid improvement of a cultivar. With the availability of a number of horticultural genome sequences, it has become relatively easier to utilize these resources to identify DNA sequences for both basic and applied research. Promoters play a key role in plant gene expression and the regulation of gene expression. In recent years, rapid progress has been made on the isolation and evaluation of plant-derived promoters and their use in horticultural crops, as more and more species become amenable to genetic transformation. Our understanding of the tools and techniques of horticultural plant biotechnology has now evolved from a discovery phase to an implementation phase. The availability of a large number of promoters derived from horticultural plants opens up the field for utilization of native sequences and improving crops using precision breeding. In this review, we look at the temporal and spatial control of gene expression in horticultural crops and the usage of a variety of promoters either isolated from horticultural crops or used in horticultural crop improvement.

Hepatocyte nuclear factor 4α regulates the expression of the murine pyruvate carboxylase gene through the HNF4-specific binding motif in its proximal promoter

Pyruvate carboxylase (PC) is the first regulatory enzyme of gluconeogenesis. Here we report that the proximal promoter of the murine PC gene contains three binding sites for hepatocyte nuclear factor 4α (HNF4α). These sites include the classical direct repeat 1 (DR1) (-386/-374), non-perfect DR1 (-118/-106) and HNF4α-specific binding motif (H4-SBM) (-26/-14). Under basal conditions, mutation of the non-perfect DR1 decreased promoter activity by 50%, whereas mutation of neither the DR1 nor the H4-SBM had any effect. In marked contrast, only mutation of the H4-SBM decreased HNF4α-transactivation of the promoter activity by 65%. EMSA revealed that HNF4α binds to the DR1site and H4-SBM with similar affinity while it binds poorly to the non-perfect DR1. Interestingly, this non-perfect DR1 also coincides with two E-boxes. Mutation of the non-perfect DR1 together with the nearby E-box reduced USF1- but not USF2-transactivation of promoter activity, suggesting that USF1 partly contributes to the basal activity of the promoter. Substitution of the H4-SBM with the DR1 marginally reduced the basal promoter activity but did not eliminate HNF4α-transactivation, suggesting that HNF4α can exert its effect via DR1 within this promoter context. ChIP-assay confirmed that HNF4α is associated with the H4-SBM. Suppression of HNF4α expression in AML12 cells down-regulated PC mRNA and PC protein by 60% and 50%, respectively, confirming that PC is a target of HNF4α. We also propose a model for differential regulation of P1 promoter of PC gene in adipose tissue and liver.

Molecular regulation of an invasion-related molecule – options for tumour staging and clinical strategies

This review provides a summary of the European Association for Cancer Research Award Lecture, presented at the ECCO13 meeting in Paris in November 2005. It is a brief overview on the biological and clinical relevance of the urokinase receptor (u-PAR), an essential molecule to promote invasive and metastatic tumour phenotype and shown to be associated with early relapse and poor prognosis in many different types of cancers. The review summarizes the most important transcriptional mechanisms regulating u-PAR gene, and will focus on the differential binding of transcription factors to u-PAR promoter elements from studies in resected tumour and normal tissues of colorectal and gastric cancer patients. These studies conducted by our group may help to understand transcriptional mechanisms, which are employed to promote invasion and metastasis, in subpopulations of cancer patients. Such studies could lead to a more target-oriented patient selection and therapy against transcriptional and oncogeneic regulators in cancer.

The rise of DNA methylation and the importance of chromatin on multidrug resistance in cancer

In recent years, the different classes of drugs and regimens used clinically have provided an improvement in tumour management. However, treatment is often palliative for the majority of cancer patients. Transformed cells respond poorly to chemotherapy mainly due to the development of the multidrug resistance (MDR) phenotype. Response to treatment does not generally result in complete remission and disease cure is uncommon for patients presenting with advanced stage cancer. Successful treatment of cancer requires a clearer understanding of chemotherapeutic resistance. Here, we examine what is known of one of the most extensively studied mechanisms of cellular drug resistance. The human multidrug resistance gene 1 (MDR1) is associated with expression of p-glycoprotein (Pgp). A transmembrane protein, Pgp acts as an efflux pump and reduces intracellular drug levels and thus its effectiveness as an antitumor agent. The precise mechanism of transcriptional regulation has been unclear due to the complex regulatory nature of the gene. It has become increasingly apparent that trans-activation or genetic amplification is by no means the only mechanism of activation. Consequently, alternative pathways have received more attention in the area of epigenetics to help explain transcriptional competence at a higher level of organization. The goal of this article is to highlight important findings in the field of methylation and explain how they impinge on MDR1 gene regulation. In this review, we cover the current information and postulate that epigenetic modification of MDR1 chromatin influences gene transcription in leukaemia. Finally, we explore transcriptional regulation and highlight recent progress with engineered ZFP's (zinc finger proteins).

Molecular regulation of urokinase-receptor gene expression as one potential concept for molecular staging and therapy

The urokinase-receptor (u-PAR) is a central molecule of invasion and metastasis promoting plasminogen-dependent extracellular matrix degradation in diverse carcinoma types such as gastric or colon cancer. Overexpression of u-PAR has been reported to occur mainly at the transcriptional level in malignant cells, and has been shown to indicate a poor clinical prognosis of cancer patients. This review will give an overview on experimental findings on u-PAR and its function, molecular mechanisms of its regulation, and its impact for future clinical decision planning and potential therapeutic concepts.

Cloning and characterization of the human UDP-glucuronosyltransferase 1A8, 1A9, and 1A10 gene promoters: differential regulation through an interior-like region

The human UDP-glucuronosyltransferases, UGT1A8, 1A9, and 1A10, are closely related in sequence and have a major role in the elimination of lipophilic chemicals by glucuronidation. UGT1A8 and 1A10 are expressed exclusively in the gastrointestinal tract, whereas UGT1A9 is expressed mainly in the liver and kidneys. To determine the factors contributing to the extrahepatic expression of these UDP-glucuronosyltransferases, we have cloned and characterized the promoters of the UGT1A8, 1A9, and 1A10 genes and studied their regulation in the colon cell line, Caco2. Their transcription start sites were mapped, and a functional overlapping Sp1/initiator-like site was identified which strongly contributed to UGT1A8 and 1A10 promoter activity. The high promoter activity of UGT1A8 and 1A10 correlated with the binding of nuclear proteins (complex B) to this region. Two-bp differences in the corresponding site in the UGT1A9 promoter prevented the binding of complex B and reduced promoter activity. Although Sp1 was able to bind to the Sp1/initiator-like site, its binding was dispensable for promoter activity. However, the binding of Sp1 to a second Sp1 site 30 bp 5' to the Sp1/initiator-like site greatly enhanced the activity of the UGT1A8 and 1A10 promoters. These results provide evidence that the UGT1A8, 1A9, and 1A10 genes are differentially regulated through an initiator element in their 5'-flanking regions.

Identification and characterization of a novel enhancer for the human MCT-1 oncogene promoter

Cloning and characterization of the promoter region for the MCT-1 oncogene is described. We used luciferase assays to identify cis-acting elements responsible for human MCT-1 promoter function. The MCT-1 promoter is TATA-less with a consensus initiator element located at the transcription start site and facilitated by two Sp1 sites that directs basal transcription. Deletion of a region of the MCT-1 promoter (-133 to -122) resulted in significant decrease in luciferase activity, suggesting that this region contains a positive cis-acting element. Using mobility shift assays with a 26-mer oligonucleotide, which contains this fragment and its flanking regions, we demonstrated the presence of sequence-specific DNA-binding protein in both Jurkat and Hela nuclear extracts that we designated as LMBF (for lymphoid MCT-1 binding factor). This 26-mer oligonucleotide containing the LMBF binding site is required for maximum transcriptional activity of the MCT-1 promoter. Although the 26-mer oligonucleotide contains a sequence with strong homology to a heat-shock factor consensus, competitive electrophoretic mobility shift assay (EMSA) analysis demonstrated that the binding protein is not a known member of heat shock family. Furthermore, this sequence when placed in reverse orientation downstream of the luciferase gene was able to enhance luciferase activity driven by a minimal promoter. These data are consistent with this sequence behaving as an enhancer. Finally, Southwestern blot analysis revealed a 96-kDa protein capable of binding a probe containing the LMBF binding site.

Transcriptional regulation of the urokinase receptor (u-PAR)--a central molecule of invasion and metastasis

The phenomenon of tumor-associated proteolysis has been acknowledged as a decisive step in the progression of cancer. This short review focuses on the urokinase receptor (u-PAR), a central molecule involved in tumor-associated invasion and metastasis, and summarizes the transcriptional regulation of u-PAR. The urokinase receptor (u-PAR) is a heavily glycosylated cell surface protein and binds the serine protease urokinase specifically and with high affinity. It consists of three similar cysteine-rich repeats and is anchored to the cell membrane via a GPI-anchor. The u-PAR gene comprises 7 exons and is located on chromosome 19q13. Transcriptional activation of the u-PAR promoter region can be induced by binding of transcription factors (Sp1, AP-1, AP-2, NF-kappa B). One current study gives an example for transcriptional downregulation of u-PAR through a PEA3/ets transcriptional silencing element. Knowledge of the molecular regulation of this molecule in tumor cells could be very important for diagnosis and therapy in the near future.

Myc recruits P-TEFb to mediate the final step in the transcriptional activation of the cad promoter

The c-Myc protein is up-regulated in many different types of cancer, suggesting that a detailed understanding of Myc function is an important goal. Our previous studies have focused on determining the mechanism by which Myc activates transcription using the target gene cad as an experimental model. Previously, we found that Myc activates cad transcription at a post-RNA polymerase II recruitment step and that the Myc transactivation domain interacts with a number of cdk-cyclin complexes. We now extend these studies to determine the role of these cyclin-cdk complexes in Myc-mediated transactivation. We have found that cyclin T1 binding to Myc localizes to the highly conserved Myc Box I, whereas cdk8 binding localizes to the amino-terminal 41 amino acids of the Myc transactivation domain. We showed that recruitment of cdk8 is sufficient for activation of a synthetic promoter construct. In contrast, the ability of Myc to activate transcription of the cad promoter correlates with binding of cyclin T1. Furthermore, recruitment of cyclin T1 to the cad promoter via a Gal4 fusion protein or through protein-protein interaction with the HIV-1 Tat protein can also activate cad transcription. These results suggest that Myc activates transcription by stimulating elongation and that P-TEFb is a key mediator of this process.

Initiation site binding protein and the initiator-like promoter element of mouse mammary tumor virus

The mouse mammary tumor virus (MMTV) promoter contains an element near its transcription initiation site that is recognized by a protein termed initiation site binding protein (ISBP). Spacing between the TATA box and the ISBP site is important for MMTV promoter function, as altered spacing results in heterogeneity in start site selection in vitro and in vivo. The sequence of the ISBP site is related to initiator elements common in many RNA polymerase II promoters. However, binding of partially purified ISBP to several promoters that contain well-characterized initiator elements was not detected; these promoters included binding sites for a number of previously identified initiator-binding proteins. Partially purified ISBP did, however, bind with high affinity to sequences near the initiation sites of the SV40 major late and adenovirus 2 E1B promoters.

Finding motifs using random projections

The DNA motif discovery problem abstracts the task of discovering short, conserved sites in genomic DNA. Pevzner and Sze recently described a precise combinatorial formulation of motif discovery that motivates the following algorithmic challenge: find twenty planted occurrences of a motif of length fifteen in roughly twelve kilobases of genomic sequence, where each occurrence of the motif differs from its consensus in four randomly chosen positions. Such "subtle" motifs, though statistically highly significant, expose a weakness in existing motif-finding algorithms, which typically fail to discover them. Pevzner and Sze introduced new algorithms to solve their (15,4)-motif challenge, but these methods do not scale efficiently to more difficult problems in the same family, such as the (14,4)-, (16,5)-, and (18,6)-motif problems. We introduce a novel motif-discovery algorithm, PROJECTION, designed to enhance the performance of existing motif finders using random projections of the input's substrings. Experiments on synthetic data demonstrate that PROJECTION remedies the weakness observed in existing algorithms, typically solving the difficult (14,4)-, (16,5)-, and (18,6)-motif problems. Our algorithm is robust to nonuniform background sequence distributions and scales to larger amounts of sequence than that specified in the original challenge. A probabilistic estimate suggests that related motif-finding problems that PROJECTION fails to solve are in all likelihood inherently intractable. We also test the performance of our algorithm on realistic biological examples, including transcription factor binding sites in eukaryotes and ribosome binding sites in prokaryotes.

Multiple transcription initiation sites, alternative splicing, and differential polyadenylation contribute to the complexity of human neurofibromatosis 2 transcripts

Northern blot analysis has shown that the human neurofibromatosis type 2 (NF2) cDNA hybridizes to multiple RNA species. To examine whether these hybridizing RNA species represent NF2 transcripts, we cloned the complete NF2 cDNA by a combination of techniques: 5' and 3' rapid amplification of cDNA ends, RT-PCR, and searching and sequencing the NF2-related cDNA clones from the IMAGE consortium. We showed that human NF2 transcripts initiate at multiple positions. Analogous to those reported previously, NF2 transcripts undergo alternative splicing in the coding exons. We isolated eight alternatively spliced NF2 cDNA isoforms, including one that contains a new exon termed exon 2', which potentially could encode proteins of different sizes. We assembled the overlapping cDNA fragments, and the longest NF2 cDNA, containing all 17 exons, consists of 6067 nucleotides, which is consistent with the size of the major RNA species hybridized to the NF2 probe. The cDNA has a 425-nucleotide 5' untranslated region upstream from the ATG start codon, and a long 3' untranslated region of 3869 nucleotides. We also isolated two shorter NF2 cDNAs that were terminated by different polyadenylation signal sequences, which indicates that differential usage of multiple polyadenylation sites also contributes to the complexity of human NF2 transcripts. By reference to the transcription initiation site mapped, we analyzed the 5' flanking sequence of the human NF2 gene. Transient transfection analysis in human 293 kidney, SK-N-AS neuroblastoma, and NT2/D1 teratocarcinoma cells with NF2 promoter-luciferase chimeric constructs revealed a core promoter region extending 400 base pairs from the major transcription initiation site. Although multiple regions are required for full promoter activity, a site-directed mutagenesis experiment identified a GC-rich sequence (position -58 to -46), which could be bound by transcription factor Sp1, as a positive cis-acting regulatory element. Cotransfection studies in Drosophila melanogaster SL2 cells showed that Sp1 could activate the NF2 promoter through the GC-rich sequence.

c-Myc mediates activation of the cad promoter via a post-RNA polymerase II recruitment mechanism

The c-Myc protein is a site-specific DNA-binding transcription factor that is up-regulated in a number of different cancers. We have previously shown that binding of Myc correlates with increased transcription of the cad promoter. We have now further investigated the mechanism by which Myc mediates transcriptional activation of the cad gene. Using a chromatin immunoprecipitation assay, we found high levels of RNA polymerase II bound to the cad promoter in quiescent NIH 3T3 cells and in differentiated U937 cells, even though the promoter is inactive. However, chromatin immunoprecipitation with an antibody that recognizes the hyperphosphorylated form of the RNA polymerase II carboxyl-terminal domain (CTD) revealed that phosphorylation of the CTD does correlate with c-Myc binding and cad transcription. We have also found that the c-Myc transactivation domain interacts with cdk9 and cyclin T1, components of the CTD kinase P-TEFb. Furthermore, activator bypass experiments have shown that direct recruitment of cyclin T1 to the cad promoter can substitute for c-Myc to activate the promoter. In summary, our results suggest that c-Myc activates transcription of cad by stimulating promoter clearance and elongation, perhaps via recruitment of P-TEFb.

The human complement C9 gene: structural analysis of the 5' gene region and genetic polymorphism studies

C9 is the last of the human complement components creating the membrane attack complex. The single chain serum protein is encoded by a gene located on chromosome 5p13 that is composed of 11 exons. With the aid of inverse PCR, the hitherto unknown regions flanking exon 1 and the 3' part of exon 11 (3'UTR) have been sequenced. A computer-based analysis of the 300-bp region located just upstream of the AUG start codon showed homologies to known DNA modules which affect the transcriptional regulation of certain genes. The most striking of these is a sequence that may substitute the missing TATA box in initiating C9 transcription. In the 3'UTR, three successive polyadenylation signals were found. Although the C9 protein is invariant, four different single nucleotide polymorphisms (SNPs) have been observed at the DNA level by exon-specific PCR and direct sequencing. None of them changes the amino acid composition of the mature protein. Due to a C --> T transition in exon 1 at cDNA position 17, the fifth amino acid of the leader peptide may be either an arginine or a tryptophane. Using either PCR/ RFLP analysis (exons 1 and 11) or allele-specific PCR (intron 1 and exon 4), each polymorphism can be characterized without sequencing. All of the exon 1, intron 1 and exon 11 variants could be detected in small population samples of European, Thai or South American Indian origin. In contrast, the exon 4 C variant was observed only once in a European. The first three SNPs can be combined to designate eight different 'C9 alleles'. Of these, six have actually be found. These data provide strong evidence that several mutation and recombination events occurred in the course of C9 gene evolution.

Structural and promoter regions of the murine pyruvate carboxylase gene

We have cloned and sequenced the gene encoding mouse pyruvate carboxylase (mPC) [EC 6.4.1.1]. The coding region contains 19 exons, one 5'-untranslated region exon, and 19 introns in 22 kb of genomic DNA. This gene's exon/intron organization is highly conserved with respect to rat and human PC genes. The mPC gene promoter lacks canonical TATA and CCAAT boxes, in common with a number of housekeeping genes. Transient expressions in COS-1 of a luciferase reporter gene under the control of 5'-nested deletions of the 5'-flanking sequence of the mPC gene have identified the 166-bp minimal sequence required for basal transcription. Alternative splicing at the 5'-untranslated region exon of the mouse PC gene results in the production of two alternate transcripts bearing different 5'-noncoding regions. Both transcripts are highly expressed in kidney and liver and moderately expressed in heart and testis and expressed at a low level in spleen.

Nd1, a novel murine Kelch family protein, may play the role of a housekeeping gene

The murine Nd1 gene encodes a novel Kelch family protein and expresses two forms of mRNA, long (Nd1-L) and short (Nd1-S), in various tissues. We characterized the genomic organization of the Nd1 gene, and found that Nd1-L and Nd1-S consist of 16 and nine exons respectively, and that exons I-VIII are shared between them. Three transcription initiation sites were identified in the 5'-flanking region and the most 3' side (+1) is likely to be a major one. Promoter analysis revealed that the region between positions -247 and -86 was sufficient for expression, and that two Sp1-binding sites and one NF-kappaB-binding site in the region were critical for promoter activity. Furthermore, the promoter region lacks a TATA and a CAAT box and has a highly GC-rich region with two important Sp1-binding sites. These characteristics of the Nd1 gene promoter are similar to the properties of housekeeping genes.

Upstream stimulatory factor 2 stimulates transcription through an initiator element in the mouse cytochrome c oxidase subunit Vb promoter

Upstream stimulatory factor (USF) is a basic helix-loop-helix-leucine zipper transcription factor that plays an important role in transcriptional activation and cell proliferation. In this article, we demonstrate that the mouse cytochrome c oxidase subunit Vb gene (Cox5b) can be transactivated by ectopic expression of USF2 through an initiator (Inr) element in the core promoter. Importantly, using a dominant-negative mutant of USF2, we demonstrate the role of endogenous USF2 proteins in the transcriptional activation of the Cox5b Inr. Domains of USF2 encoded by exon 4, exon 5 and the USF-specific region are important for maximum activation of the Cox5b Inr. Using the adenovirus E1A oncoprotein, we show that p300/CBP acts as a coactivator in the USF2-dependent activation of the Cox5b Inr. We also demonstrate that although expression of multifunctional regulatory factor, Yin Yang 1 (YY1), can stimulate transcription of the Cox5b Inr to a modest extent, expression of YY1 together with USF2 greatly reduces the level of activation of the Cox5b Inr. Furthermore, we show that the transcription factor, Sp1, represses both the YY1- and the USF2-dependent activation of the Cox5b Inr, indicating competition among Sp1, YY1, and USF2.

Human Müllerian-inhibiting substance promoter contains a functional TFII-I-binding initiator

Müllerian-inhibiting substance (MIS) plays an essential role in mammalian male sexual development; thus, it is important to determine how the tightly regulated expression of the MIS gene is transcriptionally controlled. Transcription of eukaryotic genes is dependent on regulatory elements in the enhancer and one or both distinct elements in the core promoter: the TATA box, and the initiator (Inr) element. Because the human MIS gene does not contain a consensus TATA and has not been reported to contain an Inr element, we hypothesized that the initiator region of the core promoter was essential for promoter activity. Transient transfection assays were conducted using an immortalized Embryonic Day 14.5 male rat urogenital ridge cell line (CH34) that expresses low levels of MIS. These studies revealed that promoter activity is dependent on the region around the start site (-6 to +10) but not on the nonconsensus TATA region. Electrophoretic mobility shift assays demonstrated that the human MIS initiator sequence forms a specific DNA-protein complex with CH34 cell nuclear extract, HeLa cell nuclear extract, and purified TFII-I. This complex could be blocked or supershifted by the addition of antibodies directed against TFII-I. These data suggest that the human MIS gene contains a functional initiator that is specifically recognized by TFII-I.

Characterization of the 5'-flanking region of the gene encoding bovine adenylate kinase isozyme 3

We have characterized the 5'-flanking region of the gene encoding bovine adenylate kinase isozyme 3 (AK3). S1 mapping analysis revealed multiple transcription start points in the bovine AK3 gene. The promoter activities were tested in HeLa cells using the chloramphenicol acetyltransferase (CAT) gene as a reporter. The CAT analysis showed that the basal promoter sequence was located within the region from -189 to +228. In the presence of short DNA fragments of the 5'-flanking region as competitors, the transcriptional activity of the bovine AK3 promoter changed depending on the fragments used. The results identified the basal regulatory elements in the proximal promoter region.

Molecular cloning, genomic organization, and identification of the promoter for the human pituitary tumor transforming gene (PTTG)

Recently, we cloned and sequenced cDNA of a potent pituitary tumor transforming gene (PTTG) from human testis and showed that this gene is expressed highly in various human tumors, including tumors of the pituitary and adrenal glands, and the liver, kidney, endometrium, uterus, and ovary. To determine the genomic organization of the PTTG and its transcriptional regulation in tumors, we isolated the gene. The PTTG spans more than 10kb and contains five exons and four introns. Primer extension and RNA protection assays indicated a transcription start site at an adenine residue at 37 bases upstream of the translation start site (ATG). Analysis of the 5' flanking region of the gene revealed the existence of three SP1/GC boxes, three AP1 and one AP2 binding sequences, a cyclic AMP response element sequence, and an insulin response element sequence. The promoter activity of the PTTG was evaluated by transfecting a human ovarian tumor cell line (SKOV3) and a mouse fibroblast cell line (NIH 3T3) with a chimeric fusion construct containing the 5' flanking sequence (nucleotide from -1336 to +34) and luciferase reporter gene (pluc 1370). The promoter activity of this construct was 210-fold higher in SKOV3 and 20-fold higher in NIH 3T3 cells than the promoterless vector. Deletion of sequences at the 5' end of the pluc 1370 construct from nucleotide -1336 to -1157 (pluc 1190), from nucleotide -1336 to -977 (pluc 1010) and from nucleotide -1336 to -707 (pluc 740) further increased luciferase activity. Further deletion of the 5' sequence from nucleotide -1336 to -407 (pluc 440), and from nucleotide -1336 to -127 (pluc 160) decreased activity by 95%. These results suggest that the sequence from nucleotide -126 to +34 is sufficient for PTTG promoter activity and that the sequence between nucleotide -706 and -407 contains an enhancer element. PTTG promoter activity was eight- to ten-fold higher in SKOV3 cells than NIH 3T3 cells, suggesting a basis for the tumor-specific expression of the PTTG. Knowledge of the genomic organization and the promoter region of the human tumor transforming gene will allow further studies of possible disorders of the PTTG as well as facilitate elucidation of the transcriptional control of PTTG expression in human tumors.

Molecular cloning, expression and physical mapping of the human methionine synthase reductase gene

Methionine synthase reductase (EC 2.1.1.135) is a flavoprotein essential for maintenance of methionine synthase in an active state. We characterized the human gene for methionine synthase reductase (MTRR). The gene is approximately 34kb and comprises 15 exons, varying in size from 43 to 1213bp, and 14 introns whose sizes vary from 108bp to 5kb. The positions of several junctions are conserved between the MTRR gene and the C. elegans ortholog, as well as with the rat cytochrome P450 reductase gene. A 1.3kb CpG island encompasses the 5'-flanking region and exon 1 and extends into intron 1. A short region including the transcription start site is sufficient to confer promoter activity, with a better outcome when accompanied by intron 1. The promoter region contains putative binding sites for Sp1, AP-1, AP-2 as well as CAAT motifs, but no consensus TATA box. Primer extension analysis revealed a single major transcription start site, located 137bp upstream of the previously reported initiator ATG. An alternative splicing event involving a portion of exon 1 predicts that translation can potentially be initiated at two different ATG codons. The gene was physically assigned to a narrow area between markers WI1755 and D5S1957.

Cloning and functional characterization of the promoter region of the gene encoding human adenylate kinase isozyme 3

The 5'-flanking region of the gene encoding human adenylate kinase isozyme 3 was isolated and compared with that of the bovine AK3 gene previously characterized. Four conserved DNA sequences (elements-a, -b, -c, and -d) were found in both the regions. The promoter activities were analyzed in HeLa cells using promoter-CAT reporter constructs. The proximal promoter region (-217 to +261), which contains three of four conserved elements, gave a maximum promoter activity. In a series of electrophoretic mobility-shift assays, DNA fragments and double-stranded oligodeoxyribonucleotides containing sequences of the four conserved elements interacted with nuclear extracts of HeLa cells. The a-element contained the W-element, while the d-element, which had a high G + C content, was a novel regulatory cis-element distinct from the GC box. The b- and c-elements were homologous to each other and had a motif resembling downstream promoter element. Mutations of the c- and d-elements significantly reduced the promoter activity, indicating that the c- and d-elements in the AK3 promoter are crucial. These elements may also be involved in the transcriptional regulation of other TATA-less genes.

Activation of the murine dihydrofolate reductase promoter by E2F1. A requirement for CBP recruitment

The E2F family of heterodimeric transcription factors plays an important role in the regulation of gene expression at the G1/S phase transition of the mammalian cell cycle. Previously, we have demonstrated that cell cycle regulation of murine dihydrofolate reductase (dhfr) expression requires E2F-mediated activation of the dhfr promoter in S phase. To investigate the mechanism by which E2F activates an authentic E2F-regulated promoter, we precisely replaced the E2F binding site in the dhfr promoter with a Gal4 binding site. Using Gal4-E2F1 derivatives, we found that E2F1 amino acids 409-437 contain a potent core transactivation domain. Functional analysis of the E2F1 core domain demonstrated that replacement of phenylalanine residues 413, 425, and 429 with alanine reduces both transcriptional activation of the dhfr promoter and protein-protein interactions with CBP, transcription factor (TF) IIH, and TATA-binding protein (TBP). However, additional amino acid substitutions for phenylalanine 429 demonstrated a strong correlation between activation of the dhfr promoter and binding of CBP, but not TFIIH or TBP. Finally, transactivator bypass experiments indicated that direct recruitment of CBP is sufficient for activation of the dhfr promoter. Therefore, we suggest that recruitment of CBP is one mechanism by which E2F activates the dhfr promoter.

Role of the Ets transcription factors in the regulation of the vascular-specific Tie2 gene

The Tie2 gene encodes a vascular endothelium-specific receptor tyrosine kinase that is required for normal vascular development and is also upregulated during angiogenesis. The regulatory regions of the Tie2 gene that are required for endothelium-specific gene expression in vivo have been identified. However, the transcription factors required for Tie2 gene expression remain largely unknown. We have identified highly conserved binding sites for Ets transcription factors in the Tie2 promoter. Mutations in 2 particular binding sites lead to a 50% reduction in the endothelium-specific activity of the promoter. We have compared the ability of several members of the Ets family to transactivate the Tie2 promoter. Our results demonstrate that 1 of 3 distinct isoforms of the novel Ets transcription factor NERF, NERF2, is expressed in endothelial cells and can strongly transactivate the regulatory regions of the Tie2 gene in comparison to other Ets factors, which have little or no effect. NERF2 can bind to the Tie2 promoter Ets sites in electrophoretic mobility shift assays. These studies support a role for Ets factors in the regulation of vascular-specific gene expression and suggest that the novel Ets factor NERF2 may be a critical transcription factor in specifying the expression of the Tie2 gene in vascular endothelial cells.

Organization of the gene for gelatin-binding protein (GBP28)

GBP28 is a novel human plasma gelatin-binding protein that is encoded by apM1 mRNA, expressed specifically in adipose tissue. Three overlapping clones (two lambda clones and one BAC clone) containing the human plasma gelatin-binding protein (GBP28) gene were isolated and characterized. The GBP28 gene spans 16kb and is composed of three exons from 18bp to 4277bp in size with consensus splice sites. The sizes of the two introns were 0.8 and 12kb, respectively. The gene's regulatory sequences contain putative promoter elements, but no typical TATA box. The third exon of this gene contains a long 3'-untranslated sequence containing three Alu repeats. The exon-intron organization of this gene was very similar to that of obese gene, encoding leptin. We also report the chromosome mapping of this gene by fluorescence in situ hybridization (FISH) using a genomic DNA fragment as a probe. The GBP28 gene was located on human chromosome 3q27. The nucleotide sequence data reported in this paper will appear in the DDBJ/EMBL/GenBank nucleotide sequence databases with the accession numbers ABO12163, ABO12164 or ABO12165.

Roles of an Ets motif and a novel CACGAC direct repeat in transcription of the murine dihydrolipoamide dehydrogenase (Dld) gene

The 5'-flanking region of the murine dihydrolipoamide dehydrogenase (Dld) gene was characterized for its promoter activity. DNase I footprinting analysis of the promoter region (-545 bp to +41 bp) revealed six major protein-binding domains (termed P1 to P6) that were protected by NIH3T3 fibroblast nuclear extracts. Transient transfection assays, using a series of nested deletions of the 2.5 kb 5'-flanking region ligated to the chloramphenicol acetyltransferase reporter gene, identified that the -42-bp to +41-bp region, which harbours the P1, P2, and P3 domains, had minimal transcriptional activity. When the 5'-flanking region was extended from -42 bp to -82 bp, there was an approx. 5-fold increase in promoter activity. To identify further the cis elements involved in transcription of the Dld gene (-82 bp to +41 bp), a series of mutations were introduced into this region and evaluated for functional effects using transient transfection and electrophoretic mobility shift assays. Mutation or deletion of the CACGAC direct repeat, located from -61 bp to -46 bp, resulted in minimal promoter activity. Mutation of the Ets motif, located from -37 bp to -32 bp, reduced the minimal promoter activity by approx. 50%, whereas the deletion of this motif almost abolished the promoter activity. These results indicate that: (i) the Ets motif is required for the minimal promoter activity and (ii) the CACGAC direct repeat enhances promoter activity. Database searches failed to identify the direct repeat with the CACGAC motif and hence the CACGAC sequence may represent a novel motif. The requirement of both the Ets motif and the direct repeat element for optimal promoter activity represents a unique combination for gene transcription.

Structure of the rat glucose-dependent insulinotropic polypeptide receptor gene

The Glucose-dependent insulinotropic polypeptide receptor (GIPR) is a member of the secretin-vasoactive intestinal polypeptide family of G-protein coupled receptors possessing seven transmembrane domains. We report here the cloning and the exon-intron structure of the rat GIPR gene, along with the identification and characterization of its 5'-flanking region. The coding region of the GIPR gene spans approximately 10.2 kilobases and contains 13 exons. Three additional exons, two encoding either 5' or 3' untranslated sequences and one contained in a novel alternatively spliced mRNA, were identified. The 5'-flanking sequences contained a number of transcription factor binding motifs, including a cAMP response element, an octamer binding site, three SP1 sites and an initiator element. However, neither a CAAT motif nor TATA box were found. Transient transfection assays demonstrated that the 5'-flanking region of the GIPR gene can efficiently promote transcription in RIN38 cells and that deletion of 50 base pairs containing a potential SPI binding sites leads to a 2.4-fold loss of transcriptional activity. In addition, transient transfection experiments comparing the relative promoter activities of 5'-flanking sequences of the GIPR gene in RIN38 and rat-2 cells suggests that distal negative regulatory sequences may control cell-specific expression.

Alternate promoters and developmental modulation of expression of the chicken GATA-2 gene in hematopoietic progenitor cells

We have isolated and characterized the chicken GATA-2 (cGATA-2) gene. We show that, as in the case of some other members of the GATA gene family, the gene is expressed from alternative first exons. One of the resulting mRNAs represents only a minor form of the GATA-2 mRNA in the cells and tissues we analyzed; the other is ubiquitously expressed. We have defined the minimal promoter that controls expression of this most abundant mRNA and that is necessary for full activity in hematopoietic progenitor cells. The activity of this promoter in transient assays is consistent with developmental differences of expression levels in these cells. We identify within the promoter a previously unrecognized extended CCAAT motif essential for its activity. The organization of the cGATA-2 gene, with alternative first exons and a CCAAT box in the proximal promoter, is similar to that recently described for mouse GATA-2, and the proximal promoter also resembles the only promoter so far described in Xenopus. Nonetheless, the roles of the promoters in development and tissue-specific expression are quite different in these organisms, most strikingly in the mouse, which assigns developmental roles to its proximal and distal promoters that are quite different from those in the chicken. We suggest that although the overall organization may remain the same, the role assigned to each promoter varies among organisms. We identify distant upstream regulatory elements in the cGATA-2 gene that modulate expression from the proximal promoter and that may be responsible for this variation.

Cloning and characterization of the mouse histone deacetylase-2 gene

Histone deacetylase-2 (HDAC2) is a component of a complex that mediates transcriptional repression in mammalian cells. A mouse HDAC2 cDNA was used to identify several recombinant clones containing the entire mouse HDAC2 gene. The mouse HDAC2 gene spans over 36 kilobase pairs and is composed of 14 exons (ranging from 58 to 362 nucleotides in length) and 13 introns (ranging from 75 base pairs to 19 kilobase pairs in length). Primer extension analysis with total RNA from NIH3T3 cells revealed a major transcriptional start site at 221 base pairs 5' of the ATG translational start codon. Upstream of the transcriptional start site, no canonical TATA box was found, but binding sites for several known transcription factors were identified. Transient transfection studies with 5' deletion mutants localized the promoter to no more than 76 base pairs upstream from the major transcriptional start site. Fluorescence in situ hybridization mapped mouse HDAC2 to chromosomal location 10B1, which is in close proximity to the growth factor-inducible gene fisp-12. Information concerning the genomic organization and promoter of HDAC2 will be useful in studies of the regulation of histone deacetylase activities, which in turn are important in studies of the regulation of transcriptional repression in mammalian cells.

Characterization of the initiator and downstream promoter elements of herpes simplex virus 1 late genes

Previously identified cis-acting regulatory elements of herpes simplex virus (HSV) 1 late promoters include a TATA element upstream from the start of transcription, an initiator-like element at the start of transcription, and sequences downstream from the start of transcription. To determine whether these elements are functionally equivalent to similar elements from other eukaryotic genes, model late promoters were constructed using well-characterized regulatory elements from non-HSV genes. These modular promoters were then inserted into the viral genome upstream from a lacZ marker gene. Results showed that a eukaryotic initiator element, along with a TATA element, can function as a late HSV promoter. Several initiator sequences from both viral and nonviral genes were functionally similar to the initiator-like element in HSV-1 late promoters; however, a random sequence of the same size and a similarly located sequence from the HSV-1 early thymidine kinase promoter could not substitute for the initiator element. These results indicate that eukaryotic initiator elements are functionally equivalent to HSV-1 late promoter initiator elements. In addition, the downstream element of the late glycoprotein C promoter was further analyzed by construction of a series of small deletions and insertions. The presence of the downstream glycoprotein C region in a promoter consisting of a strong TATA and initiator element increased mRNA expression by a modest amount; this effect appeared to be sequence specific and dependent on its exact alignment with the upstream elements of the promoter.

Cloning of 5'-flanking region and a polymorphic CTT trinucleotide repeat within 5'-untranslated region of mouse R-type calcium channel alpha1-subunit (Cchra1) gene, and its genetic mapping

The 5'-flanking region of the mouse R-type calcium channel (Cchra1) gene was cloned, and a transcriptional start point (tsp) was determined by rapid amplification of 5'-cDNA end (5'RACE) method. The putative promoter region of the gene contained no obvious TATA or CCAAT element in the expected positions, but multiple putative binding sites for transcriptional factors, such as Sp1, AP-1, AP-2, AP-3, EGR-1, EGR-2, NF-kappaB and HIP1, were detected. We found the existence of a tandem CTT trinucleotide repeat within the 5'-untranslated region (UTR) of the gene, and its polymorphism between C57BL/6J and Mus spretus. Using this polymorphism, the Cchra1 was mapped to the region of chromosome 1 where the synteny to human chromosome 1q was conserved.

Characterization of the human transcobalamin II promoter. A proximal GC/GT box is a dominant negative element

Deletion and mutagenesis of the 5'-flanking region of the human transcobalamin II (TC II) transfected in human intestinal epithelial Caco-2 cells have revealed that TC II promoter activity is: (a) very weak; (b) restricted to a core region (-29 to -163) that contained multiple transcription initiation sites; (c) not dependent on other potential elements, such as a distally localized CCAAT box, a CF1, a HIP1 binding motif and a MED-1 element; (d) modulated weakly by a positive-acting GC box (-568-GAGGCGGTGC) and strongly by a proximal GC/GT overlapping box (-179 CCCCCGCCCCACCCC). Gel shift and immunosupershift analyses demonstrated that both the positive-acting GC box and the negative-acting GC/GT box were recognized by Sp1 and Sp3. Co-transfection studies using Sp1 and/or Sp3 expression plasmids revealed that while Sp1 stimulated, Sp3 repressed Sp1-mediated transactivation of TC II transcription. The proximal GC/GT box also acted as a negative element in human chronic myelogenous leukemia K-562 and HeLa cells. These results suggest that tissue/cell specific expression of the TC II gene may be controlled by the relative ratios of Sp1 and Sp3 that bind to the GC/GT box and the weak promoter activity of TC II is due to the transcriptional repression caused by the binding of Sp3 to the proximal GC/GT box.

GA-binding protein-dependent transcription initiator elements. Effect of helical spacing between polyomavirus enhancer a factor 3(PEA3)/Ets-binding sites on initiator activity

Many eukaryotic RNA polymerase II promoters contain initiator elements which direct accurate transcription in a TATA-independent manner. The PEA3/Ets-binding site (PEA3/EBS) is a common enhancer element in eukaryotic genes and is also found near the transcriptional start sites of many TATA-less promoters. We demonstrate that two PEA3/EBSs driving expression of the luciferase reporter gene, function as a minimal transcriptional initiator element. Maximal levels of transcription was achieved when two PEA3/EBSs, in either orientation, were located on the same face of the DNA helix, and the sites could be separated by up to three helical turns. In vitro transcription start sites directed by PEA3/EBS elements were clustered on either side of the upstream PEA3/EBS and were abolished by immunodepletion of GA-binding protein (GABP) from FM3A cell nuclear extracts. In vivo, co-transfection of GABPalpha and GABPbeta expression vectors enhanced reporter gene expression driven from PEA3/EBS initiator elements. Like other initiator elements, the PEA3/EBS elements were activated synergistically by upstream Sp1-binding sites. Thus, our results establish GABP as both a transcriptional activator factor and as an initiator factor.

A functional YY1 binding site is necessary and sufficient to activate Surf-1 promoter activity in response to serum growth factors

The human Surf-1 and Surf-2 housekeeping genes are divergently transcribed and share a bi-directional, TATA-less promoter. Housekeeping promoters typically contain complex arrays of transcription factor binding sites and several studies have suggested that many of these sites might be functionally redundant. The Surf-1/Surf-2 promoter region contains four factor binding sites; members of the ETS family of transcription factors bind to two of these sites whilst YY1 binds to a third site immediately downstream of the major Surf-1 transcription start point. Here we show that Sp1 binds to the fourth transcription factor binding site. Although YY1 and Sp1 have previously been shown to interact both in vitro and in vivo, these proteins function independently at the Surf-1/Surf-2 promoter. The binding of Sp1 alone is sufficient to bring about full promoter activity in the Surf-2 direction. In contrast, both Sp1 and ETS proteins are required to bring about full promoter activity in the Surf-1 direction. The YY1 binding site is not required for basal transcription in either direction. The YY1 binding site is, however, both necessary and sufficient to confer growth factor inducibility on transcription in the Surf-1 direction. Our data suggest that functionally redundant transcription factor binding sites might not be a general feature of housekeeping promoters.

The rat pyruvate carboxylase gene structure. Alternate promoters generate multiple transcripts with the 5'-end heterogeneity

Pyruvate carboxylase (EC 6.4.1.1) is a biotin-containing enzyme that plays an important role in gluconeogenesis and lipogenesis. Here we report the structural organization of the rat pyruvate carboxylase gene, which spans over 40 kilobases and is composed of 19 coding exons and 4 5'-untranslated region exons. From this data, it is clear that alternative splicing of the primary transcripts from two promoters is responsible for the occurrence of the multiple mRNA species previously reported (Jitrapakdee, S., Walker, M. E., and Wallace, J. C. (1996) Biochem. Biophys. Res. Commun. 223, 695-700). The proximal promoter, which is active in gluconeogenic and lipogenic tissues, contains no TATA or CAAT boxes but includes a sequence that is typical of a housekeeping initiator protein 1 box while the distal promoter contains three CAAT boxes and multiple Sp1 binding sites. Several potential transcription factor binding sites are found in both promoters. A series of 5'-nested deletion constructs of both promoters were fused to a firefly luciferase reporter plasmid and transiently expressed in COS-1 cells. The results show that the 153 and 187 base pairs, preceding the transcription start sites of the proximal and distal promoters, respectively, are required for basal transcription. Insulin selectively inhibits the expression of the proximal promoter-luciferase reporter gene by 50% but not the distal promoter in COS-1 cells, suggesting the presence of an insulin-responsive element in the proximal promoter. A half-maximal effect was found at approximately 1 nM insulin.

Structure and expression of the murine Sp100 nuclear dot gene

The human SP100 gene encodes an autoantigen that colocalizes with two other proteins, PML and NDP52, in distinct nuclear domains, called "nuclear dots" (NDs). NDs do not overlap with other known subnuclear structures, and their function is still unknown. Patients suffering from the autoimmune disease primary biliary cirrhosis often produce antibodies against the SP100 protein. The present study describes the structure and expression of the murine Sp100 gene. In the species Mus caroli, Sp100 consists of 17 exons that are distributed over a range of 52 kb. The human and murine Sp100 promoters are very similar, and both harbor an interferon-stimulated response element. Like its human counterpart, the murine Sp100 gene is responsive to interferon treatment. The house mouse, Mus musculus, harbors the Sp100 gene and a second gene with homology to Sp100, the multicopy Sp100-rs gene. However, in contrast to the genuine mouse homolog, Sp100-rs shares only segmental homology with the human Sp100 gene. Replacement of the murine Sp100 gene by a defective copy is now feasible and should shed light on its function in an animal model.

Methods for studying the biochemical properties of an Inr element binding protein: TFII-I

Transcription initiation in eukaryotic mRNA coding genes is brought about by a host of general transcription factors, which assemble into a functional preinitiation complex (PIC) at the core promoter region, and gene-specific factors, which exert their effects on the rate and/or stability of the PIC. The core promoter region consists of a well-characterized TATA box and/or a less well-characterized pyrimidine-rich initiator element (Inr). While the biochemical mechanisms of TATA-mediated transcription initiation are extensively studied and known to be directed by the TATA binding protein, the mechanisms via the Inr element are poorly understood, as several factors have been shown to bind to an Inr. Here, we describe the biochemical properties of an Inr binding protein, TFII-I, employing the naturally occurring TATA-less but Inr-containing promoter derived from the T-cell receptor beta chain gene (V beta).

Differential regulation of major surface promoter in hepatitis B virus

The major surface promoter of human hepatitis B virus can produce three distinct groups of S transcripts. The initiation sites of these transcripts are in close proximity. Encompassing the ATG for the middle surface protein, the largest S transcript (+1) encodes the middle surface protein whereas the other two (+20 and +31) can only code for small surface protein. Sequence analysis does not reveal any TATA element. In this study, we employ deletion, linker scanning, and linker insertion analyses to study systematically the sequence requirements for the initiations of all three transcripts and their upstream regulatory sequences. Our study reveals that the sequence downstream of -16 is sufficient for precise initiation of all three groups of S transcripts. The 3' boundary of minimal promoter element is +15 for the +1 transcript, whereas it is +39 for both +20 and +31 transcripts. Furthermore, there are distinct sequence requirements for the initiations of three groups of S transcripts. The sequences from -17 to -10 and from -1 to +7 are required for the initiation of +1 transcript, the sequence from +16 to +39 is essential for the +20 transcript, and the sequences from -17 to -10 and from +24 to +39 are required for the + 31 transcript. Our results also suggest that the transcription initiations of major surface promoter may be mediated in part by initiators. The initiations of these three groups of S transcripts are under differential regulation. The region from -39 to -16 containing both negative and positive regulatory elements selectively regulates the transcription levels of the two major S transcripts. Most notably, mutation of the sequence from -17 to -10, which contains a Sp1 site, leads to an increase in the imprecise initiation at +1 site and depresses the initiation of +20 and, to a greater extent, +31 transcript. The relevance of differential regulation of major surface promoter to the varied production of different surface protein isoforms in viral life cycle is discussed.

Molecular cloning and functional characterization of the human cytosolic malic enzyme promoter: thyroid hormone responsiveness

We report the structural and functional features of the 5'-flanking region of the human cytosolic malic enzyme (ME) gene. A 2.2-kb subclone, comprising 1.5 kb upstream of the translation initiation codon, the first exon, and 0.7 kb of flanking intronic region, was sequenced and mapped to chromosome 6. The proximal promoter region is rich in G + C, lacks TATA or CCAAT boxes, and shows multiple transcription start sites, the major one 106 nucleotides upstream the ATG codon. Sequences -59/-13 and -137/-103 conferred maximal promoter activity. Deletional analysis revealed the presence of two regions positively regulated by 3,5,3'-triiodo-L-thyronine (T3). The proximal region confers the strongest T3 inducibility to the human ME as well as to a heterologous promoter. Thyroid hormone receptor beta (TRbeta) binds to an inverted palindromic T3 response element (TRE) at position -105/-87 in a manner that is prevented by T3. Nuclear extracts or in vitro-translated retinoid acid receptor alpha (RXR alpha) shifted the TRbeta retarded band to slower-mobility complexes, which are unaffected by T3. In the absence of T3, overexpression of TRbeta repressed the ME promoter activity, most probably, through binding of TRbeta homodimers to the TRE. Thus, T3 seems to control ME transcription by inducing the dissociation of TRbeta homodimers and the functional activation of liganded heterodimers.

Characterization of the mouse dihydrolipoamide dehydrogenase (Dld) gene: genomic structure, promoter sequence, and chromosomal localization

The mouse dihydrolipoamide dehydrogenase (Dld) gene has been cloned, characterized, and mapped. This nuclear gene encodes a mitochondrial protein that is shared among several alpha-keto acid dehydrogenase complexes and the glycine cleavage system. The Dld gene is contained within an approximately 21-kb region and consists of 14 exons ranging in size from 69 to 521 nucleotides. The open reading frame codes for a preprotein of 509 amino acids with a predicted mature protein of 474 amino acids that is highly conserved among mammalian species (> 90% identical). Primer extension analyses have shown the gene to have transcription initiation sites with tissue-specific differences in relative utilization. The 5' flanking region is G-C rich and lacks a TATA box, but does contain initiator element and multiple transcription factor-binding consensus sequences. Northern blot analysis shows that the Dld mRNA in various tissues is approximately 2.4 kb in size. The Dld gene has been localized to the proximal region of chromosome 12, approximately 21 cM from the centromere.

Expression and regulation of the human and mouse aspartylglucosaminidase gene

Aspartylglucosaminidase (AGA) is a lysosomal enzyme that catalyzes one of the final steps in the degradation of N-linked glycoproteins. Here we have analyzed the tissue-specific expression and regulation of the human and mouse AGA genes. We isolated and characterized human and mouse AGA 5'-flanking sequences including the promoter regions. Primer extension assay revealed multiple transcription start sites in both genes, characteristic of a housekeeping gene. The cross-species comparison studies pinpointed an approximately 450-base pair (bp) homologous region in the distal promoter. In the functional analysis of human AGA 5' sequence, the critical promoter region was defined, and an additional upstream region of 181 bp exhibiting an inhibitory effect on transcription was identified. Footprinting and gel shift assays indicated protein binding to the core promoter region consisting of two Sp1 binding sites, which were sufficient to produce basal promoter activity in the functional studies. The results also suggested the binding of a previously uncharacterized transcription factor to a 23-bp stretch in the inhibitory region.

Alternative promoters of gene MAGE4a

Gene MAGE-4 (HGMW-approved symbol MAGE4) is expressed in several types of tumors, but not in normal tissues, except testis and placenta. The 5' end of this gene contains eight homologous exons spread over a 5.8-kb region. These exons are alternatively spliced to a unique second exon and a unique third exon, which encodes a protein of 317 amino acids. The analysis of transcripts found in testis, placenta, and a sarcoma cell line showed that each of the alternative first exons is used in at least one of these tissues. Various regions of the promoter of the fifth alternative exon (1.5) were cloned in a luciferase reporter plasmid, and the constructs were transfected in a sarcoma cell line that expresses MAGE-4. Two Ets motifs located between positions -70 and -29 relative to the transcription start site were found to drive 55% of the promoter activity. A region containing a Sp1 consensus binding site located upstream of the two Ets motifs was found to be responsible for 44% of the transcriptional activity. MAGE-4a promoters 1.4 and 1.6, which also contain the Sp1 and the two Ets binding motifs, supported a level of transcription comparable to that of promoter 1.5, whereas promoter 1.1, which contains only one Ets binding site, was sixfold less active. In line with observations made with gene MAGE-1 (HGMW-approved symbol MAGE1), we found that promoter 1.5 stimulated a high level of transcription in a melanoma cell line that does not express MAGE-4. This suggests that the tumor-specific expression of MAGE genes is not determined by the presence of specific transcription factors.