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PubMed1991

Direct interaction between adenovirus E1A protein and the TATA box binding transcription factor IID.

Adenovirus E1A has long been known to activate/repress cellular and viral transcription. The transcriptional activity of nuclear extracts was depleted after chromatography on immobilized E1A protein columns that specifically retained the transcription factor (TF) IID. Stronger direct interactions between E1A and human TFIID than between E1A and yeast TFIID suggest that the unique sequences of the human protein may be involved. We have demonstrated that this interaction occurs directly between bacterially produced E1A and bacterially produced human TFIID in a protein blot assay. We propose that E1A protein may transduce regulatory signals from upstream activators to basal elements of the transcriptional machinery by contacting TFIID.

Adenovirus Early Proteins↗
PubMed2005

Full sequence of HIV type 1 Korean subtype B in an AIDS case with atypical seroconversion: TAAAA at TATA box.

A patient who presented with late stage HIV-associated diseases could not be diagnosed by commercial ELISA tests and a Western blot. However, we could amplify proviral DNA of HIV-1. We found a novel GPGGMI motif in the V3 loop, a novel insertion of a proline in the C3 region, and persistent deletion of two amino acids in the vif gene. The patient had been treated with HAART after diagnosis. Forty months after the first amplification of HIV-1 DNA, anti-HIV-1 antibody was confirmed by ELISA and Western blot and, thus, we amplified and sequenced HIV-1 full sequences. Interestingly, the sequence at the TATAA box was TAAAA, although full sequences were not CRF01_AE. The major differences in the level of the HIV-1 gene between the seronegative and seropositive states were changes at the glycosylation site (NXT) next to the inserted proline and many resistance mutations including M184V to antiretroviral drugs occurred. This is the first report on HIV-1 full sequences isolated from seronegative AIDS patients infected with subtype B in Korea.

Acquired Immunodeficiency Syndrome↗
PubMed1992

A bipartite DNA binding domain composed of direct repeats in the TATA box binding factor TFIID.

Point mutations in residues comprising the interrupted direct repeats of TFIID eliminated DNA binding in an electrophoretic mobility shift assay. In contrast, mutations in nonconserved residues within the direct repeat regions or in lysine residues comprising the intervening basic repeat had no effect on DNA binding. However, small spacing changes (addition or deletion of one to three residues) in the basic repeat eliminated DNA binding. These results argue for a bipartite DNA binding domain composed of direct repeats with a strict spacing and orientation. Surprisingly, some direct repeat mutations that inhibited DNA binding failed to show a corresponding inhibition of basal transcription, indicating compensating interactions of TFIID with other general factors. The implications of these and other recent results for TFIID structure, promoter recognition, and interactions with other factors are discussed.

Amino Acid Sequence↗
PubMed2004

The Zap1 transcriptional activator also acts as a repressor by binding downstream of the TATA box in ZRT2.

The zinc-responsive transcriptional activator Zap1 regulates the expression of both high- and low-affinity zinc uptake permeases encoded by the ZRT1 and ZRT2 genes. Zap1 mediates this response by binding to zinc-responsive elements (ZREs) located within the promoter regions of each gene. ZRT2 has a remarkably different expression profile in response to zinc compared to ZRT1. While ZRT1 is maximally induced during zinc limitation, ZRT2 is repressed in low zinc but remains induced upon zinc supplementation. In this study, we determined the mechanism underlying this paradoxical Zap1-dependent regulation of ZRT2. We demonstrate that a nonconsensus ZRE (ZRT2 ZRE3), which overlaps with one of the ZRT2 transcriptional start sites, is essential for repression of ZRT2 in low zinc and that Zap1 binds to ZRT2 ZRE3 with a low affinity. The low-affinity ZRE is also essential for the ZRT2 expression profile. These results indicate that the unusual pattern of ZRT2 regulation among Zap1 target genes involves the antagonistic effect of Zap1 binding to a low-affinity ZRE repressor site and high-affinity ZREs required for activation.

Binding Sites↗
PubMed1999

Orphan receptor Arp-1 binds to the nucleotide sequence located between TATA box and transcriptional initiation site of the human angiotensinogen gene and reduces estrogen induced promoter activity.

Human angiotensinogen gene contains a C/A polymorphism at 20 bases upstream from the transcriptional initiation site. This sequence binds to the estrogen receptor when nucleoside A is present at this site and reporter constructs containing human angiotensinogen gene promoter with nucleoside A at -20 are transactivated on co-transfection of estrogen receptor in HepG2 cells followed by estrogen treatment. We show here that orphan receptor, Arp-1, which belongs to the COUP family of transcription factors also binds to this sequence. Co-transfection of Arp-1 reduces estrogen induced promoter activity of reporter constructs containing human angiotensinogen gene promoter. On the other hand co-transfection of Arp-1 does not have a significant effect on estrogen induced promoter activity of reporter constructs containing rat angiotensinogen gene promoter. Our data suggests that human and rat angiotensinogen genes are regulated in a different manner by estrogens.

Angiotensinogen↗
PubMed2004

Small de novo duplication in the repeat region of the TATA-box-binding protein gene manifest with a phenotype similar to variant Creutzfeldt-Jakob disease.

A 20-year-old North American patient developed rapidly progressive cognitive decline and pronounced ataxia, a phenotype compatible with prion disease. No structural changes were found in the PRNP gene, which excludes genetic prion disease, but the patient's PRNP codon 129 Met/Met genotype is known to predispose to variant Creutzfeldt-Jakob disease (vCJD). Further studies identified an expanded allele with 55 CAG/CAA repeats in the TBP gene. The increase of trinucleotide repeat number in the coding region of the TBP gene has previously been associated with spinocerebellar ataxia type 17 (SCA17). The patient's unaffected parents and siblings show normal-size TBP alleles with 37-38 repeats. Haplotype and nucleotide sequence analyses clearly indicate that the mutation has occurred de novo on a paternal chromosome by insertion/duplication of a (CAA)(CAG)(CAA)(CAG)(15) sequence. This report presents a second fully investigated sporadic case of SCA17 occurring as a result of a DNA rearrangement within the polymorphic TBP trinucleotide repeat region. Our findings suggest that patients suspected of vCJD should undergo testing for SCA17, Huntington's disease and other neurodegenerative disorders having phenotypic similarities with vCJD.

Adult↗
PubMed1991

The murine adenosine deaminase promoter requires an atypical TATA box which binds transcription factor IID and transcriptional activity is stimulated by multiple upstream Sp1 binding sites.

We have explored the template and factor requirements for in vitro transcription of the GC-rich promoter of the murine adenosine deaminase gene. The core promoter consists of an A-rich sequence (TAAAAAA) 27 base pairs upstream of the initiation site which binds transcription factor IID (TFIID) and a high affinity Sp1 binding site located 27 base pairs further upstream. Multiple upstream elements increased core promoter activity 20-fold and correspond to protected regions in DNase I footprinting assays with purified Sp1 protein. Internal deletion of the TA6 element alone eliminated transcription in spite of the presence of all other promoter elements including four Sp1 binding sites. Recombinant human TFIID supported weak basal transcription in heat-treated nuclear extracts whereas a partially purified TFIID fraction from HeLa cells reconstituted a maximal level of transcription. Inclusion of 12 base pairs immediately adjacent to the proximal Sp1 site resulted in a 5-fold boost in transcriptional activity and corresponds to a second Sp1 binding site. These results serve as a basis for further exploration of the factors involved in the developmental and selective high level tissue expression of the murine adenosine deaminase gene.

Adenosine Deaminase↗
PubMed1998

Transcription from the thyroid hormone-dependent promoter of the Xenopus laevis thyroid hormone receptor betaA gene requires a novel upstream element and the initiator, but not a TATA Box.

The thyroid hormone receptor (TR) beta genes in Xenopus laevis are regulated by thyroid hormone in all organs of an animal during metamorphosis. This autoregulation appears to be critical for systematic transformations of different organs as a tadpole is transformed into a frog. To understand this autoregulation, we have previously identified a thyroid hormone response element in the hormone-dependent promoter of the X. laevis TRbetaA gene. We report here the detailed characterization of the promoter. We have now mapped the transcription start site and demonstrated the existence of an initiator element at the start site critical for promoter function. More important, our deletion and mutational experiments revealed a novel upstream DNA element that is located 125 base pairs upstream of the start site and that is essential for active transcription from the promoter. Promoter reconstitution experiments showed that this novel element does not function as an enhancer, but acts as a core promoter element, which, together with the initiator, directs accurate transcription from the promoter. Finally, we provide evidence for the existence of a protein(s) that specifically recognizes this element. Our studies thus demonstrate that the TRbetaA promoter has a unique organization consisting of an initiator and a novel upstream promoter element. Such an organization may be important for the ubiquitous but tissue-dependent temporal regulation of the gene by thyroid hormone during amphibian metamorphosis.

Animals↗
PubMed1995

Repression of the herpes simplex virus 1 alpha 4 gene by its gene product (ICP4) within the context of the viral genome is conditioned by the distance and stereoaxial alignment of the ICP4 DNA binding site relative to the TATA box.

Infected cell protein no. 4 (ICP4), the major regulatory protein encoded by the alpha 4 gene of herpes simplex virus 1, binds to a site (alpha 4-2) at the transcription initiation site of the alpha 4 gene. An earlier report described the construction of recombinant viruses that contained chimeric genes (alpha 4-tk) that consisted of the 5' untranscribed and transcribed noncoding domains of the alpha 4 gene fused to the coding sequences of the thymidine kinase gene and showed that disruption of the alpha 4-2 binding site by mutagenesis derepressed transcription of this gene (N. Michael and B. Roizman, Proc. Natl. Acad. Sci. USA 90:2286-2290, 1993). This experimental design was used to determine the effect of displacement of the alpha 4-2 binding site on the repression of alpha 4 gene transcription by ICP4. We report the following findings. (i) In the absence of the alpha 4-2 binding site, at 4 h after infection, alpha 4-tk RNA levels increased 10-fold relative to the corresponding RNA levels of a gene that contained the alpha 4-2 site at its natural location. Displacement of the alpha 4-2 binding site by approximately one, two, and three turns of the DNA helix, i.e., by 10, 21, and 30 nucleotides downstream of the original site, increased the concentration of alpha 4-tk RNA 2.4-, 3.5-, and 5.8-fold, respectively. (ii) Displacement of 16 nucleotides, i.e., approximately 1.5 helical turns, increased the accumulation of alpha 4-tk by 5.3-fold, i.e., more than predicted by displacement alone. (iii) At 8 h after infection in the absence of the binding site, the accumulation of alpha 4-tk RNA increased 13.6-fold. However, in cells infected with recombinants that carried displaced alpha 4-2 binding sites, RNA accumulation decreased relative to the levels seen at 4 h after infection. The insertion of DNA sequences in order to displace the alpha 4-2 binding site had no effect on accumulation of RNA in the presence of cycloheximide, i.e., in the absence of ICP4, or on maximum accumulation of alpha 4-tk RNA in the absence of the alpha 4-2 binding site.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2002

Cis-acting elements, CArG-, E-, CCAAT- and TATA-boxes may be involved in sexually regulated gene transcription in Schistosoma mansoni.

Schistosomes undergo various morphological and metabolic changes during their development, reflected in a finely tuned regulation of protein and/or gene expression. The mechanisms involved in the control of gene expression during the development of the parasite are not understood. Two actin genes had been previously cloned and observed to be differentially expressed during the maturation of the parasite. The SmAct gene contains four putative cis-regulatory elements (TATA-, CCAAT-, E- and CArG-boxes). Our objective was to investigate in greater detail the expression pattern of two actin genes and verify if the binding of nuclear proteins to the promoter elements of SmAct correlated with the expression profile observed. We detected little variation in the expression of actin genes during the first seven days of schistosomula culture in vitro. However, we observed significantly higher levels of expression in males compared to female adults. CArG and CCAAT elements bound to a greater extent and formed distinct complexes with male in comparison to female nuclear extracts. In contrast, female extracts bound weakly to the E-box probe while no binding was observed with male extracts. Taken together these results describe cis-acting elements that appear to be involved in sexually regulated gene expression in Schistosoma mansoni.

Animals↗
PubMed1990

UV cross-linking identifies four polypeptides that require the TATA box to bind to the Drosophila hsp70 promoter.

A protein fraction that requires the TATA sequence to bind to the hsp70 promoter has been partially purified from nuclear extracts of Drosophila embryos. This TATA factor produces a large DNase I footprint that extends from -44 to +35 on the promoter. A mutation that changes TATA to TATG interferes both with the binding of this complex and with the transcription of the hsp70 promoter in vitro, indicating that this interaction is important for transcriptional activity. Using a highly specific protein-DNA cross-linking assay, we have identified four polypeptides that require the TATA sequence to bind to the hsp70 promoter. Polypeptides of 26 and 42 kilodaltons are in intimate contact with the TATA sequence. Polypeptides of 150 and 60 kilodaltons interact within the region from +24 to +47 in a TATA-dependent manner. Both the extended footprint and the polypeptides identified by UV cross-linking indicate that the Drosophila TATA factor is a multicomponent complex.

Animals↗
PubMed1990

Isolation and characterization of the Drosophila gene encoding the TATA box binding protein, TFIID.

To investigate the biochemical mechanisms involved in interactions between regulatory factors and the general transcription complex, we have cloned, expressed, and characterized the Drosophila gene encoding the TATA binding protein, dTFIID. Comparison of the protein sequences of the Drosophila and yeast TATA binding proteins reveals a bipartite organization consisting of a highly conserved, basic carboxy-terminal domain and a nonconserved amino-terminal region rich in Gln, Gly, Ser, and Met residues. Purified dTFIID protein binds specifically to the TATA sequence and activates basal-level transcription, and the conserved carboxy-terminal half of the molecule is sufficient for both activities. Partially purified TFIID from Drosophila cells mediates activation by the transcription factor Sp1. In contrast, purified dTFIID expressed from the cloned gene is unable to support Sp1-dependent activation, suggesting that other factors may be required to mediate interactions between upstream activators like Sp1 and the TATA binding protein.

Amino Acid Sequence↗
PubMed1985

Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region.

A gene-specific transcription factor, called USF, has been partially purified from HeLa cell nuclear extracts. Addition of USF results in a 10 to 20 fold increase in transcription from the adenovirus major late promoter in an in vitro system reconstituted with transcription factors TFIIB, TFIID, TFIIE, and RNA polymerase II. Binding of USF to the promoter inhibits DNAase I cleavages over a 20 base pair region just upstream of the -45 to +35 region shown previously to interact with TFIID. More discriminating footprint analyses using methidiumpropyl-EDTA-Fe(II) as the cleaving agent indicate that USF interacts primarily with the small palindromic DNA sequence GGCCACGTGACC located between positions -63 and -52 of the major late promoter, while TFIID interacts primarily with a 10 base pair DNA region centered on the consensus TATA sequence. Dissociation rate measurements indicate a cooperative interaction between USF and TFIID when simultaneously bound to the promoter DNA.

Adenoviridae↗
PubMed1982

Nucleotide sequences of the murine retrovirus Friend SFFVp long terminal repeats: identification of a structure with extensive dyad symmetry 5' to the TATA box.

The two long terminal repeats (LTRs) of the integrated provirus of the polycythemia strain of the Friend spleen focus forming virus have been sequenced. Each of the identical LTRs is 514 nucleotides long and together confer on the provirus the features of a transposable element. They are terminated by perfect 11 base-pair inverted repeats, and the entire provirus is flanked by an apparent duplication of host DNA four nucleotides long. The assumed transcription regulatory sequences (Hogness-Goldberg box, CAAT box, polyadenylation signal) can be identified within the LTRs, as well as a region of an imperfect inverted repeat which extends from approximately 140 to 270 nucleotides 5' from the point of transcription initiation. This sequence may form a hairpin-type structure which might have some function in the promotion of transcription.

Animals↗
PubMed1983

An inverted sea urchin histone gene sequence with breakpoints between TATA boxes and mRNA cap sites.

A sea urchin histone gene fragment containing inverted regions of the normal repeat has been cloned in pBR322. Restriction enzyme mapping and homoduplex analysis of this fragment indicate that the H1-H4 spacer of one repeat is situated alongside the inverted H2A-H1 spacer of another repeat. The site of the breakpoint has been sequenced and compared with homologous stretches of the normal repeat. The breakpoints in the original duplexes were found to be within 4-6 bp of the H4 mRNA cap site and 8-10 bp of the H1 mRNA cap site in the standard repeat. The breakpoints in both original duplexes contain short direct repeats and an overlap of 3 bases. As this is the first breakpoint resulting in the apposition of inverted sequence to be analyzed at the level of DNA sequence, we speculate whether structural features described here are typical of such rearrangements. The structure observed is consistent with, but does not prove, that the sequence is the endpoint of a true inversion since only one junction has been isolated and characterized.

Animals↗
PubMed1983

The repeated GC-rich motifs upstream from the TATA box are important elements of the SV40 early promoter.

We have constructed deletion and point mutations within the Simian virus 40 (SV40) early promoter region which contains two tandemly repeated 21 bp sequences and a related 22 bp sequence (the "upstream" 21 bp repeat region). After transfection into permissive CV-1 cells and non-permissive mouse 3T3-4E cells, the effect of the mutations on early gene expression was studied by measuring T-antigen production, using indirect immunofluoresence. Our results demonstrate that the 21 bp repeat region, and in particular the six GC-rich motifs 5'-CCGCCC-3' which are repeated in this region constitute an important element of the SV40 early promoter. Surprisingly, we found that the requirement for the 21 bp repeat region for early gene expression was partially fulfilled even when it was in the inverted orientation.

Animals↗