Lack of an initiator element is responsible for multiple transcriptional initiation sites of the TATA-less mouse thymidylate synthase promoter

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation

We assess the role of DNA breathing dynamics as a determinant of promoter strength and transcription start site (TSS) location. We compare DNA Langevin dynamic profiles of representative gene promoters, calculated with the extended non-linear PBD model of DNA with experimental data on transcription factor binding and transcriptional activity. Our results demonstrate that DNA dynamic activity at the TSS can be suppressed by mutations that do not affect basal transcription factor binding–DNA contacts. We use this effect to establish the separate contributions of transcription factor binding and DNA dynamics to transcriptional activity. Our results argue against a purely ‘transcription factor-centric’ view of transcription initiation, suggesting that both DNA dynamics and transcription factor binding are necessary conditions for transcription initiation.

Transcriptional regulation of the major zinc uptake protein hZip1 in prostate cancer cells

hZip1 has been characterized as the major zinc uptake transporter regulating the accumulation of zinc in prostate cells. The mechanisms regulating expression of hZip1 have not been described. To explore the mechanisms of transcriptional regulation of the hZip1 gene, we determined the putative promoter sequence for hZip1 and identified the potential transcription start site within the predicted hZip1 promoter region. To further characterize the promoter region for basal hZip1 transcription, 3' and 5' deletion constructs and constructs with mutated binding sites for putative transcription factors were generated by PCR amplification and assessed for transcriptional activity with a luciferase reporter assay in PC-3 prostate cancer cells. The ability of the specific transcription factors to bind the hZip1 core promoter was confirmed by EMSA, GelSupershift and ChIP assays. Our experiments identified the core promoter region responsible for constitutive expression of hZip1 and demonstrated critical roles for SP1 and CREB1 in transcriptional regulation of the hZip1 gene in prostate cancer cells.

Introduction of an initiator element in the mouse thymidylate synthase promoter alters S phase regulation but has no effect on promoter bidirectionality

The promoter of the mouse thymidylate synthase (TS) gene lacks a TATAA box and an initiator element, is bidirectional and initiates transcription at multiple start sites across broad initiation windows upstream and downstream of the 30 nt essential promoter region. The TS promoter also plays an essential role in the post-transcription regulation of TS gene expression during the G(1)-S phase transition. The goal of this study was to determine if the addition of a TATAA box or an initiator element would have a significant effect on start-site pattern, promoter bidirectionality and S phase regulation of the TS gene. A TATAA box and/or an initiator element were inserted downstream of the TS essential promoter region, and the modified promoters were used to drive expression of indicator genes. The engineered genes were transfected into cultured mammalian cells, and the effects of the mutations were determined. Addition of the TATAA box and especially the initiator element had a significant effect on the transcription start site pattern, indicating that the elements were functional. Unexpectedly, addition of one or both of these elements had no effect on promoter bidirectionality. However, inclusion of the initiator element led to a significant reduction in S phase regulation of TS mRNA levels, indicating that changes in promoter architecture can perturb normal S phase regulation of TS gene expression.

Characterisation of the mulibrey nanism-associated TRIM37 gene: transcription initiation, promoter region and alternative splicing

The TRIM37 gene encodes a peroxisomal protein of unknown function. Mutations in TRIM37 underlie mulibrey nanism, a rare autosomal recessively inherited disorder with severe growth failure of prenatal onset, constrictive pericardium, hepatomegaly and characteristic dysmorphic features. Eleven mulibrey nanism-associated mutations have been identified. We here characterised TRIM37 further by mapping the transcription initiation site and promoter region as well as by analysing splice variants. By primer extension analysis, several transcription initiation sites were localised to a region between -246 and -373 relative to the ATG codon for translation initiation. Basal promoter activity was mapped within 600 nucleotides upstream from the translation initiation site using promoter-luciferase reporter constructs. Several alternative splice variants of TRIM37 exist in databases. Most of these predict non-functional protein products, are expressed at low levels and are thus likely to be targets for nonsense-mediated mRNA decay. A novel splice variant, TRIM37b, with an alternative termination codon and 3'untranslated region (UTR) transcribed from an exon 16 kb downstream from exon 24, predicts an identical protein product with the previously identified transcript, TRIM37a. As seen by Northern blot analysis and quantitative real-time PCR, both transcripts are highly expressed in testis, whereas in other tissues TRIM37a is prominent. The 3'UTR of the PPM1E gene in the opposite strand overlaps TRIM37b. These data suggest that TRIM37 expression is regulated by several mechanisms: through nonsense surveillance of non-functional transcripts, as well as through 3'UTR regulatory sequences and/or naturally occurring antisense RNAs especially in testis.

CCAAT/enhancer binding protein-beta (C/EBP-beta), a pivotal regulator of the TATA-less promoter in the rat catalase gene

The rat catalase gene carries a TATA-less promoter and its transcriptional mechanism is interesting because of downregulation in liver injury. We characterized the core element in the promoter and found that C/EBP-beta binding downstream of the transcription initiation site plays a crucial role for transcription. The multiple complexes binding to the promoter were composed of homodimers and heterodimers of C/EBP-beta isoforms. Transduction of the C/EBP-beta gene showed complete reconstitution of multiple binding complexes in HeLa cells, similar to normal liver. Furthermore, C/EBP-beta was observed to bind to the endogenous catalase promoter. These data suggest that multiple complex formation of C/EBP-beta regulates transcription in the TATA-less catalase promoter.

Bystander gene activation by a locus control region

Random assortment of genes within mammalian genomes establishes the potential for interference between neighboring genes with distinct transcriptional specificities. Long-range transcriptional controls further increase this potential. Exploring this problem is of fundamental importance to understanding gene regulation. In the human genome, the Igbeta (CD79b) gene is situated between the pituitary-specific human growth hormone (hGH) gene and its locus control region (hGH LCR). Igbeta protein is considered B-cell specific; its only known role is in B-cell receptor signaling. Unexpectedly, we found that hIgbeta is transcribed at high levels in the pituitary. This Igbeta transcription is dependent on pituitary-specific epigenetic modifications generated by the hGH LCR. In contrast, expression of Igbeta at its native site in B cells is independent of hGH LCR activity. These studies demonstrated that a gene with tissue-restricted transcriptional determinants (B cell) can be robustly activated in an unrelated tissue (pituitary) due to fortuitous positioning within an active chromatin domain. This 'bystander' gene activation pathway impacts on current concepts of tissue specificity and models of active chromatin domains.

Isolation and characterization of the 5'-flanking region of the growth hormone secretagogue receptor gene from black seabream Acanthopagrus schlegeli

Ghrelin, the recently discovered endogenous ligand for growth hormone secretagogue receptor (GHSR), is widely expressed and involved in regulating diverse physiological functions in addition to stimulation of growth hormone (GH) secretion. Previous studies have demonstrated the functional significance of the ghrelin/GHSR system, yet the transcriptional regulation of the ghrelin and GHSR genes are poorly understood. We have recently cloned the GHSR cDNA from the pituitary of black seabream Acanthopagrus schlegeli. In the present study, we have isolated a 2.1 kb 5'-flanking region of the GHSR gene from the same species and have investigated, for the first time, the transcriptional regulation of GHSR from a non-human species. The 5'-flanking region of the seabream GHSR gene was found to contain a number of unique putative transcription factor-binding sites different from the human counterpart. Functional characterization of the 5'-flanking region in several cell lines indicates that the region between -1423 and +19 contains sufficient elements for promoter function. Moreover, progressive 3'-deletion analysis suggests the presence of negative regulatory element(s) and essential cis-acting element(s) at -514/+19 and -928/-515, respectively. Furthermore, we have shown that the promoter activity is significantly enhanced by a GHSR agonist in a cell line stably expressing the seabream GHSR, and this stimulatory effect could be completely blocked by a GHSR antagonist. These results suggest that homologous up-regulation plays an important role in the transcriptional control of the teleostean GHSR gene. This is in big contrast to the human situation in which a homologous down-regulation of the GHSR gene transcription by its own ligand has been previously demonstrated.

Structure and expression of the ovine Hoxc-13 gene

HOXC-13 has an important role in controlling hair formation through regulating keratin differentiation-specific genes. In this study, we describe the isolation and characterisation of the Hoxc-13 gene from sheep wool follicles and its expression in the skin. We show that the gene organisation of ovine Hoxc-13 is similar to other homeobox genes of the Abd-B type I Homeobox class with two exons split by an intron next to the homeobox. The gene spans 7.5 kilobases (kb) and has a relatively large intron, which divides an open reading frame of 2361 nucleotides. The predicted ovine Hoxc-13 protein of 330 amino acids has over 97% sequence identity with the human and mouse proteins. A second novel transcript was identified, which could produce a truncated Hoxc-13 protein lacking 15 amino acids from the N-terminus. A positionally conserved Hoxc-13 binding site in the Hoxc-13 proximal promoters of sheep, human, mouse and newt suggests that Hoxc-13 expression is autoregulatory. Positionally conserved motifs for LEF-1 and Whn/Foxn1 suggest that Hoxc-13 may be a downstream target of these transcription factors known to regulate hair growth. In addition to expression in the follicle, we detected Hoxc-13 in cells of the blood sinus surrounding vibrissal follicles and in scattered cells in the upper dermis of the skin. Thus, in addition to a role in controlling transcription of hair keratins, Hoxc-13 may have other roles in skin function.

Functional cooperation between multiple regulatory elements in the untranslated exon 1 stimulates the basal transcription of the human GnRH-II gene

The wide distribution of GnRH-II and conservation of its structure over all vertebrate classes suggest that the neuropeptide possesses vital biological functions. Although recent studies have shown that the expression of the human GnRH-II gene is regulated by cAMP and estrogen, the molecular mechanisms governing its basal transcription remain poorly understood. Using the neuronal TE-671 and placental JEG-3 cells, we showed that the minimal human GnRH-II promoter was located between nucleotide -1124 and -750 (relative to the translation start codon) and that the untranslated exon 1 was important to produce full promoter activity. Two putative E-box binding sites and one Ets-like element were identified within the first exon, and mutational analysis demonstrated that these cis-acting elements functioned cooperatively to stimulate the human GnRH-II gene transcription. EMSAs, UV cross-linking, and Southwestern blot analyses indicated that the basic helix-loop-helix transcription factor AP-4 bound specifically to the two E-box binding sites, whereas an unidentified protein bound to the Ets-like element. The functional importance of AP-4 in controlling human GnRH-II gene transcription was demonstrated by overexpression of sense and antisense full-length AP-4 cDNAs. Taken together, our present data demonstrate a novel mechanism in stimulating basal human GnRH-II gene transcription mediated by cooperative actions of multiple regulatory elements within the untranslated first exon of the gene.

Mouse vesicular GABA transporter gene: genomic organization, transcriptional regulation and chromosomal localization

The vesicular GABA transporter (VGAT) loads GABA from neuronal cytoplasm into synaptic vesicles and is selectively expressed in inhibitory neurons that contain GABA and/or glycine. To elucidate the molecular mechanisms of mouse VGAT (mVGAT) gene expression, we have isolated and characterized the mVGAT gene. The mVGAT gene was found to be 4.7 kilobases in size and to contain three exons and two introns by comparison of the cloned genomic DNA with the cDNA (termed mVGATa) sequence reported by Sagne et al. [FEBS Lett. 417 (1997) 177]. Analysis of transcripts and genomic DNA revealed an alternatively spliced mVGAT isoform (termed mVGATb) that retains intron 2 of mVGATa as an exon. This alternative transcript specifies 514 amino acid residues identical to VGATa followed by a unique C-terminal sequence of 11 amino acids encoded by intron 2. Fluorescent in situ hybridization studies showed that the mVGAT gene is localized on chromosome 2. One major transcription start site of the mVGAT gene is an A residue 209 bp upstream from the translational initiation site, as shown using the 5'-RACE method. RT-PCR analysis revealed that the mVGAT gene was expressed at a high level in retinoic acid-treated P19 embryonal carcinoma cells, at a very low level in non-treated P19 cells, and not detectably expressed in Neuro-2a neuroblastoma cells. Sequence analysis of the 5'-flanking region revealed a number of putative regulatory elements including Sp1, Egr-1 and Pitx binding sites. In transient transfection assays, 2 kilobases of the mVGAT 5'-flanking region generated similar levels of luciferase reporter activity in three kinds of cultured cells. Deletion analysis and gel mobility shift assays demonstrated that the region -161 to +155 contained the basal promoter activity of the mVGAT gene and that an activating region from -49 to -27 bound an Sp1-like protein. These results suggest a possible mechanism for regulation of the expression of the mVGAT gene.

Human cytomegalovirus infection induces cellular thymidylate synthase gene expression in quiescent fibroblasts

Productive infection of non-proliferating cells by cytomegalovirus (CMV) requires the coordinated stimulation of host biochemical pathways that prepare cells to synthesize DNA. Here we illustrate the ability of human CMV (HCMV) to stimulate cellular thymidylate synthase (TS) gene expression in quiescent human embryonic lung fibroblasts. TS mRNA and protein levels are nearly undetectable in quiescent cells, but are greatly increased following HCMV infection. Inhibition of TS activity was shown to impair HCMV DNA synthesis, demonstrating that TS upregulation is required for efficient HCMV replication in quiescent cells. The increase in TS gene expression was due to an increase in gene transcription, since the expression of a reporter gene driven by the human TS promoter was strongly induced by HCMV infection. Deletion analysis of the human TS promoter identified two positive elements that are important for this increased transcription. We have previously shown that murine CMV (MCMV) stimulates the mouse TS promoter by a mechanism that depends on the presence of an E2F element in the promoter region. However, deletion of the two potential E2F binding sites in the human TS promoter did not prevent the virus-induced increase in TS promoter activity. Our data suggest that HCMV activates human TS gene transcription by mechanisms that are independent of E2F and different from those used by MCMV to stimulate the mouse TS promoter.

Thymidylate synthase as a translational regulator of cellular gene expression

Studies from our laboratory have shown that the folate-dependent enzyme, thymidylate synthase (TS), functions as an RNA binding protein. There is evidence that TS, in addition to interacting with its own TS mRNA, forms a ribonucleoprotein complex with a number of other cellular mRNAs, including those corresponding to the p53 tumor suppressor gene and the myc family of transcription factors. Using both in vitro and in vivo model systems, we have demonstrated that the functional consequence of binding of TS protein to its own cognate mRNA, as well as binding of TS to the p53 mRNA, is translational repression. Herein, we review current work on the translational autoregulatory control of TS expression and discuss the molecular elements that are required for the TS protein-TS mRNA interaction. TS may play a critical role in regulating the cell cycle and the process of apoptosis through its regulatory effects on expression of p53 and perhaps other cell cycle related proteins. Finally, the ability of TS to function as a translational regulator may have important consequences with regard to the development of cellular resistance to various anticancer drugs.

Synergistic activation of the TATA-less mouse thymidylate synthase promoter by the Ets transcription factor GABP and Sp1

The mouse thymidylate synthase (TS) promoter lacks a TATA box and an initiator element and directs transcriptional initiation at multiple sites over a 90-nucleotide region. The minimum sequence required for wild-type promoter activity has been mapped to a 30-nucleotide essential promoter region that partially overlaps the 5' end of the transcriptional initiation window. The essential promoter region contains two potential binding sites for members of the Ets family of transcription factors as well as a binding site for Sp1. Promoter mutation analyses revealed that all three of these sites are important for promoter activity. Transient cotransfection assays showed that GABP, a heterodimeric Ets factor, is able to stimulate expression of reporter genes driven by the wild-type mouse TS promoter whereas several other Ets factors have no effect. Electrophoretic mobility shift assays revealed that recombinant GABP binds to both Ets elements in the essential promoter region. Stimulation of promoter activity by GABP is diminished when either Ets element is inactivated and is prevented when both Ets elements are inactivated. Transient cotransfection assays revealed that Sp1 and GABP stimulate TS promoter activity in a highly synergistic manner.

Two CCAAT boxes in a novel inverted repeat motif are required for Hlx homeobox gene expression

Hlx is a homeobox transcription factor gene required for normal intestinal and hepatic growth in development. We previously found high sequence identity and 17 conserved consensus cis-regulatory/transcription factor binding elements in the mouse and human Hlx 5' regions. A 594 bp sequence in the Hlx 5' region possessing the same activity in driving luciferase expression as larger Hlx 5' sequences had three segments each necessary but not sufficient for luciferase expression in NIH 3T3 cells (which express Hlx). Nine of the conserved putative regulatory elements are positioned within these segments, including two CCAAT boxes on opposite strands within a conserved 44 bp inverted repeat sequence. To test the hypothesis that these elements are required for promoter activity, we compared the reporter expression activity of segments containing mutations of these elements with activity of the parent Hlx promoter sequence. We found that mutation of either CCAAT box or a conserved AP-2 site resulted in a significant decrease in promoter activity. Restoration of the inverted repeat with complementary mutations of both CCAAT boxes did not restore activity. Further, mutation of other portions of the inverted repeat did not affect promoter activity. Mutation of other elements had no effect on promoter activity.

Transcription of eukaryotic protein-coding genes

The past decade has seen an explosive increase in information about regulation of eukaryotic gene transcription, especially for protein-coding genes. The most striking advances in our knowledge of transcriptional regulation involve the chromatin template, the large complexes recruited by transcriptional activators that regulate chromatin structure and the transcription apparatus, the holoenzyme forms of RNA polymerase II involved in initiation and elongation, and the mechanisms that link mRNA processing with its synthesis. We describe here the major advances in these areas, with particular emphasis on the modular complexes associated with RNA polymerase II that are targeted by activators and other regulators of mRNA biosynthesis.

Identification and functional characterization of the human and murine fibroblast growth factor receptor 4 promoters

Fibroblast growth factor receptors (FGFRs) play crucial roles in signal transduction of adult tissues and during embryonic development. To study the transcriptional control, we isolated and characterized the promoter of human FGFR4. Two transcription initiation sites were identified. The deletion analysis in different cell types defined a core promoter reaching from -9 to -198, lacking TATA and CCAAT boxes but displaying high GC content (77%) in a stretch of 300 bp upstream of the major mRNA start. This region harbors multiple binding motifs for transcription factors. Moreover, the region between -1085 and -1140 contains a potential repressor element, which downregulates transcriptional activity. To identify conserved regulatory elements, we isolated and analyzed also the murine FGFR4 promoter. Only one transcription start was identified using RNase protection assays. Sequence alignment of human and mouse shows a striking similarity in the core promoter region of both genes, encompassing conserved transcription factor binding sites and a splice acceptor site. Furthermore, the region containing the putative repressor element is also conserved suggesting a functional role for gene expression.

Transcriptional control elements of the rat thymidylate synthase promoter: evolutionary conservation of regulatory features

The sequence elements that are important for the transcription and regulation of the rat thymidylate synthase (TS) gene were analyzed. The rat TS promoter lacks a TATA box and directs transcriptional initiation at multiple sites between 60 and 20 nt upstream of the AUG translational start codon. Promoter deletion analyses showed that the region between -100 and -42 nt relative to the AUG codon was both necessary and sufficient for high level promoter activity and was designated the essential promoter region. The essential region also had bidirectional promoter activity. Site-directed mutagenesis revealed that four elements were especially important for promoter activity. These include Ets motifs at -85 and -50, an Sp1 motif at -80, and an LSF motif that overlapped the upstream Ets and Sp1 motifs. Inactivation of E2F motifs that are upstream and downstream of the essential promoter region had no measurable effect on promoter activity in transient transfection assays. The rat TS promoter region directed S-phase-specific expression of a stably transfected minigene if a spliceable intron was included in the transcribed region. When the intron was deleted or the E2F motifs were inactivated, expression of the minigene changed very little during the G1 to S transition.

Cloning and initial characterization of the human DPYD gene promoter

Dihydropyrimidine dehydrogenase (DPD) is the rate-limiting enzyme in the degradation of pyrimidine bases and pyrimidine-based antimetabolites. Reduced DPD activity is associated with toxicity to 5-fluorouracil (5FU) therapy in cancer patients and with neurological abnormalities in paediatric patients. Although variant DPYD alleles have been identified in DPD-deficient patients, they do not adequately explain polymorphic DPD activity or associated clinical phenotypes in vivo. DPD may be transcriptionally regulated as mRNA levels correlate with activity and are differentially regulated in human tissues. A 1.85 kb 5' flanking region of the human DPYD gene was cloned and has transcriptional activity in cultured cells. Analysis of this 5' flanking region in rhesus and cynomolgus monkeys demonstrated conservation (>96%) between humans and primates. Putative binding sites for ubiquitous and cell-specific factors were identified. A polymorphism that disrupts a putative gamma-interferon response element was identified in a cancer patient with reduced DPD activity and severe 5FU toxicity. Further insight into regulation of DPD expression may identify new avenues for the treatment of clinical problems associated with DPD deficiency.

Transcriptional control elements and complex initiation pattern of the TATA-less bidirectional human thymidylate synthase promoter

The nucleotide sequences that are important for transcription of the human thymidylate synthase gene were analyzed by deletion and site-directed mutagenesis of the promoter region. Deletion analyses from the 5' and 3' ends indicated the presence of multiple positive and negative elements. The promoter had approximately the same strength in the normal or inverted orientation. The region between 161 and 141 nt upstream of the translational start codon was found to be both necessary and sufficient for high-level promoter activity in both directions and was designated the essential promoter region. This region, which is highly conserved in human, mouse and rat TS promoters, contains potential binding sites for Ets, Sp1, and LSF transcription factors. Site directed mutagenesis of each of these elements led to large decreases in promoter strength. However, inactivation of potential Sp1 and E2F elements adjacent to the essential promoter region led to increases in promoter strength. The transcriptional start site pattern was analyzed by S1 nuclease protection assays of mRNA isolated from cells transiently transfected with TS minigenes. Multiple start sites were detected, most of which were between 160 and 120 nt upstream of the AUG codon.

Complex transcriptional initiation pattern of the thymidylate synthase promoter in mouse tissues

Thymidylate synthase (TS) is an essential enzyme that must be expressed in all proliferating cells. The mouse TS promoter lacks a TATA box and an initiator element and initiates transcription over a broad region in cultured fibroblasts. The goal of this study was to determine if expression of the TS gene in a variety of cells and tissues involves the use of alternative promoters or different patterns of transcriptional initiation sites. The amount of TS mRNA and the pattern of initiation sites were determined using S1 nuclease protection assays. We found that even though the amount of TS mRNA varied over a wide range, reflecting differences in cell proliferation rates, the pattern of initiation sites was nearly identical in all of the cell lines and tissues that were examined. Therefore transcription of the TS gene is directed by a single promoter that is capable of being expressed in a wide variety of cellular environments.

Myeloid cell-lineage and premylocytic-stage-specific- expression of themouse myeloperoxidase gene is controlled at initiation as well as elongation levels of transcription

The myeloperoxidase (MPO) is an important microbicidal protein present at high concentration in the primary granule of mature granulocyte and its expression is regulated in both myeloidcell-lineage and premyelocytic-stage-specific manners. A better understanding of the underlying control mechanisms should provide insights into the temporal and co-ordinate regulation of the gene expression during granulopoiesis. We have identified its promoter by mapping the start(s) of transcription using various molecular approaches together with demonstrating the promoter function of the relevant DNA segment in a transient transfection reporter assay. Besides the major start of transcription mapped at G residue, 11 nucleotide upstream of the 3' end of exon 0, the usage of that is specific to the MPO expressing cell lines, we have shown that irrespective of the MPO-expression status of the hematopoietic cells, transcription occurs broadly within a two kb region upstream of the 5' proximity of the gene, and is largely terminated in intron 2. These data support a model of the premyelocytic-stage-specific MPO expression, the control of which is operated at initiation as well as elongation levels of transcription.

Inactivation of MED-1 elements in the TATA-less, initiator-less mouse thymidylate synthase promoter has no effect on promoter strength or the complex pattern of transcriptional start sites

The mouse thymidylate synthase (TS) promoter is a member of a family of promoters that lack a TATA box as well as an initiator element and that initiate transcription at many sites over a broad initiation window. An element (MED-1) downstream of the initiation window of almost all promoters of this family has been proposed to be important for promoter activity, as well as for multiple start site utilization. Two consensus MED-1 elements are located downstream of the initiation window of the TS promoter. To determine the role of the MED-1 elements in the TS promoter, one or both elements were inactivated by site-directed mutagenesis and the effects on promoter function were determined. We found that inactivation of the MED-1 elements had no measurable effect on promoter strength, the boundaries of the initiation window, or the pattern of transcriptional start sites. Furthermore, inactivation of the elements did not affect the ability of the TS promoter to direct S phase-specific expression of the gene in growth-stimulated cells. We conclude that the MED-1 element does not play a significant role in TS promoter function and therefore is not an essential component of all TATA-less promoters with complex transcriptional initiation patterns.

Identification of conserved promoter elements for aldB and isozyme specific residues in aldolase B

The comparison of three complete aldolase B genes-including known and putative regulatory elements-is presented. The third aldolase B gene was provided by the complete aldB gene sequence (14803 bp) encoding the rabbit aldolase B isozyme. The promoter sequence alignment included the nonmammalian chicken aldolase B gene and confirms the promoter sequence conservation of those elements where trans-factor binding has been demonstrated in rat aldB. Moreover, the alignment reveals conserved sequences that may represent previously unidentified promoter elements that are present in all aldBs or specifically in the mammalian aldB promoters. One remarkable feature is a poly-purine segment found between the CAAT and TATA elements. In the mammalian promoters, this is exclusively a 9-10 bp poly-dA stretch. The avian promoter has an additional stretch of eight dG-bases immediately upstream of the poly-dA. Alignment of a portion of intron 1 of the chicken, human, and rabbit aldB genes reveals conserved sequences that are likely candidates for a reported positive activation sequence. In addition, the amino acid sequences of all eight known aldolase B isozymes is compared to the other vertebrate aldolases. A number of aldolase B-specific residues are identified that cluster in the carboxyl-portion of the sequence. With the exception of residue C268, these residues are not found near the active site, although, they are likely to be responsible for the substrate specificity of aldolase B.

Genomic organization of the murine polysialyltransferase gene ST8SiaIV (PST-1)

Polysialic acid (PSA) is an important regulator of cellular interactions. Two enzymes (ST8SiaII and ST8SiaIV) are capable of synthesizing PSA. In the present study, the gene encoding the murine ST8SiaIV (PST-1) has been isolated and characterized. In contrast to the ST8SiaII (STX) gene which contains six exons and spans about 80 kb, the ST8SiaIV gene comprises only five exons spanning over at least 55 kb. However, alignment of the two genes revealed that exon-intron boundaries of exons 2-5 of ST8SiaIV and exons 3-6 of ST8SiaII are located at identical sites. Differences are restricted to the 5'-region encoded by one exon in the case of ST8SiaIV, whereas the corresponding region of ST8SiaII is interrupted by a very long intron. 5'-RACE analysis of the ST8SiaIV transcript using mRNA from AtT20 cells identified two transcription start sites at positions -324 and -204 relative to the translation start codon. The promoter region of ST8SiaIV lacks TATA- and CAAT-like sequences and is enriched in G+C (60%). The promoter contains putative Sp1, AP-1, AP-2, and PEA3 binding sites, as well as a purine- and a pyrimidine-rich region. Luciferase reporter gene assays demonstrated that the region between nucleotides -443 and -162 is sufficient to direct gene expression. The induction of luciferase activity was 30- and 10-fold in the PSA-positive AtT20 and CHO cells, but only 5- and 7-fold in the PSA-negative NIH-3T3 cells and in a PSA-negative subline of AtT20. Thus, although decreased in activity in PSA-negative cell lines, the basal promoter is not sufficient for the strong cell-type and tissue specific regulation of the ST8SiaIV gene, suggesting regulatory elements in the more upstream 5'-region.

Analysis of transcripts derived from sequences upstream of the bidirectional mouse thymidylate synthase promoter

The promoter of the mouse thymidylate synthase (TS) gene lacks a TATAA box and an initiator element and is capable of directing transcriptional initiation with approximately equal strength and over broad initiation windows in both directions. The goal of the present study was to determine if the TS promoter directs the transcription of a second gene that is upstream of the TS gene by characterizing the transcripts that correspond to the upstream sequences. RNA blot analyses revealed the presence of 1.4 and 5 kb cytoplasmic, polyadenylated transcripts that include sequences upstream of the TS promoter. The transcripts were much more abundant in a cell line in which the TS gene is amplified. S1 nuclease protection assays showed that the transcripts have multiple 5' termini. An exon trap approach identified a potential splice donor site that might correspond to the 3' end of the first exon of the upstream gene. A cDNA library was probed with a sequence from the putative first exon, and six different cDNA clones were isolated. However, analysis of the sequences of the cDNAs revealed that the upstream transcripts were not spliced at the potential 3' donor site but instead extended into a repetitive LINE (long interspersed nuclear element) sequence that begins 0.3 kb upstream of the TS promoter. RNase protection assays confirmed that the in vivo transcripts extend into the LINE element. Therefore it appears that the upstream transcripts are unlikely to correspond to a functional mRNA molecule.

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.

Inhibition of mouse thymidylate synthase promoter activity by the wild-type p53 tumor suppressor protein

The p53 tumor suppressor protein is an important negative regulator of the G1 to S transition in mammalian cells. We have investigated the effect of p53 on the expression of the mouse thymidylate synthase (TS) gene, which normally increases as cells enter S phase. A luciferase indicator gene that was driven by the wild-type or various modified forms of the TATA-less mouse TS promoter was transiently cotransfected with a p53 expression plasmid into TS-deficient hamster V79 cells and the level of luciferase activity was determined. We found that wild-type p53 inhibited TS promoter activity by greater than 95% but had a strong stimulatory effect on an artificial promoter that contained multiple p53-binding sites. In contrast, an expression plasmid that encodes a mutant form of p53 or a wild-type retinoblastoma tumor suppressor protein had little effect on TS promoter activity. Deletion of sequences upstream or downstream of the TS essential promoter region, or inactivation of each of the known elements within the essential promoter region, had no effect on the ability of wild-type p53 to inhibit TS promoter activity. Our observations indicate that the inhibition of TS promoter activity by p53 is not due to the presence of a specific p53 negative response element in the TS promoter. Rather, it appears that p53 inhibits the TS promoter by sequestering ("squelching") one or more general transcription factors.

Identification of functional elements in the promoter region of the human gene for thymidylate synthase and nuclear factors that regulate the expression of the gene

To identify the essential motifs of the promoter of the human gene for thymidylate synthase (TS), we constructed a set of deletion mutants from the 5'-terminal region of the human TS gene. From the results of assays of the expression of chloramphenicol acetyltransferase (CAT), we identified two functional elements with positive effects on the promoter activity: a CACCC box (CCACACCC) and an Sp1-binding motif (GAGGCGGA) that was homologous to the Sp1-binding site in the mouse TS gene. In addition, negative regulatory sequences were identified between the two positive elements and in the region upstream of the CACCC box. The results of gel mobility shift analyses suggested that Sp1 binds to the Sp1-binding motif of the human TS gene promoter and that multiple nuclear factors that are related to Sp1 bind to the CACCC box. Furthermore, the binding of Sp1 to mutated Sp1-binding motifs in the promoter region of the human TS gene was correlated with the promoter activity, as measured by the CAT assay. Therefore, the Sp1 motif seems to be a major contributor to the basic promoter activity of the human TS gene, although multiple positive and negative regulatory elements are involved in the regulated expression of this gene.

The promoters for human and monkey poliovirus receptors. Requirements for basic and cell type-specific activity

The cellular receptors for poliovirus (PVR) are glycoproteins belonging to the immunoglobulin superfamily. Functional receptors for poliovirus are only expressed by primates; known rodent homologues lack the ability to bind virus due to amino acid differences. Human poliovirus infections are targeted to the gastrointestinal tract and, rarely, to motor neurons in the central nervous system. Available evidence suggests that poliovirus uses only one cellular receptor, implying that the tissue tropism of poliovirus is likely to be related to the expression of the human PVR (hPVR). However, low levels of expression of hPVR-specific mRNAs can be detected in many human tissues other than the apparent target cells. The nonpathogenic function of hPVR is unknown. For a study of the transcriptional control of hPVR expression, we have isolated and characterized the promoter of the hPVR gene. Deletion analysis defined an approximately 280 base pair minimal promoter fragment that: 1) lacks TATA- and CAAT-like elements, 2) is distinguished by a high GC content, and 3) promotes transcription at multiple start sites. The pattern of activity caused by transfection of serial 5'- and 3'-promoter deletions is almost identical in HEp2, HeLa, COS-1, and mouse L929 cells, indicating a similar transcriptional regulation of the hPVR promoter in these cell lines. However, on transfection of Raji cells, a Burkitt's lymphoma cell line harboring a transcriptionally inactive hPVR gene, all promoter reporter constructs tested exerted only residual activity. These results suggest that the cis-element(s) governing cell type-specific hPVR expression resides in the minimal promoter region. We also report the sequences of the promoters of two monkey homologues to hPVR (AGMalpha1 and AGMalpha2). Transcripts encoding the monkey poliovirus receptors originate from a region analogous to that identified for hPVR transcripts.

The initiator element and proximal upstream sequences affect transcriptional activity and start site selection in the amyloid beta-protein precursor promoter

The TATA-less human amyloid beta-protein precursor promoter contains an initiator element with the sequence CGTCA+1GTT. Primary transcriptional start sites were identified at positions +1 and -4. Deletion of the upstream activator elements APBbeta and APBalpha did not affect the selection of transcriptional start sites, although total transcriptional activity was reduced both in vitro and in vivo. Mutations within the initiator element shifted the transcriptional start sites and reduced transcriptional activity. Mutations between positions -6 and -35 changed the relative utilization of start sites +1 and -4 without affecting the total level of transcriptional activity. A 10-base pair deletion between position -40 and -31 increased in vitro transcriptional activity with a preeminent utilization of the start site at position -4. In contrast, a 20-base pair deletion between position -40 and -21 resulted in a reduction in transcriptional activity and in the primary utilization of the start site at position +1. Furthermore, transactivation by APBbeta and APBalpha was eliminated. DNase I footprinting provided evidence for the existence of two binding domains designated UE (position -12 to -30) and Inr (position +7 to -7). The positions of these binding domains are altered in mutations and deletions that affect transcriptional activity.

Identification and characterization of a hepatitis delta virus RNA transcriptional promoter

Transcription and replication of hepatitis delta virus (HDV) RNA are performed by the cellular enzyme RNA polymerase II (Pol II). As DNA is the normal template for Pol II, the enzyme must undergo template switching. The mechanism for this is unknown, but since HDV RNA can form a rod-like molecule by extensive intramolecular base pairing, it has been suggested that a double-stranded region(s) of HDV RNA serves as a recognition site for Pol II. A bidirectional promoter has been identified previously on HDV cDNA (T. B. Macnaughton, M. R. Beard, M. Chao, E. J. Gowans, and M. M. C. Lai, Virology 196:629-636, 1993). In the present study, genomic RNA corresponding to this region was able to direct the synthesis of antigenomic RNA in a nuclear extract transcription reaction, whereas genomic RNA species containing a mutation that resulted in a replication-defective phenotype were unable to do so. Thus, this region, the location of which is defined as nucleotides 1608 to 1669 on the basis of a highly conserved structure, represents a RNA-RNA promoter. Computer analysis of the RNA secondary structure predicted that the promoter contains two bulge regions in a stem-loop structure which encompasses a GC-rich motif. This predicted model was confirmed by enzyme digestion and primer extension analysis. The promoter is located at one end of the rod and has some homology with the simian virus 40 late promoter. A number of other mutations were introduced within this region, and expression plasmids were constructed to examine the effects of mutations in the promoter on HDV replication. Disruption of the overall secondary structure, particularly the bulge regions, totally inhibited HDV RNA replication.

Expression of the smooth muscle cell calponin gene marks the early cardiac and smooth muscle cell lineages during mouse embryogenesis

Although several genes are considered markers for vascular smooth muscle cell (SMC) differentiation, few have been rigorously tested for SMC specificity in mammals, particularly during development where considerable overlap exists between different muscle gene programs. Here we describe the temporospatial expression pattern of the SMC calponin gene (formerly h1 or basic calponin) during mouse embryogenesis and in adult mouse tissues and cell lines. Whereas SMC calponin mRNA expression is restricted exclusively to SMCs in adult tissues, during early embryogenesis, SMC calponin transcripts are expressed throughout the developing cardiac tube as well as in differentiating SMCs. Transcription of the SMC calponin gene initiates at two closely juxtaposed sites in the absence of a consensus TATAA or initiator element. Transient transfection assays in cultured SMC demonstrated that high level SMC calponin promoter activity required no more than 549 nucleotides of 5 sequence. In contrast to the strict cell type-specificity of SMC calponin mRNA expression, the SMC calponin promoter showed activity in several cell lines that do not express the endogenous SMC calponin gene. These results demonstrate that SMC calponin responds to cardiac and smooth muscle gene regulatory programs and suggest that the cardiac and smooth muscle cell lineages may share a common gene regulatory program early in embryogenesis, which diverges as the heart matures. The finding that the isolated SMC calponin promoter is active in a wider range of cells than the endogenous SMC calponin gene also suggests that long-range repression or higher order regulatory mechanism(s) are involved in cell-specific regulation of SMC calponin expression.

Regulation of the leukocyte integrin gene CD11c is mediated by AP1 and Ets transcription factors

The leukocyte integrin gene, CD11c, encodes the chi subunit of the p150,95 (CD11c.CD18) receptor. Expression of the CD11c gene is predominately seen in monocytes, but has also been detected in some B- and T-cell neoplasms and in some large-cell lymphomas of uncertain origin. To elucidate the molecular mechanisms that govern the expression of CD11c, we have cloned and characterized the promoter region of this gene. The DNase I footprint and mobility shift analyses revealed five sites within the -86 to +40 region that interact with nuclear proteins. The -62 to -44 region contains two consensus sequences for AP1 (referred to as AP1-1 and AP1-2) and were shown to bind purified c-jun protein. Co-transfection of c-fos and c-jun expression constructs with a CD11c promoter-CAT fusion into HL60 cells led to a 6.7-fold increase in CD11c promoter activity. We show that c-fos and c-jun mediate their effects through both AP1-1 and AP1-2 which function in an additive manner. Regions -42 to -34 and -13 to -5 contain consensus sequences for Ets factors (referred to as Ets C and Ets A, respectively). Deletion of Ets resulted in a significant reduction in phorbol ester-induced expression of CD11c, whereas deletion of Ets A led to only a modest loss in CD11c expression. We show that Ets C cooperates with the AP1 sites to regulate CD11c expression.

Pancreatic islet expression of the homeobox factor STF-1 relies on an E-box motif that binds USF

The commitment of cells to specific lineages during development is determined in large part by the relative expression of various homeodomain (HOX) selector proteins, which mediate the activation of distinct genetic programs. But the mechanisms by which individual HOX genes are themselves targeted for expression in different cell types remain largely uncharacterized. Here, we demonstrate that STF-1, a homeodomain protein that functions in pancreatic morphogenesis and in glucose homeostasis is encoded by an "orphan" homeobox gene on mouse chromosome 5. When fused to a beta-galactosidase reporter gene, a 6.5-kilobase genomic fragment of 5'-flanking sequence from the STF-1 gene shows pancreatic islet specific activity in transgenic mice. Two distinct elements within the STF-1 promoter are required for islet-restricted expression: a distal enhancer sequence located between -3 and -6.5 kilobases and a proximal E-box sequence located at -104, which is recognized primarily by the helix loop helix/leucine zipper nuclear factor USF. As point mutation within the -104 E-box that disrupt USF binding correspondingly impair STF-1 promoter activity, our results demonstrate that USF is an important component of the regulatory apparatus which directs STF-1 expression to pancreatic islet cells.

A conserved downstream element defines a new class of RNA polymerase II promoters

Although many TATA-less promoters transcribed by RNA polymerase II initiate transcription at multiple sites, the regulation of multiple start site utilization is not understood. Beginning with the prediction that multiple start site promoters may share regulatory features and using the P-glycoprotein promoter (which can utilize either a single or multiple transcription start site(s)) as a model, several promoters with analogous transcription windows were grouped and searched for the presence of a common DNA element. A downstream protein-binding sequence, MED-1 (Multiple start site Element Downstream), was found in the majority of promoters analyzed. Mutation of this element within the P-glycoprotein promoter reduced transcription by selectively decreasing utilization of downstream start sites. We propose that a new class of RNA polymerase II promoters, those that can utilize a distinctive window of multiple start sites, is defined by the presence of a downstream MED-1 element.

The TATA-less promoter of mouse ribonucleotide reductase R1 gene contains a TFII-I binding initiator element essential for cell cycle-regulated transcription

Mammalian ribonucleotide reductase shows S-phase specific expression and consists of two non-identical subunits, proteins R1 (large subunit) and R2 (small subunit). A comparison between the human and mouse TATA-less R1 gene promoters revealed four highly conserved DNA regions, while the remaining sequence showed a low degree of conservation. Two regions, alpha and beta, were earlier identified as protein binding regions in the mouse R1 promoter by using DNase footprinting technique. The two new regions are located to the transcription start and to a DNA sequence about 40 base pairs downstream from the start. Gel shift assays using TFII-I antibodies and competition with an oligonucleotide representing the terminal deoxynucleotidyl transferase inhibitor element identified the start region as a TFII-I binding initiator element. The conserved downstream region, called gamma, also formed specific DNA-protein complexes in gel shift assays. Functional studies, using synchronized cells stably transformed by R1 promoter-luciferase reporter gene constructs, indicated that the initiator and the gamma elements together were necessary for cell cycle-regulated R1 promoter activity. Earlier published data, indicating Sp1 binding to the R1 alpha/beta regions, could not be confirmed, suggesting that the R1 initiator element may function independent of Sp1.

Isolation and expression of rat thymidylate synthase cDNA: phylogenetic comparison with human and mouse thymidylate synthases

Two cDNA clones representing rat hepatoma thymidylate synthase (rTS) were isolated from a lambda ZAP II cDNA library using as a probe a fragment of the human TS cDNA. The two were identical except that one was missing 50 bp and the other 23 bp corresponding to the 5' coding region of the protein. The missing region was obtained by screening a rat genomic library. The open reading frame of rTS cDNA encoded 921 bp encompassing a protein of 307 amino acids with a calculated molecular mass of 35,015 Da. Rat hepatoma TS appears identical to normal rat thymus TS and the two sequences differ from mouse TS in the same eight amino acid residues. Six of these differences are in the first 21 amino acids from the amino-end. The human enzyme differed from rat and mouse TS at 17 residues where the latter two were identical, with most changes being conservative in nature. The three species differed completely at only four sites. Because the mouse TS shares four amino acids with human TS at sites which differ from rTS and a comparable situation does not exist between rTS and human TS, it is suggested that mouse TS is closer to human TS phylogenetically than rTS. The polymerase chain reaction was used to subclone the protein coding region of rTS into a high expression vector, which expressed rTS in Escherichia coli to the extent of 10 to 20% of its cellular protein. Although the amino-end of the amplified TS was unblocked, that isolated from a FUdR-resistant rat hepatoma cell line contained mostly N-acetylmethionine on its N-terminal end, a finding that may have significant regulatory consequences, which are discussed. The TS level in the resistant cell line was 60 to 70-fold higher than normal which was found to be associated with both multiple gene copies and an expanded TS mRNA pool.

Characterization of the promoter region of the human MDR3 P-glycoprotein gene

The human MDR3 (or MDR2) P-glycoprotein is probably involved in the transport of phospholipids from liver hepatocytes into bile (Smit et al. (1993) Cell 75, 451-462). In accordance with this function, MDR3 is highly expressed in human liver, but lower mRNA levels were also found in adrenal, heart, muscle and cells of the B-cell compartment. We have cloned and analyzed the MDR3 promoter region. It is GC-rich, and contains neither a TATA nor a CAAT box, but it does contain multiple putative SP1 binding sites, features also found in so-called housekeeping genes. RNase protection and primer extension analyses indicate that the MDR3 gene has multiple transcription start sites in a GC-rich region with considerable homology to the putative mouse mdr2 promoter. A 3 kb genomic fragment containing the MDR3 start sites directs transcription of a chloramphenicol acetyltransferase (CAT) reporter gene upon transient transfection in the human hepatoma cell line HepG2. This transcription is orientation dependent, and stimulated by a SV40 enhancer, indicating that the 3 kb insert contains the core promoter elements of the MDR3 gene. The promoter region contains several consensus sequences where known or putative liver-specific (C/EBP, HNF5) or lymphoid specific (Pu.1, ets-1) transcription factors may bind.

Initiation of transcription at the human terminal deoxynucleotidyl transferase gene promoter: a novel role for the TATA binding protein

Control of initiation of transcription of the human terminal deoxynucleotidyl transferase (TdT) gene was investigated by using an in vitro transcription assay. The precise contribution of discrete basal promoter elements to transcription initiation was determined by testing deletion and substitution mutations. The primary element, contained within the region spanning -34 to -14 bp relative to the transcription start site, accounted for 80% of basal promoter activity. TdT promoter activity required the sequence ACCCT at -24 to -20 bp since a dramatic decrease in transcription initiation was observed after mutation of this sequence, whereas mutation of the adjacent sequence from -32 to -25 bp did not alter promoter activity. The secondary element contained sequences surrounding the transcription start site and had 20% of promoter activity. Deletion of both elements completely abolished transcription initiation. Initiator characteristics of the secondary element were revealed by using the in vitro assay: promoter sequences at the transcription start site were sufficient to direct accurate initiation at a single site. Mutation of the sequence GGGTG spanning the transcription start site resulted in loss of transcription initiation. Both the primary and secondary elements were nonhomologous to corresponding regions from the mouse TdT gene promoter. While the human basal promoter functioned in the absence of TATA consensus sequences or GC-rich SP1 binding sites, it was dependent on active TFIID. In contrast to other TATA-less promoters, purified TATA binding protein substituted for the TFIID complex and restored promoter activity to TFIID-inactivated nuclear extracts.

In vitro transcription of the TATAA-less mouse thymidylate synthase promoter: multiple transcription start points and evidence for bidirectionality

The mouse thymidylate synthase (TS) promoter (pTS) lacks a TATAA box and an initiator element, and has multiple transcription start points (tsp) located across a 90-bp region. We have developed an in vitro transcription system for pTS using circular templates and nuclear extracts from HeLa cells or mouse 3T6 fibroblasts. The amount of RNA synthesized and the locations of the tsp were determined by S1 nuclease protection assays. The transcription system reproduced the complex pattern of in vivo tsp, except that the downstream tsp were used preferentially. The reaction temperature, concentrations of DNA template and MgCl2, and incubation time were optimized. The pTS core region contains binding sites for the Sp1 and Ets transcription factors. Inactivation of the Sp1-binding element led to a twofold reduction in transcription and a preferential use of upstream tsp. Inactivation of the Ets-binding element, which reduced promoter activity tenfold in vivo, had only a minor effect in vitro. Addition of a strong initiator element introduced a new tsp, but did not eliminate the complex tsp pattern. To determine if pTS had bidirectional promoter activity, the promoter was inverted and analyzed for transcriptional activity. The inverted promoter was found to initiate transcription at multiple tsp and had approximately the same strength as the normal pTS.