Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Transcription initiation by mammalian RNA polymerase II is effected by multiple common factors interacting through minimal promoter elements and regulated by gene-specific factors interacting with distal control elements. Minimal promoter elements that can function independently or together, depending on the specific promoter, include the upstream TATA box and a pyrimidine-rich initiator (Inr) overlapping the transcription start site. The binding of TFIID to the TATA element promotes the assembly of other factors into a preinitiation complex but factors which function at the Inr have not been defined. We show here that a novel factor (TFII-I) binds specifically to Inr elements, supports basal transcription from the adenovirus major late promoter and is immunologically related to the helix-loop-helix activator USF. We further show that TFII-I also binds to the upstream high-affinity USF site (E box), that USF also binds to the Inr, and that TFII-I and USF interact cooperatively at both Inr and E box sites. Thus, TFII-I represents a novel type of transcription initiation factor whose interactions at multiple promoter elements may aid novel communication mechanisms between upstream regulatory factors and the general transcriptional machinery.
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PMID:Cooperative interaction of an initiator-binding transcription initiation factor and the helix-loop-helix activator USF. 196 Dec 51

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.
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PMID:Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. 407 92

Ornithine decarboxylase (ODC) plays an important role in cell proliferation. Its expression is tightly regulated at the mRNA and protein levels and is found to be deregulated in various malignancies. The rapid and dramatic induction of cellular ODC mRNA upon serum addition raised the possibility that a transcriptional attenuation mechanism may be involved in the regulation of ODC gene expression. Using transcription in HeLa nuclear extract and isolated transcription complexes, we have identified two sites of transcription arrest downstream to the transcription start site: Attenuator 1 (Att.1) located at +220, near two repeats of a USF/Myc-Max binding consensus sequence and attenuator 2 (Att.2) located at +1590 near a long stretch of T-residues. The two attenuators exhibit distinct properties as revealed by elongation of briefly initiated and partially purified transcription complexes: Att.1 serves as a transient pause site while arrest at Att.2 is more prolonged. The arrest at both attenuators is modulated by the general elongation factor TFIIS. In a promoter independent transcription system, using partially purified RNA polymerase II, only Att.2 was recognized efficiently. This suggests that the recognition of Att.2 is an intrinsic property of the polymerase while Att.1 recognition has to be facilitated by an auxiliary factor/s.
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PMID:Transcription elongation of the murine ornithine decarboxylase (ODC) gene is regulated in vitro at two downstream elements by different attenuation mechanisms. 753 63

Upstream stimulatory factor USF is a human transcriptional activation factor, which uses a basic/helix-loop-helix/ leucin zipper (b/HLH/Z) motif to homodimerize and recognize specific sequences in the promoter region of both nuclear and viral genes transcribed by RNA polymerase II. Steady state fluorescence spectroscopy demonstrated that the basic/helix-loop-helix/leucin zipper domain of USF binds its DNA targets with high affinity and specificity, whereas removal of the leucine zipper yielding the basic/helix-loop-helix minimal DNA binding region reduces both affinity and specificity. Stopped flow method provided kinetic evidence for a two-step binding process involving rapid formation of a protein-DNA intermediate followed by a slow isomerization step, which is consistent with the basic region undergoing a random coil to alpha-helix folding transition on specific DNA recognition. The leucine zipper is also necessary for USF to function as a bivalent homotetramer, capable of binding two distinct recognition sites simultaneously and mediating DNA looping under physiologic conditions. Titration studies revealed that the first binding event has a equilibrium constant Keq = (2.2 +/- 2.0) x 10(9) M-1 for major late promoter DNA, whereas the second binding event occurs with a remarkable reduced affinity, Keq = (1.2 +/- 0.8) x 10(8) M-1. This anticooperative feature of DNA binding by the homotetramer suggests that USF stimulates transcription by mediating DNA looping between nearby recognition sites located in class II nuclear and viral gene promoters.
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PMID:Anti-cooperative biphasic equilibrium binding of transcription factor upstream stimulatory factor to its cognate DNA monitored by protein fluorescence changes. 764 9

The tandemly repeated gene set encoding the sea urchin U6 gene has been cloned from the sea urchin Strongylocentrotus purpuratus. The U6 gene is transcribed by RNA polymerase III in a sea urchin nuclear extract. Like that of the vertebrate U6 genes, transcription of the sea urchin U6 gene does not require any internal sequences or 3' sequences but requires only 5' flanking sequences. Only 88 nucleotides of 5' flanking sequence are required for maximal expression in vitro. Mutagenesis experiments demonstrated the requirement for three elements, a CACGTG element at -80, a proximal sequence element at about -55, and the TATA-like box at -25. The major protein in sea urchin extracts that interacts with the CACGTG element is sea urchin USF, and immunodepletion of sea urchin USF greatly reduces transcription. The USF binding site in the U6 gene is highly homologous (11 of 13 nucleotides) with the USF binding sites found in the promoter of the S. purpuratus spec genes.
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PMID:Transcription of the sea urchin U6 gene in vitro requires a TATA-like box, a proximal sequence element, and sea urchin USF, which binds an essential E box. 811 49

We have previously demonstrated that the core promoter of rat ribosomal RNA gene (rDNA) contains an E-box-like sequence to which the core promoter binding factor CPBF binds and that the 44 kDa subunit of this protein is immunologically related to USF1, the helix--loop--helix-zipper DNA binding protein. Further, we showed that RNA polymerase I (pol I) transcription in vitro is competed by oligonucleotides containing USF-binding site, which suggested a key role for USF in rDNA transcription. To prove the potential role of USF in pol I transcription in vivo, USF1 and USF2 homodimers and USF1/USF2 heterodimer were overexpressed in CHO cells by transfection of the respective cDNAs. Co-transfection of a plasmid containing rDNA followed by primer extension analysis showed that overexpression of USF1 and USF2 as homodimers resulted in inhibition of rDNA transcription by as much as 85-90% whereas overexpression of USF1/USF2 in the heterodimeric form activated transcription approximately 3.5-fold. Transfection of mutant USF2 cDNA that is devoid of the basic DNA-binding domain produced only minimal inhibition of rDNA transcription. These data show that USF can modulate transcription of rRNA gene in vivo by functioning as a repressor (homodimer) or activator (heterodimer) of pol I transcription in vivo and suggest that inhibition of rDNA transcription may be responsible for the antiproliferative action of USF homodimers.
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PMID:The dual role of helix-loop--helix-zipper protein USF in ribosomal RNA gene transcription in vivo. 905 57

Insoluble functional synthetic random copolymers are able to develop at their surfaces specific interactions with biologic components. Crosslinked phosphorylated polystyrene derivatives were previously shown to mimic DNA antigen because they interacted with anti-DNA antibodies found in the sera of systemic lupus erythematosus patients. These biospecific surfaces were postulated to be able to bind other DNA-binding proteins such as RNA polymerase II transcription factors. Indeed, these proteins play a major role in gene regulation in mammalian cells. This hypothesis was checked by adsorption and elution of HeLa cell nuclear extracts on a 72% phosphorylated resin. The composition of the eluted fractions were analyzed by electrophoresis, and the biologic activity of the transcription factors was tested using an in vitro transcription assay. The results showed that USF, TATA-binding protein (TBP), and TFIIB were specifically adsorbed on the polymer and that all eluted factors kept their biologic activity. Therefore, randomly phosphorylated polystyrene derivatives may be useful for the fractionation of RNA polymerase II transcription factors.
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PMID:Randomly phosphorylated polystyrene derivatives interact with RNA polymerase II transcription factors: part I. 905 26

PTF/SNAPc is a multisubunit complex which specifically recognizes the PSEs of small nuclear RNA genes and activates transcription by RNA polymerase II or III. Here we describe the isolation and characterization of genomic clones encoding the human PTFgamma/SNAP43 gene. The gene spans approximately 29 kilobases, and is composed of 9 exons and 8 introns. A major transcription initiation site was identified at the position 58 base pairs upstream of the AUG translation initiator codon on primer extension analysis with HeLa mRNA. The 5' flanking region lacks a typical TATA box but contains many putative binding sites for various transcription factors, such as Sp1, Oct1, NF1, AP1, E2F, and USF. Immediately downstream of the transcription start site, we found a VNTR of a 17-bp sequence rich in (G+C). Four different alleles with two to five copies of the tandem repeat were identified in 10 individuals examined, indicating a high degree of variation at the PTFgamma/SNAP43 locus. In addition, the PTFgamma/SNAP43 gene was mapped to human chromosome 14q22 by fluorescence in situ hybridization.
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PMID:The human PTFgamma/SNAP43 gene: structure, chromosomal location, and identification of a VNTR in 5'-UTR. 964 40

To investigate the regulation of CD30 at the level of transcription, we have isolated and compared the promoter sequence of human and murine CD30. Analysis of the human and mouse promoter identified a number of potential transcription factor binding sites, including ETS, MZF, AP-1, IK2, CREB, Stat, USF, and Spl. The absence of TATA or CAAT boxes and the identification of one major and three minor transcription initiation sites for CD30 suggest that it is a member of the class of TATA-less promoters that use initiator elements to correctly position the RNA polymerase. Comparison of the murine and human CD30 promoters identified a number of highly conserved regions, including an Spl site 40 bp upstream from the major start site and a downstream promoter element (DPE) that may be involved in directing transcriptional initiation of the CD30 gene. Functional analysis of the human CD30 promoter in transfected Jurkat T cells provided further evidence that these conserved regions are important regulatory elements in the CD30 promoter.
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PMID:Analysis of the human and mouse promoter region of the non-Hodgkin's lymphoma-associated CD30 gene. 985 12

The c-Myc oncoprotein and its dimerization partner Max bind the DNA core consensus sequence CACGTG (E-box) and activate gene transcription. However, the low levels of induction have hindered the identification of novel Myc target genes by differential screening techniques. Here, we describe a computer-based pre-selection of candidate Myc/Max target genes, based on two restrictive criteria: an extended E-box consensus sequence for Myc/Max binding and the occurrence of this sequence within a potential genomic CpG island. Candidate genes selected by these criteria were evaluated experimentally for their response to Myc. Two Myc target genes are characterized here in detail. These encode nucleolin, an abundant nucleolar protein, and BN51, a co-factor of RNA polymerase III. Myc activates transcription of both genes via E-boxes located in their first introns, as seen for several well-characterized Myc targets. For both genes, mutation of the E-boxes abolishes transcriptional activation by Myc as well as repression by Mad1. In addition, the BN51 promoter is selectively activated by Myc and not by USF, another E-box-binding factor. Both nucleolin and BN51 are implicated in the maturation of ribosomal RNAs, albeit in different ways. We propose that Myc, via regulation of these and probably many other transcriptional targets, may be an important regulator of ribosome biogenesis.
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PMID:Myc induces the nucleolin and BN51 genes: possible implications in ribosome biogenesis. 1060 42


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