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PubMed1989

Yeast upstream activator protein GCN4 can stimulate transcription when its binding site replaces the TATA element.

We replaced the required TATA element of a yeast gal-his3 promoter by a binding site for GCN4, a protein that normally activates transcription when bound upstream of a TATA element. Surprisingly, GCN4 efficiently activates his3 transcription from wild-type initiation sites, though in a pattern associated with constitutive his3 transcription rather than GCN4 upstream activation through a TATA element. Transcriptional stimulation by GCN4 requires both the DNA-binding domain and the acidic activation function but is not affected by changing the spacing or helical relationship between the GCN4 binding site and the mRNA start sites. GCN4 is not sufficient for this TATA-independent activation; a sequence in the gal fragment distinct from the GAL4 binding sites is also required. Thus, GCN4 functions both when bound upstream of a TATA element and also when bound at the position of a TATA element. In the latter case, we suggest the possibility that GCN4 might be able to stimulate transcription by an alternate mechanism that does not involve a conventional TATA-binding transcription factor.

Bacterial Proteins↗

PubMed1991

Several different upstream promoter elements can potentiate transactivation by the BPV-1 E2 protein.

The enhancer and upstream promoter regions of RNA polymerase II transcribed genes modulate the rate of transcription initiation and establish specific patterns of gene expression. Both types of region consist of clusters of DNA binding sites for nuclear proteins. To determine how efficiently the same factor can activate transcription when acting as an enhancer or promoter factor, we have studied transactivation by the BPV-1 E2 protein, a papillomavirus transcriptional regulator. By cotransfecting a BPV-1 E2 expression vector and a series of reporter plasmids containing well-defined chimeric promoters we have found that whilst E2 can strongly stimulate complex promoters such as that of the HSV tk gene, it does not efficiently activate constructions containing only a TATA box and initiation site. We show that insertion of upstream promoter elements, but not of spacer DNA, between E2 binding sites and the TATA box greatly increases E2 activation. This effect was observed with more than one type of upstream promoter element, is not related to the strength of the promoter and is unlikely to result from co-operative DNA binding by E2 and the transcription factors tested. These results would suggest that E2 has the properties of an enhancer rather than promoter factor and that in certain cases promoter and enhancer factors may affect different steps in the process of transcriptional activation.

Base Sequence↗

PubMed1995

Upstream sequence elements enhance poly(A) site efficiency of the C2 complement gene and are phylogenetically conserved.

Poly(A) signals of mammalian pre-mRNA have been defined as an AAUAAA sequence 10-30 nt upstream of the cleavage/poly(A) site followed by a GU/U-rich element immediately downstream. However, a number of viral poly(A) signals have been shown to possess additional signals upstream of AAUAAA that increase poly(A) site efficiency. We describe the first non-viral example of such an upstream sequence element (USE) for the poly(A) site of the human C2 complement gene. As this gene is very closely spaced to the related Factor B gene [the C2 poly(A) site is only 421 bp from the transcription start site of Factor B] we have isolated this same intergenic sequence from four other mammals (mouse, cat, rabbit and cow). We show that the USE of the C2 poly(A) site is highly conserved between these five different mammals. Furthermore, extensive mutagenesis of the human USE indicates that most of the 53 nt sequence is required for full activity. The human C2 poly(A) site does not possess any obvious downstream GU/U-rich sequences, although sequences immediately 3' to AAUAAA as well as 13 nt of sequence following the cleavage site are both required for full activity. Interestingly the other mammalian C2 poly(A) sites do possess significant downstream GU/U-rich sequences. Finally we show that all five mammalian C2 poly(A) signals are immediately followed by conserved signals for transcriptional termination, consistent with the close proximity of the downstream Factor B gene.

Animals↗

PubMed2004

Comparison of genomic and cDNA sequences of guinea pig CYP2B18 and rat CYP2B2: absence of a phenobarbital-responsive enhancer module in the upstream region of the CYP2B18 gene.

Potential mechanisms were investigated whereby CYP2B18, a cytochrome P450 gene exhibiting high constitutive expression but only low levels of phenobarbital-inducibility in the guinea pig liver, may be differentially regulated versus the highly inducible rat CYP2B2 gene. To comparatively assess potential regulatory sequences associated with CYP2B18, a guinea pig genomic library was screened enabling isolation of the CYP2B18 gene. The genomic screening process resulted in the identification of at least four closely-related CYP2B18 genes, designated here as CYP2B18A-D. Of these isolates, CYP2B18A exhibited sequence identical to that of the CYP2B18 cDNA. Further, the deduced amino acid sequence of the CYP2B18 cDNA was identical to that of N-terminal and internally-derived peptide sequences obtained in this investigation from CYP2B18 protein isolated from guinea pig liver. Genomic structural sequences were derived for CYP2B18A, together with the respective 5'-upstream and intronic regions of the gene. Comparison of the CYP2B18A and CYP2B2 gene sequences revealed the lack of repetitive LINE gene sequences in CYP2B18A, putative silencing elements that effect neighboring genes, although these sequences were present in both 5'-upstream and 3'-downstream regions of CYP2B2. We determined that the phenobarbital-responsive enhancer module was absent from the 5'-upstream region as well as the intronic regions of CYP2B18A gene. We hypothesize that the compromised phenobarbital inducibility of CYP2B18A stems from its lack of a functional phenobarbital responsive enhancer module.

Amino Acid Sequence↗

PubMed1995

Regulation of the rat S100 beta gene expression: the role of the 2 kb 5'-upstream sequence in glial specific expression.

We have studied the role of the 2047 bp 5'-upstream region and 232 bp first exon sequence of the rat S100 beta gene in glial specific expression. S100 beta luciferase expression vectors carrying serial deletions of the S100 beta 5' upstream sequence were constructed and transiently transfected into the peripheral nervous system (PNS) glial-type cell line RT4-D6, the PNS neuronal-type cell line RT4-E5, and the central nervous system (CNS) glial-type cell line C6. The hepatoma cell line HTC was also transfected as a nonneural control. From this functional analysis, we found a glial-specific positive regulatory sequence(s) mapped between -583 and -106 relative to the transcriptional start site. This region confers a significantly higher level of luciferase expression in the glial-type cell lines RT4-D6 and C6 than in the neuronal cell line RT4-E5 and the hepatoma cell line HTC. Also, a non-cell type specific positive regulatory element was identified in the first exon sequence between +78 and +232. Though non-cell type-specific, it was found to have a predominant effect in glial cells. From these observations, we have concluded that the 2047 bp 5'-upstream region and 232 bp of the first exon sequence confers the high levels of S100 beta expression in glial cells through these two positive elements.

Animals↗

PubMed1989

Sequence-directed DNA bending upstream of the streptokinase promoter.

A 450-base pair (bp) HinfI restriction fragment from the chromosome of Streptococcus equisimilis H46A contains the early coding region of the streptokinase gene (skc), the skc promoter, and a stretch of DNA 5' to the--35 region of the skc promoter. Two-dimensional polyacrylamide (PA) gel electrophoresis at two different temperatures showed that this fragment migrates anomalously slowly on PA gels, suggesting the existence of a bent DNA conformation. Inspection of the nucleotide sequence confirmed this suggestion by revealing numerous oligomeric dA.dT tracts, some of which are in phase with the helix screw. Computer analysis of the sequence predicted the existence of two bending loci, one of which is located upstream of the skc promoter. In addition to showing DNA bending, the 450-bp HinfI fragment contains multiple 13-bp sequences homologous to the Escherichia coli integration host factor DNA-binding consensus sequence. Insertion of IS1 into a site immediately upstream of the--35 region decreased the expression level of skc in E. coli, suggesting that DNA conformation upstream of the promoter has a role in skc expression.

Base Sequence↗

PubMedDate not supplied

An essential gene in Saccharomyces cerevisiae shares an upstream regulatory element with PRP4.

ORF2 is an essential gene immediately upstream of PRP4 (formerly RNA4), a gene involved in nuclear mRNA processing in Saccharomyces cerevisiae. The two genes are arranged head-to-head. An 8 base-pair conserved sequence element is found upstream of both genes, as well as upstream of certain other genes that are known to be involved in pre-mRNA processing. Through deletion analysis we have found that both of the conserved sequence elements are important for transcription of both genes. We have cloned ORF2 and have isolated temperature-sensitive orf2 mutants. The phenotype of these mutants does not suggest a role for ORF2 in mRNA processing. The deduced amino acid sequence of ORF2 indicates significant similarity to DPR1, a gene encoding a protein that is involved in the carboxy-terminal processing of G-protein.

Amino Acid Sequence↗

PubMed1997

Two Sp sites are important cis elements regulating the upstream promoter region of the gene for rat type I hexokinase.

Multiple transcriptional start sites have been identified for the gene encoding the rat Type I isozyme of hexokinase (White, J.A., Liu, W., and Wilson, J. E., Arch. Biochem. Biophys. 335, 161-172, 1996); these are clustered at positions approximately -460, -300, and -100 relative to the translational start codon (ATG, with A being +1). PC12 cells and H9c2 cells were transfected with luciferase reporter constructs containing genomic sequence between positions -3366 and -171. Marked (85%) decrease in promoter activity was associated with deletion of sequence between -742 and -516. In DNase I footprinting experiments, two regions, called P1 (-552 to -529) and P2 (-480 to -458) boxes, were protected by proteins present in nuclear extracts from PC12 cells. Mutation or deletion of the P2 box had no effect on promoter activity; protection in this region, which includes the most upstream cluster of transcriptional start sites, is attributed to binding of RNA polymerase II or associated factors. In contrast, mutations or deletions in the P1 box had markedly detrimental effects on promoter activity and on binding of proteins in PC12 cell nuclear extracts. Maintenance of a consensus Sp1 binding site centrally located in the P1 box was critical for both promoter activity and binding. A second Sp1 site (-570), just upstream from the P1 box, was also shown to be functionally important but no protection of this region was detected in footprinting experiments, presumably reflecting lower affinity at this site under the conditions used. Supershift experiments demonstrated the involvement of Sp1, Sp3, and Sp4 in formation of complexes with the P1 box region and implicate these transcription factors in regulating promoter activity associated with this region. Another series of reporter constructs, including sequence between -171 and -1, permitted detection of an additional promoter activity downstream from -364. While not yet extensively characterized, it is already evident that the cis elements influencing the downstream promoter activity are distinct from the Sp factors determined to be important in expression from the upstream promoter region.

Animals↗

PubMed2001

Posttranscriptional regulation of human ADH5/FDH and Myf6 gene expression by upstream AUG codons.

Upstream open-reading frames are unusual in mammalian mRNAs. The 5' untranslated region of ADH5 mRNA contains an upstream open-reading frame (uORF) with two possible AUG start codons. Myf6 mRNA contains three tandem AUG repeats at the translation start site, a rare feature. Mutation at one or both of the upstream AUG codons in the ADH5 mRNA increased gene expression twofold in CV-1, NIH/3T3, HeLa, and SL2 cells. Mutation of these AUG codons led to 3- to 5-fold increases in activity as measured by in vitro translation assays using capped mRNAs. RNA toeprint analysis demonstrated many stalled ribosomes flanking the AUG codons and secondary structures near the AUGs. Secondary structures may increase the ability of ribosomes to recognize the two AUGs, despite their poor initiation context. The degree of repression by uAUGs varied significantly depending on the cell lines tested, which may partly explain the differential tissue expression. Myf6 is a critical myogenic transcription factor with the striking feature of three tandem AUG codons at the translation initiation site. This structure reduced expression; removing two of these AUGs led to a doubling of activity in CV-1, HeLa, and NIH/3T3 cells.

3T3 Cells↗

PubMed1995

Upstream structure of human ADH7 gene and the organ distribution of its expression.

The ADH7 gene encoding human class IV (sigma) alcohol dehydrogenase (ADH) was cloned from a Caucasian genomic DNA library and its upstream structure was determined. Moreover, the organ distribution of its expression was examined. Northern hybridization analysis with a specific probe for sigma-ADH showed that expression of the gene is organ specific rather than ubiquitous, and occurs in the stomach but not in the liver. The lack of CG rich sequence and presence of TATA and CCAAT boxes in the upstream region of ADH7 may reflect the organ specific expression. The findings that this region lacks hepatocyte nuclear factor and has only one CCAAT enhancer binding protein consensus site may account for the fact that this gene is not expressed in the liver. The upstream region had sequences which are compatible with a glucocorticoid response element, a metal binding factor-1, and an active gene regulatory protein-1, suggesting that sex hormones, zinc, and retinoic acid may be involved in the regulation of the expression of this gene.

Alcohol Dehydrogenase↗

PubMed1996

DNA bending between upstream activator sequences increases transcriptional synergy.

To determine if DNA bending enhances transcriptional synergy between tandem upstream activators, we constructed a series of synthetic promoters containing either an AP1 or an NF1 site linked to four copies of the putative transcription factor binding site ACGTGA incorporated into an intrinsic DNA bending sequence. In transient transfection, the intrinsic bending sequence between AP1 and the TATA box or between NF1 and the TATA box elicited a strong synergistic activation of transcription. The synergistic activation of transcription was greatly reduced when the intrinsic bending sequence was replaced with a mutant sequence which retains the binding site, but does not bend the DNA, and when the intrinsic bending sequence was upstream of the AP1 or NF1 sites. These data indicate that bent DNA located between upstream activator sequences can facilitate transcriptional synergism between bound activators.

Animals↗

PubMed1993

Upstream elements involved in the embryonic regulation of the sea urchin CyIIIb actin gene: temporal and spatial specific interactions at a single cis-acting element.

The sea urchin Strongylocentrotus purpuratus CyIIIb actin gene codes for a cytoskeletal type actin and is activated in the early embryo specifically in the cells destined to become the aboral ectoderm. Deletion constructs of its upstream region fused to the bacterial chloramphenicol acetyltransferase (CAT) gene were expressed in developing embryos following microinjection into eggs. These studies revealed the segments of the upstream region which are necessary for embryonic expression. We mapped the protein:DNA interaction sites in this upstream region by DNase I footprinting. At least five binding sites were identified in the 2173 nucleotide flanking sequence, which seem to include all the necessary elements for quantitative expression. One of these elements (E1) showed different patterns of association in vitro with nuclear proteins isolated from different stages in development. These different interactions are separated when nuclear extracts from ectodermal or endodermal-mesodermal tissues were used. When S. purpuratus eggs were injected with a CAT fusion construct mutated at this site, a decrease in CAT activity was observed only in late stage embryos (plutei), whereas early stage embryos (blastulae) exhibited wild-type CAT activity. These results suggest that the E1 element is involved in the temporal regulation of the CyIIIb gene.

Actins↗

PubMed1997

Thyroid hormone deiodination in various tissues of larval and upstream-migrant sea lampreys, Petromyzon marinus.

Properties and activities of four potential thyroid hormone (TH) monodeiodinating pathways (T4ORD, L-thyroxine (T4) outer-ring (5') deiodination to 3,5,3'-triiodo-L-thyronine (T3); T4IRD, T4 inner-ring (5) deiodination to 3,3',5'-triiodo-L-thyronine (reverse T3); T3ORD, T3 outer-ring deiodination to 3,5-diiodo-L-thyronine; T3IRD, T3 inner-ring deiodination to 3,3'-diiodo-L-thyronine) were studied in microsomes of liver, kidney, muscle, and intestine of unmetamorphosed larvae and nontrophic upstream-migrant (spawning-phase) sea lampreys, Petromyzon marinus. T4ORD properties (pH optimum, dithiothreitrol cofactor requirement, apparent K(m), substrate preference and potency of potential inhibitors) were similar in most respects to those described previously for teleosts. T4ORD activity was detected in all larval tissues examined and was highest in intestine. In upstream migrants, T4ORD was also greatest in intestine, but low in muscle and kidney and undetectable in liver. T3ORD activity was not found in any tissue of either developmental stage. T4IRD and T3IRD activities were negligible in larval tissues, but present in kidney and particularly intestine of upstream migrants. We conclude that depending on developmental/physiological state, sea lampreys possess low-K(m) outer-ring and inner-ring monodeiodinases, which in most respects correspond functionally with those of teleosts. However, in contrast to teleosts, deiodination is particularly active in larval intestine, perhaps reflecting the release from the endostyle of TH into the lumen of the alimentary canal.

Animals↗

PubMed1997

Role of upstream activation sequences and integration host factor in transcriptional activation by the constitutively active prokaryotic enhancer-binding protein PspF.

PspF, the transcriptional activator of the pspA operon of Escherichia coli, which belongs to the enhancer binding protein (EBP) family of sigma54 activator proteins, is constitutively active in an in vitro transcription assay. PspF protein, together with RNA polymerase holoenzyme containing sigma54, is required for in vitro transcription from the pspA promoter. EBP proteins are typically subject to regulation either by post-translational modification or interaction of a specific ligand with an N-terminal regulatory domain. However, unlike other members of the EBP family, PspF lacks this domain. pspA is positively regulated by IHF in vitro, and this regulation is dependent on the topology of the DNA; a linear template is much more dependent on IHF than a supercoiled template. EBP binding to upstream activating sequences (UAS) in their target promoters is mediated by the C-terminal domain which contains a helix-turn-helix DNA-binding motif. A mutant PspF protein lacking the C-terminal DNA-binding domain is active in vitro, although at much higher concentrations than the wild-type protein. In vitro transcription from pspA templates missing one or both of the UAS sites is reduced relative to wild-type templates, but is still appreciable; however, IHF acts as a negative regulator of pspA transcription on these mutant templates. Thus, PspF bound to non-specific sequences upstream of the pspA promoter can activate pspA transcription, but this activation is inhibited by IHF. These data, taken together, support the model that a precise promoter geometry is necessary for IHF to positively regulate transcription and that IHF may act to prevent activation from inappropriately spaced upstream sites.

Bacterial Proteins↗

PubMed1999

Minor groove DNA-protein contacts upstream of a tRNA gene detected with a synthetic DNA binding ligand.

Transcription factor IIIB (TFIIIB) is composed of the TATA box binding protein (TBP) and class III gene-specific TBP-associated factors (TAFs). TFIIIB is brought to a site centered approximately 35 bp upstream from the transcription start site of tRNA genes via protein-protein interactions with the intragenic promoter-recognition factor TFIIIC. Since TBP interacts with TATA elements through the minor groove of DNA, we asked whether TFIIIB interacts with DNA in the minor groove. Polyamides containing pyrrole (Py) and imidazole (Im) amino acids are synthetic DNA ligands that bind to predetermined sequences in the minor groove of double helical DNA. These small molecules have been shown to interfere with protein-DNA interactions in the minor groove. A series of DNA constructs was generated in which the binding site for a Py-Im polyamide was placed at various distances upstream from a tRNA gene transcription start site. We find that a match polyamide will effectively inhibit tRNA gene transcription when its binding site is located within 33 bp of the transcription start site of the Xenopus TyrD tRNA gene. Moreover, in the presence of polyamide, RNA polymerase III is redirected to a new transcription initiation site located approximately one DNA helical turn downstream from the native start site. Our results suggest that a subunit of TFIIIB, possibly TBP, makes an essential minor groove DNA contact centered approximately 30 bp upstream from the tRNA gene.

Animals↗

PubMed2000

Upstream flanking sequences and transcription of SINEs.

SINEs, short interspersed repeated DNA elements, undergo amplification through retroposition and subsequent integration into a new location in the genome. Each new SINE insertion will be located in a new chromosomal environment, with different flanking sequences. Modulation of transcription by different flanking sequences may play an important role in determining which SINE elements are preferentially active in a genome. We evaluated the ability of upstream flanking sequences to regulate the transcription of three different SINEs (Alu, B2 and ID) by constructing chimeric constructs with known 5' flanking sequences of RNA polymerase III-transcribed genes. Upstream sequences from the 7SL RNA gene, U6 RNA gene, vault RNA gene, and BC1 gene increase transcription of Alu, B2 and BC1 in transient transfections of NIH3T3, HeLa, Neuro2a and C6 glioma cell lines. The 7SL sequence proved most efficient in increasing SINE transcription. The 7SL upstream fused to the BC1 RNA gene (an ID element) was used to create a transgenic mouse line. In contrast to the tissue-specific endogenous BC1 transcription, BC1 transgene transcripts were detected in all tissues tested. However, expression was much higher in those tissues that express the endogenous gene, demonstrating both transcriptional and post-transcriptional regulation. The BC1 RNA was detected in a similar ribonucleoprotein complex in the different tissues.

Alu Elements↗

PubMed2002

Identification of two middle promoters upstream DNA ligase gene 30 of bacteriophage T4.

Bacteriophage T4 DNA ligase gene 30 lies in the cluster of prereplicative genes located counterclockwise from map units 149 to 121. Based on the early transcription studies this gene has been considered as a typical early gene of bacteriophage T4. In agreement with this assignment, two strong T4 early promoters, P(E )30.8 (128.6) and P(E )30.7 (128.2), located about 3.1 and 2.7 kb upstream from gene 30 have been revealed by promoter mapping and sequence analysis. In addition, the existence of a putative early promoter just upstream of gene 30 was proposed from the sequence data. However, here we show that the putative early promoter just upstream of gene 30 is, in fact, a T4 middle promoter. Furthermore, we detected one more middle promoter located in the genomic region between early promoter P(E )30.7 (128.2) and DNA ligase gene 30 in the coding region of gene 30.3. Both new middle promoters have differences from the consensus MotA box, while their -10 regions match the sigma(70) consensus sequence very well. The 5' ends of MotA-dependent transcripts directed from these promoters, as well as the kinetics of 5' end accumulation in the cells, have been determined by primer extension analysis. The results of these analyses indicate that both MotA-dependent and MotA-independent promoters control the transcription of T4 DNA ligase gene 30 in vivo. Moreover, we show that the first transcripts for gene 30 are directed from its own middle promoter, P(M)30.

Bacteriophage T4↗

PubMed1994

Mapping of upstream regulatory elements in the P4 promoter of parvovirus minute virus of mice.

The early promoter (P4) of the autonomous parvovirus minute virus of mice (prototype strain) directs the expression of the transcription unit coding for the nonstructural proteins NS1 and NS2. Although proximal promoter elements (GC and TATA boxes) are essential for P4 activity in vivo, additional upstream sequences appear to be required for optimal transcription. Therefore, associations of proteins with the upstream regulatory region of promoter P4 were studied in the rat fibroblast cell line FREJ4 by gel retardation and in vitro as well as in vivo footprinting assays. This led to the identification of at least four distinct upstream elements that interacted with cellular proteins. The functionality of these elements was supported by the reduced level of gene expression driven by corresponding linker-substitutive mutants of promoter P4.

Animals↗