Run-off Transcription Research Articles

Monitoring mis-acylated tRNA suppression efficiency in mammalian cells via EGFP fluorescence recovery.

A reporter assay was developed to detect and quantify nonsense codon suppression by chemically aminoacylated tRNAs in mammalian cells. It is based on the cellular expression of the enhanced green fluorescent protein (EGFP) as a reporter for the site-specific amino acid incorporation in its sequence using an orthogonal suppressor tRNA derived from Escherichia coli. Suppression of an engineered amber codon at position 64 in the EGFP run-off transcript could be achieved by the incorporation of a leucine via an in vitro aminoacylated suppressor tRNA. Microinjection of defined amounts of mutagenized EGFP mRNA and suppressor tRNA into individual cells allowed us to accurately determine suppression efficiencies by measuring the EGFP fluorescence intensity in individual cells using laser-scanning confocal microscopy. Control experiments showed the absence of natural suppression or aminoacylation of the synthetic tRNA by endogenous aminoacyl-tRNA synthetases. This reporter assay opens the way for the optimization of essential experimental parameters for expanding the scope of the suppressor tRNA technology to different cell types.

A Modified pBluescript-Based Vector for Facile Cloning and Transcription of RNAs

We report here the generation of a vector that would permit efficient in vitro transcription of RNAs and ensure that unwanted additional sequences at the 59 termini are minimized in the final transcripts. Several vectors (such as the Bluescript and GEM series) are currently available for cloning genes under the control of a bacteriophage RNA polymerase promoter and subsequent in vitro transcription. During the cloning process, if recognition sequences for the type IIS restriction enzymes (e.g., FokI, BsmAI) are adroitly placed at the end of the coding region, templates with the desired 39 end for runoff transcription can be easily generated (1, 2). In contrast to the precision with which the 39 end can be engineered, the use of restriction enzymes for directional cloning downstream to the promoter sequence frequently results in additional nucleotides being introduced 59 to the sequence encoding gene of interest. Consequently, the 59 end of the resulting transcript has unwanted sequences. The commercially available LITMUS vectors (New England Biolabs) sought to address this limitation by engineering restriction sites into the 26 to 21 region of the T7 RNA polymerase promoter (PT7) sequence (3). However, this approach resulted in reductions in transcriptional efficiency owing to modifications in the consensus sequence of PT7 that is required for initiation (3, 4). Yet another solution to circumvent addition of unwanted 59 sequences in the transcript is by including the PT7 sequence in the sense primer used in PCR-based cloning of the gene of interest (1). Al-

Defining the Bacillus subtilis σ W regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches

The Bacillus subtilis extracytoplasmic function (ECF) σ factor σ W controls a large regulon that is strongly induced by alkali shock. To define the physiological role of σ W we have sought to identify the complete set of genes under σ W control. Previously, we described a promoter consensus search procedure to identify σ W controlled genes. Herein, we introduce a novel method to identify additional target promoters: run-off transcription followed by macroarray analysis (ROMA). We compare the resulting list of targets with those identified in conventional transcriptional profiling studies and using the consensus search approach. While transcriptional profiling identifies genes that are strongly dependent on σ W for in vivo expression, some σ W-dependent promoters are not detected due to the masking effects of other promoter elements, overlapping recognition with other ECF σ factors, or both. Taken together, the consensus search, ROMA, and transcriptional profiling approaches establish a minimum of 30 promoter sites (controlling ∼60 genes) as direct targets for activation by σ W. Significantly, no single approach identifies more than ∼80 % of the regulon so defined. We therefore suggest that a combination of two or more complementary approaches be employed in studies seeking to achieve maximal coverage when defining bacterial regulons. Our results indicate that σ W controls genes that protect the cell against agents that impair cell wall biosynthesis but fail to reveal any connection to operons likely to function in adaptation to alkaline growth conditions. This is consistent with the observation that a sigW mutant is unaffected in its ability to survive alkali shock. We conclude that in B. subtilis sudden imposition of alkali stress activates the σ W stress response, perhaps by impairing the ability of the cell wall biosynthetic machinery to function.

Virus-induced silencing of FtsH gene in Nicotiana benthmiana causes a striking bleached leaf phenotype.

A recombinant Potato virus X (PVX) vector, pTXS.FtsH, harboring partial sequence of FtsH gene of Nicotiana benthamiana was constructed to silence the expression of endogenous FtsH homologous gene in N. benthamiana. Inoculation with in vitro runoff transcript of pTXS.FtsH to N. benthamiana plants allowed silencing of FtsH, causing striking bleaching of upper leaves reminiscent of var2 mutant phenotype of Arabidopsis thaliana. FtsH-silenced plants exhibited no resistance against Tobacco mosaic virus (TMV) and a phytopathogenic fungus Botrytis cinerea. Virus-induced gene silencing (VIGS) of N. benthamiana with PVX as demonstrated here would be an efficient and rapid method to study the function of other elements of photosystem II (PSII) in planta.

NF-κB1 (p50) Homodimers Contribute to Transcription of thebcl-2 Oncogene

The bcl-2 proto-oncogene is frequently expressed in human cancer. Although bcl-2 was first cloned as the t(14;18) translocation breakpoint from human follicular B-cell lymphoma, it has become apparent that many cell types express bcl-2 because of transcriptional regulation. As such, several transcription factors have been demonstrated to activate expression of bcl-2, including NF-kappaB. We investigated the role of NF-kappaB1 (p50) homodimers in the expression of Bcl-2 in two murine B-cell lymphoma cell lines: LY-as, an apoptosis-proficient line with low Bcl-2 protein expression and no nuclear NF-kappaB activity, and LY-ar, a nonapoptotic line with constitutive p50 homodimer activity and 30 times more Bcl-2 protein expression than LY-as. We found that nuclear p50 homodimer activity correlated with Bcl-2 expression in these cell types and identified several sites within the bcl-2 5'-flanking region that p50 was capable of binding. In vitro transcription revealed that recombinant p50 enhanced the production of run-off transcripts from the bcl-2 P1 promoter. Additional in vitro transcription experiments suggested the sites by which p50 afforded this effect. We conclude that the p50 homodimer is capable of transcriptional activation of the bcl-2 gene and suggest that its nuclear activity contributes to the expression of bcl-2 in LY-ar cells.

Host RNA polymerase requirements for transcription of the human hepatitis delta virus genome.

Replication of the genome of hepatitis delta virus (HDV) requires RNA-directed RNA synthesis using a host polymerase(s). This manuscript reviews the relevant published evidence. It also provides two new studies, both of which made use of transiently transfected Huh7 cells undergoing HDV RNA-directed RNA synthesis. For the first study, RNA transcription inhibitors were added to the transfected cells for periods of 1 to 2 days, after which assays of the effects on the accumulation of processed unit-length genomic HDV RNA were performed. For the second study, nuclei were isolated at 6 days after transfection, and then in vitro runoff transcription was used to assay the effects of RNA transcription inhibitors. Overall, the data support the interpretation that HDV transcription does not require host polymerase I or III (pol I or III) but at least primarily involves an enzyme resembling pol II.

Inhibition of protein translocation across the endoplasmic reticulum membrane by sterols.

Cholesterol and related sterols are known to modulate the physical properties of biological membranes and can affect the activities of membrane-bound protein complexes. Here, we report that an early step in protein translocation across the endoplasmic reticulum (ER) membrane is reversibly inhibited by cholesterol levels significantly lower than those found in the plasma membrane. By UV-induced chemical cross-linking we further show that high cholesterol levels prevent cross-linking between ribosome-nascent chain complexes and components of the Sec61 translocon, but have no effect on cross-linking to the signal recognition particle. The inhibiting effect on translocation is different between different sterols. Our data suggest that the protein translocation machinery may be sensitive to changes in cholesterol levels in the ER membrane.

Genotyping of dinucleotide tandem repeats by MALDI mass spectrometry of ribozyme-cleaved RNA transcripts.

We describe a method for high-throughput typing of short tandem repeat (STR) polymorphisms. Current gel electrophoresis techniques allow only moderate throughput with long hands-on and analysis time, and the output is on a relative scale of electrophoretic mobility, prone to artifacts. Matrix-assisted laser- desorption/ionization mass spectrometry (MALDI-MS) enables an automated high throughput and delivers accurate data directly depicting the molecular nature of the analyte. Analysis of large DNA fragments, however, is limited by adduct formation and fragmentation, which result in peak broadening and low signal intensity. MALDI typing of polymorphic STRs has been reported for tri- and tetranucleotide repeats with sufficient resolution to distinguish alleles. For dinucleotide repeats, essential in animal genome studies, an enhanced resolution is necessary. Increased mass resolution was reported for RNA (ref. 7) and modified DNA (refs 8-10) due to substituents that disfavor intramolecular reactions leading to fragmentation. RNA transcripts can be synthesized enzymatically from PCR products containing a promoter sequence, requiring no specialty reagents or primer labels. Furthermore, RNA transcripts are single-stranded, a prerequisite for high-resolution mass spectrometry of nucleic acids. The 3' heterogeneities produced by viral RNA polymerases, however, impede exact sizing of RNA runoff transcripts. Non-templated multiple-base extensions as well as premature termination have been reported. PCR of dinucleotide repeats tends toward the deletion of repeat units, generating a complex pattern of interleaved extensions (from RNA polymerase) and deletions (from PCR) that obscure the true allele size. We overcome this obstacle by adding a 3' sequence encoding a catalytic RNA sequence, the so-called hammerhead ribozyme, that cleaves itself co-transcriptionally, creating a homogeneous 3' end.

Elevation of β-Amyloid Peptide 2–42 in Sporadic and Familial Alzheimer's Disease and Its Generation in PS1 Knockout Cells

Urea-based beta-amyloid (Abeta) SDS-polyacrylamide gel electrophoresis and immunoblots were used to analyze the generation of Abeta peptides in conditioned medium from primary mouse neurons and a neuroglioma cell line, as well as in human cerebrospinal fluid. A comparable and highly conserved pattern of Abeta peptides, namely, 1-40/42 and carboxyl-terminal-truncated 1-37, 1-38, and 1-39, was found. Besides Abeta1-42, we also observed a consistent elevation of amino-terminal-truncated Abeta2-42 in a detergent-soluble pool in brains of subjects with Alzheimer's disease. Abeta2-42 was also specifically elevated in cerebrospinal fluid samples of Alzheimer's disease patients. To decipher the contribution of potential different gamma-secretases (presenilins (PSs)) in generating the amino-terminal- and carboxyl-terminal-truncated Abeta peptides, we overexpressed beta-amyloid precursor protein (APP)-trafficking mutants in PS1+/+ and PS1-/- neurons. As compared with APP-WT (primary neurons from control or PS1-deficient mice infected with Semliki Forest virus), PS1-/- neurons and PS1+/+ neurons overexpressing APP-Deltact (a slow-internalizing mutant) show a decrease of all secreted Abeta peptide species, as expected, because this mutant is processed mainly by alpha-secretase. This drop is even more pronounced for the APP-KK construct (APP mutant carrying an endoplasmic reticulum retention motif). Surprisingly, Abeta2-42 is significantly less affected in PS1-/- neurons and in neurons transfected with the endocytosis-deficient APP-Deltact construct. Our data confirm that PS1 is closely involved in the production of Abeta1-40/42 and the carboxyl-terminal-truncated Abeta1-37, Abeta1-38, and Abeta1-39, but the amino-terminal-truncated and carboxyl-terminal-elongated Abeta2-42 seems to be less affected by PS1 deficiency. Moreover, our results indicate that the latter Abeta peptide species could be generated by a beta(Asp/Ala)-secretase activity.

Transcriptional activation by the human Hsp70-associating protein Hap50.

We investigated human Hap50, the large isoform of the previously characterized Hsp70/Hsc70-associating protein Hap46, also called BAG-1, for effects on transcriptional activities. Overproduction by transient transfection led to enhanced expression of reporter gene constructs in various cell types using different promoters, suggesting independence of promoter type. Similarly, overexpression of Hap50 resulted in increased levels of poly(A)(+ )mRNAs in HeLa, COS-7, 3T3 and HTC cells. Concomitantly, the expression of some selected endogenous genes, such as those coding for c-Jun and the glucocorticoid receptor, was enhanced significantly relative to actin. Nuclear runoff transcription assays using HeLa cells showed that the effect is caused by increased transcription rates rather than mRNA stabilization. Activation of transcription by Hap50 occurred at 37 degrees C and did not require prior thermal stress, as is the case for Hap46. In accordance with these biological effects, Hap50 is localized exclusively in the nuclear compartment of different cell types, whereas Hap46 is mostly cytoplasmic in unstressed cells, as revealed by use of fusion constructs with green fluorescent protein. High cellular levels of Hap50 were found to make cells less susceptible to adverse environmental effects such as heat stress. Our data suggest that Hap50 is a nuclear protein that acts in cells to increase the transcription of various genes.

5'-coterminal subgenomic RNAs in citrus tristeza virus-infected cells.

Three unusual 5' coterminal positive-stranded subgenomic (sg) RNAs, two of about 0.8 kb and one of 10 kb (designated LMT1, LMT2, and LaMT, respectively), from Citrus spp. plants and Nicotiana benthamiana protoplasts infected with Citrus tristeza virus (CTV) were characterized. The 5' termini of the LMT RNAs were mapped by runoff reverse transcription and found to correspond with the 5' terminus of the genomic RNA. The LMT 5'-coterminal sgRNAs consisted of two modal lengths of 744--746 and 842--854 nts. The 3' of the LaMT RNAs terminated near the junction of ORF 1b and ORF 2 (p33). None of the 5' sgRNAs had detectable amounts of corresponding negative-sense RNAs, as occurs with the genomic and 3' coterminal subgenomic RNAs of CTV. The abundance of the short and long 5' sgRNAs differed considerably in infected cells. The LMT RNAs were considerably more abundant than the genomic RNAs, while the larger LaMT RNA accumulated to much lower levels. The kinetics of accumulation of LMT1 and LMT2 in synchronously infected protoplasts differed. The larger RNA, LMT1, accumulated earlier with a strong hybridization signal at 2 days postinfection, a time when only traces of genomic and 3' sgRNAs were detected. The lack of corresponding RNAs, that could be 3' cleavage products corresponding to the 5' coterminal sgRNAs and the lack of complementary negative strands, suggest that these sgRNAs were produced by termination during the synthesis of the genomic positive strands.

Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes.

In the effort to prepare the mouse full-length cDNA encyclopedia, we previously developed several techniques to prepare and select full-length cDNAs. To increase the number of different cDNAs, we introduce here a strategy to prepare normalized and subtracted cDNA libraries in a single step. The method is based on hybridization of the first-strand, full-length cDNA with several RNA drivers, including starting mRNA as the normalizing driver and run-off transcripts from minilibraries containing highly expressed genes, rearrayed clones, and previously sequenced cDNAs as subtracting drivers. Our method keeps the proportion of full-length cDNAs in the subtracted/normalized library high. Moreover, our method dramatically enhances the discovery of new genes as compared to results obtained by using standard, full-length cDNA libraries. This procedure can be extended to the preparation of full-length cDNA encyclopedias from other organisms.

Kinetic analysis of Sp1-mediated transcriptional activation of the human DNA polymerase beta promoter.

In the present studies, we have examined the effect of Sp1 on the activation of the human DNA polymerase beta (beta-pol), a TATA-less promoter. A HeLa cell nuclear extract (NE) based in vitro runoff transcription system of core beta-pol promoter human DNA (pbetaP8) three-step kinetic model of transcription initiation were used to describe the kinetic effect of Sp1. The results showed that distal Sp1-binding sites in the core beta-pol promoter are important for transcriptional activation of the pbetaP8 promoter. A detailed kinetic analysis showed that Sp1 stimulates the activity of the pbetaP8 promoter through distal Sp1-binding sites by increasing the amount of recruitment, instead of stimulating the apparent rate of RPc assembly (k1). There was no significant effect of Sp1 on the apparent rate of open complex (RPo) formation (k2) or on the apparent rate of promoter clearance (k3) of the pbetaP8 promoter. These studies define the kinetic mechanisms by which Sp1 may regulate the rate of transcript formation of the pbetaP8 promoter, and these results may have implications for Sp1 regulation of TATA-less promoters.

Recombinant constructions and infectivity analysis of tobacco mosaic virus and attenuated tomato mosaic virus N14 genomes

The recombinant clones of pTN and pNT have been constructed by exchanging the coding regions of the movement proteins (MP), coat proteins (CP) and 3− noncoding regions between the cDNAs of the tobacco mosaic virus (Chinese Isolate, TMV-Cv) and the attenuated tomato mosaic virus N14 genomes, and used as templates forin vitro runoff transcription. Their transcripts have been used for tobacco infection assays. The infection results show that the transcripts of pTN and pNT are infectious. Local lesions were observed in the leaves ofNicotiana tabacum cv. Samsun NN inoculated with pTN transcript, but were fewer than those in the same kind of plant induced by pTMV-Cv transcript. Systemic symptoms were also observed inN. tabacum cv. Huangmiaoyu induced by pTN transcript, but were slighter than those on the same kind of tobacco induced by pTMV-Cv transcript. Local lesions were shown inN. tabacum cv. Samsun NN inoculated with pNT transcript, but were more than those in the same kind of plant induced by pN14 transcript while no systemic symptom was displayed inN. tabacum cv. Huangmiaoyu. These results suggest that the recombinant viruses of TN and NT are able to propagate in the assayed tobaccos, and they keep the most same phenotypic character with pTMV-Cv and pN14 transcripts, and TMV-Cv and N14 as well. The conjunctions between the replicase and the MP, CP and 3− noncoding regions are not stringent. Apparently there is a compatible function complementation between the homologous subgenomes of TMV-Cv and N14. From those above it could be probably presumed that the mutagenized replicase gene of N14 plays a major role In contributing to the virus attenuation while its mutagenized MP gene could avianize the symptoms of the infected tobaccos.

Early perturbations in keratin and actin gene expression and fibrillar organisation in griseofulvin-fed mouse liver

Background/Aims: Long-term feeding of mice with a diet containing griseofulvin results in the formation of Mallory bodies, keratin K8 and K18 containing aggregates in hepatocytes. These bodies are biochemically and morphologically identical to the Mallory bodies that emerge in several human liver disorders. The aim of this study was to examine the contribution of K8 and K18 and actin to Mallory body formation.Methods: Mice were fed griseofulvin over a period ranging from 1 day to 20 months. Hepatocyte morphology was monitored by immunocytochemistry, gene expression by Northern and run-off transcription assays, and protein level by Western blotting.Results: Griseofulvin feeding induced a series of morphological alterations in hepatocytes that could be grouped into 3 phases: appearance of cholestasis during the first week (phase I), partial hepatocyte recovery at 3 months (phase II), and development of typical Mallory bodies after 3 to 5 months (phase III). All these cellular alterations were associated with perturbations in keratin and actin fibrillar status, coupled with increases in K8, K18 and actin mRNA steadystate level and, in K8 and K18 protein content. The transcriptional activity of the genes was not affected.Conclusions: Perturbations in keratin and actin gene expression and fibrillar organisation constitute early events in the griseofulvin-induced pathological process that in the long-term leads to Mallory body formation. The higher keratin and actin mRNA levels reflect significant increases in mRNA stability taking place at the early phase of griseofulvin intoxication in hepatocytes.

Generation of catalytically active 6-phosphofructokinase from Saccharomyces cerevisiae in a cell-free system.

PFK1 and PFK2 coding for the subunits of 6-phosphofructokinase from Saccharomyces cerevisiae were cloned into plasmids suitable for runoff transcription. In vitro translation products of both kinds of subunit were obtained using rabbit reticulocyte lysate as the synthesis and folding system. They were monitored by chemiluminescent Western-blot analysis. Folding and assembly of the alpha-subunit and beta-subunit of 6-phosphofructokinase were found to occur in the cell-free system resulting in an enzymatically active protein. The in vitro generated enzyme exhibits a folding state that is similar to that of the heterooctameric form of 6-phosphofructokinase in the presence of fructose 6-phosphate, ATP and ammonium sulfate, as demonstrated by size-exclusion HPLC followed by ELISA.

Infectious Pancreatic Necrosis Virus RNA Cleavage In Vitro by Hammerhead Ribozymes and Enhancement of Ribozyme Catalysis by Oligonucleotide Facilitators.

Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus, has a bisegmented double-stranded RNA genome consisting of a 3.2-kb A segment and a 2.9-kb B segment. To determine the function of IPNV's viral proteins and to study the effects of viral RNA cleavage by hammerhead ribozymes, we cloned and sequenced the IPNV E1S strain of the A segment. After sequencing, we continued to study the virus pathogens inhibited by ribozyme cleavage and analyzed the cleavage of the virus RNA in vitro. The templates (VP2, 1220 bp) for in vitro transcription of S569 and S969 (substrates 569 and 969 bp in length) were synthesized by polymerase chain reaction. The DNA templates of hammerhead ribozymes targeted different sites in the partial sense RNA of IPNV. These templates were chemically synthesized RNAs prepared by runoff transcription of amplification products or synthetic DNA templates containing a T7 RNA polymerase promoter, and were used to characterize several properties of the cleavage reaction at 25 degrees C in 12 mM Mg(2+). Under this condition (25 degrees C, 12 mM Mg(2+)), the hammerhead ribozymes formed an estimated fraction of product during the reaction of only 30% in cleaving long RNA substrates in vitro. Short DNA facilitators (12 or 24-mers) that bind adjacent to either the 3' or 5' end of the ribozyme enhanced the rate of cleavage of the long RNA substrates containing 569 and 969 nucleotides, respectively, in trans. The hammerhead ribozymes with 3'-end facilitators reacted more efficiently (i.e., 65%).

Elf-pulsed magnetic fields modulate opioid peptide gene expression in myocardial cells.

Magnetic fields have been shown to affect cell proliferation and growth factor expression in cultured cells. Although the activation of endorphin systems is a recurring motif among the biological events elicited by magnetic fields, compelling evidence indicating that magnetic fields may modulate opioid gene expression is still lacking. We therefore investigated whether extremely low frequency (ELF) pulsed magnetic fields (PMF) may affect opioid peptide gene expression and the signaling pathways controlling opioid peptide gene transcription in the adult ventricular myocyte, a cell type behaving both as a target and as a source for opioid peptides. Prodynorphin gene expression was investigated in adult rat myocytes exposed to PMF by the aid of RNase protection and nuclear run-off transcription assays. In PMF-exposed nuclei, nuclear protein kinase C (PKC) activity was followed by measuring the phosphorylation rate of the acrylodan-labeled MARCKS peptide. The effect of PMF on the subcellular distribution of different PKC isozymes was assessed by immunoblotting. A radioimmunoassay procedure coupled to reversed-phase high performance liquid chromatography was used to monitor the expression of dynorphin B. Here, we show that PMF enhanced myocardial opioid gene expression and that a direct exposure of isolated myocyte nuclei to PMF markedly enhanced prodynorphin gene transcription, as in the intact cell. The PMF action was mediated by nuclear PKC activation but occurred independently from changes in PKC isozyme expression and enzyme translocation. PMF also led to a marked increase in the synthesis and secretion of dynorphin B. The present findings demonstrate that an opioid gene is activated by myocyte exposure to PMF and that the cell nucleus and nuclear embedded PKC are a crucial target for the PMF action. Due to the wide ranging importance of opioid peptides in myocardial cell homeostasis, the current data may suggest consideration for potential biological effects of PMF in the cardiovascular system.

Characterization of avian reovirus non structural protein σNS synthesized in Escherichia coli

The coding region of avian reovirus S1133 genomic segment S4, encoding the non structural protein σNS, was inserted into expression vector pET28a and the protein was expressed in Escherichia coli BL21(DE3) as a fusion protein containing a C-terminal peptide with six tandem histidines (His-tag). The expressed protein (eσNS) consistent with the expected molecular size of the avian reovirus protein σNS synthesized in infected cells was readily purified by His-Bind Resin. The eσNS was further confirmed to be indistinguishable from viral σNS by immunoblot analysis. The eσNS binds 32P-labeled ssRNA probe produced by run-off transcription of clone pGEM-3Zf(+)S4. The binding activity is blocked by heterologous yeast rRNA, but not by homologous avian reovirus dsRNA and heterologous infectious bursal disease virus dsRNA and salmon sperm dsDNA. Therefore, the ssRNA-binding activity of the expressed protein σNS is non sequence-specific, similar to that previously described for viral σNS purified from avian reovirus infected cell extracts. In addition, the recent data also show that the optimal salt (NaCl) concentration and pH for its binding are 100–150 mM and 7.0, respectively, in terms of the UV cross-linking and RNase A treatment of the reaction mixtures prior to the denaturing gel analysis.

Kinetic analysis of Sp1-mediated transcriptional activation of a TATA-containing promoter.

Using a HeLa cell nuclear extract (NE)-based in vitro runoff transcription system, we have examined the effect of Sp1 on the activation of a TATA-containing chimeric DNA polymerase beta (pAS8) promoter. The results demonstrated that the TATA element-dependent basal activity of the pAS8 promoter was stimulated 4-fold by supplementation of a Sp1-depleted HeLa cell nuclear extract (NEd) with purified human Sp1, indicating that pAS8 promoter activity is dependent upon Sp1. A detailed kinetic analysis based on a three-step kinetic model of transcription initiation showed that Sp1 stimulates the activity of the pAS8 promoter by increasing the amount of closed preinitiation complex (RP(c)) assembly as well as by enhancing the rate of promoter clearance (k(3)). There was no significant effect of Sp1 on the apparent rate of open complex (RP(o)) formation (k(2)) of the pAS8 promoter. These studies define more precisely the kinetic mechanisms by which Sp1 may regulate the rate of transcript formation of a TATA-containing promoter.