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PubMed2001

[In vitro modelling of the interactions between the promoter and enhancer complexes].

The aim of this work is to study in vitro mechanisms of interactions between the promoter and enhancer complexes of the transcriptional apparatus. We used retardation assay for the labeled TATA-box containing oligonucleotide with an unfractionated nuclear extract and with a second unlabeled oligonucleotide carrying an enhancer sequence. As an enhancer sequence we have chosen e5 element that is known to interact with members of Pax family transcription factors. We showed that the presence of unlabeled e5 element led to a significant decrease in the mobility of TATA-box associated complex. E5 element with a mutated homeodomen binding site does not produce such an effect, while a mutation in the paired binding site does not change the ability of e5 element to influence the formation of promoter-associated complex. We observed the same complex using crude nuclear extracts from cells that express chimeric protein Pax7-FKHR with higher molecular weight. The fact that the increase in the size of the transcription factor does not influence the size of the TATA-box associated complex led us to conclude that this complex did not result from association of original promoter and enhancer components, but rather the role of enhancer may be to stabilize the slowly migrating complex on the TATA-box via short-term interactions inducing conformational changes in the included proteins.

3T3 Cells↗
PubMed2006

SAGA binds TBP via its Spt8 subunit in competition with DNA: implications for TBP recruitment.

In yeast, the multisubunit SAGA (Spt-Ada-Gcn5-acetyltransferase) complex acts as a coactivator to recruit the TATA-binding protein (TBP) to the TATA box, a critical step in eukaryotic gene regulation. However, it is unclear which SAGA subunits are responsible for SAGA's direct interactions with TBP and precisely how SAGA recruits TBP to the promoter. We have used chemical crosslinking to identify Spt8 and Ada1 as potential SAGA subunits that interact with TBP, and we find that both Spt8 and SAGA bind directly to TBP monomer in competition with TBP dimer. We further find that Spt8 and SAGA compete with DNA to bind TBP rather than forming a triple complex. Our results suggest a handoff model for SAGA recruitment of TBP: instead of binding together with TBP at the TATA box, activator-recruited SAGA transfers TBP to the TATA box. This simple model can explain SAGA's observed ability to both activate and repress transcription.

Adaptor Proteins, Signal Transducing↗
PubMed1996

Paclitaxel activation of the GADD153 promoter through a cellular injury response element containing an essential Sp1 binding site.

The GADD153 promoter is transcriptionally activated by paclitaxel-induced injury. Promoter deletion from -786 to -85 base pairs relative to the start of transcription had no significant effect on activation, but deletion to the TATA box abolished it. Placement of the 39 bases from -74 to the TATA box (cellular injury response element, CIRE) upstream of the adenovirus E4 TATA box conferred paclitaxel inducibility. The only consensus sequence present in the CIRE is an Sp1 site; mutation of this site inhibited paclitaxel activation. Paclitaxel failed to activate a SV40-driven luciferase construct containing five Sp1 sequences, and Sp1 sites further upstream in the GADD153 promoter were not essential for activation. Pure Sp1 and nuclear extracts from uninjured and paclitaxel-injured cells protected the same region from -62 to -48 bases on the noncoding strand and -74 to -53 on the coding strand. Nuclear extracts shifted the CIRE to the same extent as purified Sp1 but had no effect on a CIRE with a mutated Sp1 site in gel shift assays. Immunodepletion of Sp1 abolished the shift; antibody to Sp1 produced a supershift. These data indicate that paclitaxel activates the GADD153 promoter through a constitutively occupied Sp1 site at -61 bases.

Base Sequence↗
PubMed1990

Immediate early protein of pseudorabies virus is a general transactivator but stimulates only suboptimally utilized promoters. A clue to specificity?

Pseudorabies virus, a herpesvirus, encodes an immediate early (IE) protein that is known to be a general and strong transactivator of transcription. We have tested the activity of this IE protein with a set of well-defined promoters containing a TATA box and one type of upstream factor binding site (for Sp1, NF-kappa B, heavy metal responsive factors, octamer factors or glucocorticoid receptor). All promoters were strongly activated by IE protein, i.e. the IE protein did not preferentially activate transcription via a particular type of upstream element. Activation did not require a bona fide TATA box, since a promoter construct with three Sp1 sites but no TATA box was also activated. Our data are not compatible with a model in which IE protein would bypass the need for upstream factors. Rather, the properties of IE protein, especially a failure to induce strong transcription from a promoter with only a TATA box but no upstream sequences, mimic the action of a remotely placed, cis-active, enhancer DNA. The IE protein was found to have no effect on transcription units that are expressed to their maximal potential, irrespective of whether this was high or low. Such optimal transcription conditions are observed in the presence of a strong enhancer, or with multiple tandem copies of an upstream binding site and/or a high concentration of the corresponding factor. The property of stimulating only "suboptimally" utilized promoters may be exploited by pseudorabies virus to restrict the specificity of the IE protein to the viral early promoters and a subset of cellular promoters.

Base Sequence↗
PubMed2006

Tissue- and tumor-specific targeting of murine leukemia virus-based replication-competent retroviral vectors.

Replication-competent retrovirus vectors based on murine leukemia virus (MLV) have been shown to effectively transfer therapeutic genes over multiple serial infections in cell culture and through solid tumors in vivo with a high degree of genomic stability. While simple retroviruses possess a natural tumor selectivity in that they can transduce only actively dividing cells, additional tumor-targeting strategies would nevertheless be advantageous, since tumor cells are not the only actively dividing cells. In this study, we used the promiscuous murine cytomegalovirus promoter, a chimeric regulatory sequence consisting of the hepatitis B virus enhancer II and the human alpha1-antitrypsin (EII-Pa1AT) promoter, and a synthetic regulatory sequence consisting of a series of T-cell factor binding sites named the CTP4 promoter to generate replicating MLV vectors, whereby the last two are transcriptionally restricted to liver- and beta-catenin/T-cell factor-deregulated cells, respectively. When the heterologous promoters were used to replace almost the entire MLV U3 region, including the MLV TATA box, vector replication was inefficient since nascent virus particle production from infected cells was greatly decreased. Fusion of the heterologous promoters lacking the TATA box to the MLV TATA box, however, generated vectors which replicated with almost-wild-type kinetics throughout permissive cells while exhibiting low or negligible spread in nonpermissive cells. The genomic stability of the vectors was shown to be comparable to that of a similar vector containing wild-type MLV long terminal repeats, and tropism analysis over repeated infection cycles showed that the targeted vectors retained their original specificity.

Animals↗
PubMed2000

PRH represses transcription in hematopoietic cells by at least two independent mechanisms.

PRH (proline-rich homeodomain protein) is strongly expressed in the hematopoietic compartment. Here we show that PRH is a repressor of transcription in hematopoietic cells. A fragment of PRH that includes the homeodomain can bind to TATA box sequences in vitro and can also bind to the TATA box-binding protein. PRH represses transcription from TATA box-containing promoters in intact cells but does not repress transcription from a promoter lacking a TATA box. A mutation in the PRH homeodomain that blocks binding to DNA but that has little or no effect on binding to the TATA box-binding protein significantly reduces the ability of the protein to repress transcription and provides the first clear demonstration that a homeodomain can bring about transcriptional repression in vivo by binding to a TATA box. However, we also show that mutation of the PRH homeodomain does not block the ability of PRH to repress transcription when this protein is tethered upstream of the TATA box via a heterologous DNA-binding domain. PRH also contains an N-terminal proline-rich repression domain that is separate from the homeodomain. Deletion mapping suggests that this repression domain contains at least two regions that both independently contribute to transcriptional repression.

Binding Sites↗
PubMed2000

Transactivation activity of the human cytomegalovirus IE2 protein occurs at steps subsequent to TATA box-binding protein recruitment.

The IE2 protein of human cytomegalovirus transactivates viral and cellular promoters through a wide variety of cis-elements, but the mechanism of its action has not been well characterized. Here, IE2-Sp1 synergy and IE2-TATA box-binding protein (TBP) interaction are examined by artificial recruitment of either Sp1 or TBP to the promoter. It was found that IE2 could cooperate with DNA-bound Sp1. A 117 amino acid glutamine-rich fragment of Sp1, which can interact with Drosophila TAF(II)110 and human TAF(II)130, was sufficient for the augmentation of IE2-driven transactivation. In binding assays in vitro, IE2 interacted directly with the C-terminal region of Sp1, which contains the zinc finger DNA-binding domain, but not with its transactivation domain, suggesting that synergy between IE2 and the transactivation domain of Sp1 might be mediated by other proteins such as TAF or TBP. It was also found that TBP recruitment to the promoter markedly increased IE2-mediated transactivation. Thus, IE2 acts synergistically with DNA-bound Sp1 and DNA-bound TBP. These results suggest that, in human cytomegalovirus IE2 transactivation, Sp1 functions at an early step such as recruitment of TBP and IE2 acts to accelerate rate-limiting steps after TBP recruitment.

Animals↗
PubMed1991

Functional analysis of E2-mediated repression of the HPV18 P105 promoter.

Transcription of the transforming genes E6 and E7 of the human papillomavirus type 18 (HPV18) can be repressed by the product of the E2 open reading frame. Mutations were introduced in the cis-responsive elements upstream from the E6 and E7 transcriptional promoter, P105. The effect of these mutations in the absence or presence of E2 was examined in the human cervical carcinoma cell line C33, transfected with expression plasmids. In the presence of HPV18 E2, repression was relieved only when both of the two E2 binding motifs, immediately proximal to the P105 TATA box, were mutated. Mutation of a third E2 binding site, 110 nucleotides upstream of the TATA box, led to a slight but consistent activation in the presence of the full-length E2. Therefore, three E2 binding sites appear to be involved in the negative regulation of the P105 promoter by HPV18 E2. In the presence of the BPV1 E2 protein, only the E2 binding site most proximal to the promoter TATA box was involved in the P105 repression. The comparative analysis of the in vitro and in vivo properties of the human and bovine E2 proteins on the HPV18 P105 promoter provides new insights into the mechanism of transcriptional repression, which appears to involve steric hindrance at the site of transcriptional initiation.

Base Sequence↗
PubMed1989

Cloning of the gene encoding the yeast protein BTF1Y, which can substitute for the human TATA box-binding factor.

An activity (designated BTF1Y) in extracts of Saccharomyces cerevisiae can substitute for the human TATA box-binding factor BTF1 in a reconstituted transcription system containing the adenovirus 2 major late promoter, RNA polymerase B (II), and the basic transcription factors BTF2, BTF3, and STF. We have purified BTF1Y to homogeneity, using as assays reconstitution of in vitro transcription and DNase I footprinting on the TATA element. Both activities copurified with a 27-kDa polypeptide as determined by SDS/PAGE. Gel filtration indicated a molecular mass of 28 +/- 5 kDa under nondenaturing conditions, suggesting that the native BTF1Y protein is a monomer. BTF1Y was enzymatically cleaved, several peptides were sequenced, and appropriate oligonucleotide probes were synthesized to clone the BTF1Y gene from a yeast genomic library. The BTF1Y gene contains a 720-base-pair open reading frame encoding a protein of 27,003 Da. The recombinant protein expressed in HeLa cells exhibited the same chromatographic characteristics and in vitro transcriptional activity as BTF1Y prepared from yeast extracts, confirming the identity of the gene. Gene-disruption experiments indicated that the yeast BTF1Y gene is a single-copy essential gene.

Adenoviruses, Human↗
PubMed1994

Species-specific interaction of the glutamine-rich activation domains of Sp1 with the TATA box-binding protein.

We have used protein-blotting and protein affinity chromatography to demonstrate that each of the two glutamine-rich activation domains of the human transcription factor Sp1 can bind specifically and directly to the C-terminal evolutionarily conserved domain of the human TATA box-binding protein (TBP). These activation domains of Sp1 also bind directly to Drosophila TBP but bind much less strongly to TBP from the yeast Saccharomyces cerevisiae. The abilities of the Sp1 activation domains to interact directly with the TBPs of various species correlate well with their abilities to activate transcription in extracts derived from the same species. We also show that a glutamine-rich transcriptional activating region of the Drosophila protein Antennapedia binds directly to TBP in a species-specific manner that reflects its ability to activate transcription in vivo. These results support the notion that TBP is a direct and important target of glutamine-rich transcriptional activators.

Animals↗
PubMed2000

TATA-flanking sequences influence the rate and stability of TATA-binding protein and TFIIB binding.

The kinetics of TATA-binding protein (TBP) and TFIIB binding were measured on a series of promoter constructs that had varying sequences within and flanking the TATA box. The flanking sequences were found to influence TBP stability even though they do not contact the protein. This occurs by altering the decay rate rather than the association rate. TFIIB association is accompanied by protein-protein cooperativity as indicated by the simultaneous release of both proteins in challenge experiments. The sequence of the TATA box and the sequences that flank it can influence the kinetics of the TFIIB.TBP.DNA complex. TFIIB can contribute to tighter TATA binding in two ways. It always slows the decay rate of TBP, but it can also increase the rate of association at promoters with certain combinations of TATA and flanking sequences. The results imply that the interplay between the TATA box and flanking elements leads to variations in the kinetics of preinitiation complex formation that may account for the observed effects of all of these diverse sequences on transcription.

DNA↗
PubMed1993

Intron-exon structure, alternative use of promoter and expression of the mouse collagen X gene, Col10a-1.

The entire mouse collagen X gene (Col10a-1) has been isolated. The gene is composed of three exons and two introns spanning 7.0 kb of the DNA sequence. Exons 2 and 3 together encode 15-bp of 5' untranslated sequence, a 2040-bp open reading frame and an 895-nucleotide 3' non-coding region. In the 5' flanking region of the gene, two consensus TATA-box sequences were found. Identification of the first exon by ribonuclease-protection assays and the determination of the 5' end of Col10a-1 mRNA transcripts by primer-extension analyses show that the more 3' TATA box is probably predominantly used and that there are at least three transcription start sites in the exon 1 sequence 3' to this, resulting in 5' untranslated regions of 78, 77 and 55 nucleotides. By means of rapid amplification of cDNA ends by polymerase chain reaction, an additional mRNA species was detected which overlapped the other Col10a-1 transcripts, including the 3' TATA box sequence, giving a 5' untranslated sequence of approximately 235 bases. This latter transcript starts approximately 20 bp 3' to the more 5' TATA box. The data suggest alternative use of promoters and transcription starts for the Col10a-1 gene. Comparison of the combined nucleotide and deduced amino acid sequences of exons 2 and 3 with chicken, bovine and human collagen X genes, showed a high degree of similarity indicating conservation of this gene throughout evolution. Mouse Col10a-1 mRNA was shown to be approximately 3.0 kb and the pepsinized protein, as detected by SDS/PAGE, was approximately 45 kDa. The mRNA and protein sizes correlate with that predicted by the open reading frame. Reverse-transcription polymerase chain reaction assays indicate that the mouse collagen X gene is first expressed at 13.5 days post coitum, temporally preceding the onset of endochondral ossification. In agreement with the generally accepted association of type-X collagen with endochondral ossification, in situ hybridization analyses indicate that Col10a-1 mRNA are restricted to the hypertrophic regions of growth cartilage.

Amino Acid Sequence↗
PubMed2004

Methyl jasmonate induced expression of the tobacco putrescine N -methyltransferase genes requires both G-box and GCC-motif elements.

Putrescine N-methyltransferase (PMT) catalyzes the first committed step of nicotine biosynthesis, converting putrescine into N-methylputrescine. A variety of chemical, environmental, and developmental cues have been implicated in its regulation. Here we have examined the differential expression of beta-glucuronidase (GUS) transgenes under the control of the transcriptional regulatory sequences of four distinct members of the NtPMT gene family from tobacco (Nicotiana tabacum L.). BY-2 cell cultures expressing various NtPMT promoter-GUS constructs were examined for their response to treatment with various combinations of methyl jasmonate (MeJA), auxin (AUX), and ethylene (ETH). All four NtPMT gene promoters examined were inducible by MeJA, although the extent of the induction varied dramatically, with the NtPMT1a promoter being the most responsive. High AUX levels in the cell growth media repressed NtPMT::GUS transgene expression and inhibited their MeJA-induced transcription. Treatment of BY-2 cells with ETH alone did not result in a significant alteration in NtPMT::GUS expression. However, similar to AUX, ETH treatment led to the suppression of MeJA-induced transcription. Detailed deletion analysis of the NtPMT1a gene promoter showed that as little as 111 bp upstream of the transcriptional start site were sufficient to confer MeJA-responsiveness. Deletion of a conserved G-box element (GCACGTTG) at -103 to -96 bp completely abolished MeJA-responsiveness. Further mutagenesis studies revealed that in addition to a functional G-box, MeJA-responsiveness of the NtPMT1a promoter also required a TA-rich region and a GCC-motif (TGCGCCC) located at -80 to -69 bp and -62 to -56 bp relative to the start site, respectively. A synthetic G-box tetramer (4 X syn G-box) fused to a -83 bp fragment from the NtPMT1a promoter (containing the TA-rich region, GCC-box, and TATA-box) displayed a 30-fold induction by MeJA treatment, whereas when the 4 X syn G-box was fused to a minimal (-46 bp) promoter fragment derived from the CaMV 35S gene, no induction by MeJA treatment was detected. Our results indicate that multiple intersecting signal transduction pathways and different transcriptional regulatory factors are involved in mediating JA-responsiveness of NtPMT expression in tobacco.

Acetates↗
PubMed1996

Regulation of the human bilirubin UDP-glucuronosyltransferase gene.

The human UGT1 gene is a single copy gene consisting of four common exons and more than 13 variable exons which span more than 200 kb of the human genome. A single variable exon is spliced to the four common exons to form the mRNA for synthesis of a single UDP-glucuronosyltransferase (UGT) isoenzyme. Treatment of humans or hepatoma cell lines with drugs such as phenobarbital causes the induction of hepatic bilirubin UGT by increased transcription from the UGT1 gene. The upstream region of UGT1*1 (bilirubin UGT) was sequenced and found to contain consensus sequences for several transcriptional regulatory elements including a 'BARBIE box'. An unusual 'TATA' promoter sequence A(TA)6TAA was also observed. The 5' region flanking the UGT1*1 exon when cloned into reporter constructs and transfected into four cells lines was capable of promoting reporter gene expression, but not when transfected into monkey kidney cell fibroblasts (COS-7 cells) indicating a cell specific expression. Sequential deletion of the 5' flanking region in the plasmid constructs did not cause any significant reduction in reporter expression. Treatment of cells transfected with these plasmid constructs with drugs did not cause a significant increase in reporter expression except with retinoic acid plus WY 14643. Introduction of an additional two base pairs (TA) into the 'TATA' box of the 5' gene sequence (as observed in Gilbert's patients) did not significantly change reporter expression levels. The regulation of the biliruibin UGT gene by drugs is not yet understood and it will be important to identify additional genetic elements possibly further than -2kb upstream of the UGT1*1 coding region, which regulate the expression of this gene.

Base Sequence↗
PubMed1991

Structure and expression of the duck alpha-enolase/tau-crystallin-encoding gene.

In the duck, the glycolytic enzyme, alpha-enolase (alpha ENO) and the lens structural protein, tau-crystallin (tau CRY), are products of the same gene, an example of protein multi-functionality. We report that duck alpha ENO/tau CRY mRNA levels are developmentally regulated: alpha ENO/tau CRY mRNA levels in the lens increase over those in the liver by embryonic day 14 and, within the lens, are higher in the lens epithelium than in fiber cells. We determined the structure of the duck alpha ENO/tau CRY-encoding gene (alpha ENO/tau CRY), sequenced 1 kb of 5'-flanking region, and demonstrated that this region contains a functional promoter. The gene is 13 kb in size and is composed of twelve exons; the exon organization is identical to that of mammalian enolase-encoding genes. A fragment of 5'-flanking region (-803/+3) containing three CCAAT boxes and a TATA box was able to activate transcription of a heterologous reporter gene when transfected into cultured lens cells. However, in spite of greater quantities of alpha ENO/tau CRY mRNA and protein in the lens, the promoter was equally active in primary cultures of embryonic lens, liver and fibroblast cells. Since the cultured cells unexpectedly lost the restricted pattern of alpha ENO/tau CRY mRNA levels observed in vivo, evaluation of the promoter's tissue specificity was precluded.

Animals↗
PubMed1993

Isolation and characterization of a rat HSP 27 gene.

A gene encoding the rat heat shock protein 27 protein was isolated and characterized. The gene is composed of three exons and two introns. The proximal 5' untranslated region of this gene contains consensus heat shock elements, multiple SP1 sites, and basal regulatory elements including a CCAAT box and a TATA box. Comparison of this heat shock gene with the murine heat shock protein 25 and human heat shock protein 27 genes revealed the conserved presence of a putative heat shock element in the first intron of these mammalian small M(r) heat shock protein genes. While preliminary expression studies indicate the promoter directs heat shock induced expression of heat shock protein 27, the functional significance of the intronic heat shock element to the expression of this gene remains to be determined.

Amino Acid Sequence↗
PubMed1992

Characterization of the human pleiotrophin gene. Promoter region and chromosomal localization.

The protein (PTN) encoded by the pleiotrophin (PTN) gene belongs to a recently described family of heparin-binding cytokines whose expression is temporally and spatially regulated during development. We have now isolated genomic clones of the human PTN gene, characterized its promoter region, determined its transcription initiation site(s), and established functional activity of the PTN promoter. A fragment -550/+191 that contains a CAAT box, no apparent TATA box, and four consensus sites for the binding of MyoD is sufficient to provide optimal promoter activity. A serum response element is found at -559 to -568. We also have identified the human PTN gene on chromosome 7, band q33 and the mouse Ptn gene on chromosome 6, respectively. The data thus identify and characterize the 5' end of the PTN gene and its promoter region, suggest potential regions that may contribute to the regulation of its transcriptional activity, and localize the PTN gene in human and mouse chromosomes.

3T3 Cells↗
PubMed1994

Human interferon regulatory factor 2 gene. Intron-exon organization and functional analysis of 5'-flanking region.

Interferon regulatory factor 2 (IRF-2) is a transcriptional regulatory protein that terminates interferon beta expression initiated by interferon regulatory factor 1. In this study, we isolated the genomic DNA for human IRF-2 gene, determined the intron-exon structure of the human IRF-2 gene, mapped the major transcription initiation site, identified a number of potential regulatory elements in the 5'-flanking region, and localized the IRF-2 gene on human chromosome 4. The IRF-2 promoter region contains a CpG island, with several GC boxes, a putative NF-kappa B-binding site, and a CAAT box, but no TATA box. When the promoter region was linked with a heterologous reporter gene, we found that the promoter region is inducible by both interferons (interferon-alpha and -gamma) and interferon regulatory factor 1. The region which induced these inductions was identified as being confined to 40 nucleotides 5' to the major transcriptional initiation site by testing a series of clones with truncated promoter of IRF-2. This region contains elements which are shared with the transcriptional enhancers of other genes including interferon regulatory factor 1, interferon beta, and interferon-inducible genes. These data suggest that interferon regulatory factor 1 not only triggers the activation of the interferon signal transduction pathway, but also may play a role in limiting the duration of this response by activating the transcription of IRF-2.

Amino Acid Sequence↗