Purification of a factor specific for the upstream element of the adenovirus-2 major late promoter

Hematopoietic upstream stimulating factor 1 deficiency is associated with increased atherosclerosis susceptibility in LDL receptor knockout mice

Total body upstream stimulatory factor 1 (USF1) deficiency in mice is associated with brown adipose tissue activation and a marked protection against the development of obesity and atherosclerotic lesions. Functional expression of USF1 has also been detected in monocytes and monocyte-derived macrophages. In the current study we therefore tested whether selective hematopoietic USF1 deficiency can also beneficially impact the development of atherosclerosis. For this purpose, LDL receptor knockout mice were transplanted with bone marrow from USF1 knockout mice or their wild-type littermate controls and subsequently fed a Western-type diet for 20 weeks to stimulate atherosclerotic lesion development. Strikingly, absence of USF1 function in bone marrow-derived cells was associated with exacerbated blood leukocyte (+ 100%; P < 0.01) and peritoneal leukocyte (+ 50%; P < 0.05) lipid loading and an increased atherosclerosis susceptibility (+ 31%; P < 0.05). These effects could be attributed to aggravated hyperlipidemia, i.e. higher plasma free cholesterol (+ 33%; P < 0.001) and cholesteryl esters (+ 39%; P < 0.001), and the development of hepatosteatosis. In conclusion, we have shown that hematopoietic USF1 deficiency is associated with an increased atherosclerosis susceptibility in LDL receptor knockout mice. These findings argue against a contribution of macrophage-specific USF1 deficiency to the previously described beneficial effect of total body USF1 deficiency on atherosclerosis susceptibility in mice.

Dynamic proteomic analysis of Phanerochaete chrysosporium under copper stress

The model white rot fungus Phanerochaete chrysosporium is frequently preferred for heavy metal accumulation studies due to its high resistance to heavy metals, including copper (Cu). Here, the response of P. chrysosporium under Cu stress at different time points was investigated for the first time by a detailed proteomic analysis using 2DE MALDI-TOF/MS and nanoLC-MS/MS techniques. A total of 123 Cu-responsive protein spots were determined using 2DE approach, and 104 of them were corresponded to 73 distinct open reading frames (ORFs). Of identified ones, 88 spots were over-, and 16 spots were underrepresented. The majority of these proteins showed to the strongest response at 8th h of Cu exposure. Using nanoLC-MS/MS analysis, a total of 167 differentially produced proteins were identified from Cu-exposed cultures after enrichment of the membrane proteins followed by SILAC. Seventy four, 66, and 69 overrepresented, and 56, 71, and 64 underrepresented proteins were identified at 2 h, 4 h, and 8 h of Cu exposure, respectively. The bioinformatic analysis of these proteins revealed that intracellular trafficking proteins such as Ran GTPase and a p24 family protein, and certain proteins involved in posttranslational modification, protein turnover and folding were Cu-responsive. Three important transcription factors (TFs), NAC, BTF3, and homeobox TFs, 40S and 60S ribosomal proteins, chaperones such as Hsp26/Hsp42 and mortalin, as well as 20S proteasome, 14-3-3 proteins and Hsp90 involve in Cu-stress response of P. chrysosporium. Moreover, certain elements of translation machinery, the proteins related with aspartate, methionine, and pyruvate metabolisms, transketolase, and trehalase related with carbohydrate metabolism, citrate synthase, fumarase, V-ATPase, and F0F1-type ATPase playing role in energy production and conversion, transport proteins such as multidrug resistance and p24 family proteins as well as actin-related proteins involved in cytoskeleton remodeling were determined to be Cu-responsive. The present proteome analysis revealed that P. chrysosporium mainly regulates translational and posttranslational processes, certain transport processes, many metabolic pathways and cytoskeleton to overcome the Cu-induced oxidative stress.

Role of upstream stimulating factors in the transcriptional regulation of the neuron-specific K-Cl cotransporter KCC2

The neuron-specific K-Cl cotransporter (KCC2) maintains a low intracellular Cl(-) concentration in neurons and is necessary for fast hyperpolarizing responses to GABA and glycine. The mammalian KCC2 gene (alias Slc12a5) generates two neuron-specific isoforms by using alternative promoters and first exons. Expression of the major isoform, KCC2b, is strongly upregulated during neuronal maturation, and is modulated by neuronal activity, trauma, and neurotrophic factors. In the present study, we have focused on the regulatory influence of the upstream stimulating factors USF1 and USF2 via an E-box control element in the KCC2b promoter (E-boxKCC2b). Electrophoretic mobility shift assay in cell lines and chromatin immunoprecipitation in neurons demonstrated binding of endogenous USF1 and USF2 to the E-box(KCC2b) element. Mutation of the E-boxKCC2b site resulted in reduced KCC2b promoter activity in cell lines and cortical neurons. Overexpression of a dominant-negative form of USF confirmed the involvement of endogenous USF proteins in the regulation of the KCC2b gene. The results suggest that binding of USF proteins to the E-boxKCC2b may contribute to the upregulation of KCC2b gene expression in developing brain.

The adenovirus L4 33-kilodalton protein binds to intragenic sequences of the major late promoter required for late phase-specific stimulation of transcription

The adenovirus late IVa2 protein is required for maximally efficient transcription from the viral major late (ML) promoter, and hence, the synthesis of the majority of viral late proteins. This protein is a sequence-specific DNA-binding protein that also promotes the assembly of progeny virus particles. Previous studies have established that a IVa2 protein dimer (DEF-B) binds specifically to an intragenic ML promoter sequence necessary for late phase-specific stimulation of ML transcription. However, activation of transcription from the ML promoter correlates with binding of at least one additional infected-cell-specific protein, termed DEF-A, to the promoter. Using an assay for the DNA-binding activity of DEF-A, we identified the unknown protein by using conventional purification methods, purification of FLAG-tagged IVa2-protein-containing complexes, and transient synthesis of viral late proteins. The results of these experiments established that the viral L4 33-kDa protein is the only component of DEF-A: the IVa2 and L4 33-kDa proteins are necessary and sufficient for formation of all previously described complexes in the intragenic control region of the ML promoter. Furthermore, the L4 33-kDa protein binds to the promoter with the specificity characteristic of DEF-A and stimulates transcription from the ML promoter in transient-expression assays.

The Yeast Ccr4-Not Complex Controls Ubiquitination of the Nascent-associated Polypeptide (NAC-EGD) Complex

In this work, we determine that the Saccharomyces cerevisiae Ccr4-Not complex controls ubiquitination of the conserved ribosome-associated heterodimeric EGD (enhancer of Gal4p DNA binding) complex, which consists of the Egd1p and Egd2p subunits in yeast and is named NAC (nascent polypeptide-associated complex) in mammals. We show that the EGD complex subunits are ubiquitinated proteins, whose ubiquitination status is regulated during cell growth. Egd2p has a UBA domain that is not essential for interaction with Egd1p but is required for stability of Egd2p and Egd1p. Ubiquitination of Egd1p requires Not4p. Ubiquitination of Egd2p also requires Not4p, an intact Not4p RING finger domain, and all other subunits of the Ccr4-Not complex tested. In the absence of Not4p, Egd2p mislocalizes to punctuate structures. Finally, the EGD complex can be ubiquitinated in vitro by Not4p and Ubc4p, one of the E2 enzymes with which Not4p can interact. Taken together our results reveal that the EGD ribosome-associated complex is ubiquitinated in a regulated manner, and they show a new role for the Ccr4-Not complex in this ubiquitination.

Upstream stimulating factors: highly versatile stress-responsive transcription factors

Upstream stimulating factors (USF), USF-1 and USF-2, are members of the eucaryotic evolutionary conserved basic-Helix-Loop-Helix-Leucine Zipper transcription factor family. They interact with high affinity to cognate E-box regulatory elements (CANNTG), which are largely represented across the whole genome in eucaryotes. The ubiquitously expressed USF-transcription factors participate in distinct transcriptional processes, mediating recruitment of chromatin remodelling enzymes and interacting with co-activators and members of the transcription pre-initiation complex. Results obtained from both cell lines and knock-out mice indicates that USF factors are key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism, and in melanocytes USF-1 has been implicated as a key UV-activated regulator of genes associated with pigmentation. This review will focus on general characteristics of the USF-transcription factors and their place in some regulatory networks.

Upstream stimulatory factors are mediators of Ca2+-responsive transcription in neurons

To identify molecular mechanisms that control activity-dependent gene expression in the CNS, we have characterized the factors that mediate activity-dependent transcription of BDNF promoter III. We report the identification of a Ca(2+)-responsive E-box element, CaRE2, within BDNF promoter III that binds upstream stimulatory factors 1 and 2 (USF1/2) and show that USFs are required for the activation of CaRE2-dependent transcription from BDNF promoter III. We find that the transcriptional activity of the USFs is regulated by Ca(2+)-activated signaling pathways in neurons and that the USFs bind to the promoters of a number of neuronal activity-regulated genes in vivo. These results suggest a new function for the USFs in the regulation of activity-dependent transcription in neurons.

Identification of a transcription factor, an 80-kDa protein that interacts with the HLH recognition motif of the rat p53 promoter

The p53 promoter has been shown to contain a number of potential regulatory motifs. It was previously reported that the upstream stimulating factor (USF) played a central role in regulating the p53 expression. The USF binding site, E-box, is located around 40 bp upstream of the major transcription start site. In this study, it was confirmed that the E-box binds to proteins by DNase I footprinting assay. In the electrophoretic mobility shift assay (EMSA), two retarded bands were detected. One band was abolished by the competition of USF consensus oligonucleotide, but the other band was not. This result indicated that a factor, other than USF, was bound to the E-box. The molecular masses of the binding proteins were determined by a Southwestern-blotting assay. As a result, 46- and 80-kDa proteins were detected. The 46-kDa protein was eliminated by the competition of USF consensus oligonucleotide. Also, the Southwestern-blotting assay with 32P-labeled USF consensus oligonucleotide showed only a 46-kDa protein. Therefore, the 46-kDa protein was USF. These results showed that USF and the 80-kDa protein were bound to the E-box. In addition, it was proved by in vitro transcription assay that this 80-kDa protein had a basal transcriptional activity.Key words: E-box, HLH, rat p53 promoter, transcription factor, upstream stimulating factor (USF).

Multiple modes of repression by the Smad transcriptional corepressor TGIF

TGIF is a DNA-binding homeodomain protein that has been demonstrated to play a role in transforming growth factor beta-regulated transcription and implicated in the control of retinoid-responsive transcription. We investigated the intrinsic transcriptional activity of TGIF fused to a heterologous DNA-binding domain. Our results demonstrate that TGIF is a transcriptional repressor able to repress transcription from several different promoters. Repression by TGIF is insensitive to the distance at which it is bound from the promoter. Moreover, the wild type TGIF effectively represses transcription when bound to its cognate DNA-binding site via its homeodomain. Deletion analysis revealed the presence of at least two separable repression domains within TGIF. Repression by one of these is dependent on the activity of histone deacetylases (HDACs), whereas the other appears not to require HDAC activity. Finally, we demonstrate that TGIF interacts with HDACs via its carboxyl-terminal repression domain. Together, these results suggest that TGIF is a multifunctional transcriptional repressor, which acts in part by recruiting HDAC activity.

The E-box of the human glycophorin B promoter is involved in the erythroid-specific expression of the GPB gene

Previous studies performed on the glycophorin B (GPB) expression demonstrated that this gene is expressed in erythroid cells only and that the ubiquitous factor Ku70 is involved in the process. Here, we investigated the contribution of the -70 E-box sequence toward the GPB promoter expression. We found that the E-box bound two factors, the USF1/USF2 protein and an unidentified ubiquitous protein which was named factor U. Site-directed mutagenesis performed on the -70 E-box showed that the USF factor had an activating effect in CAT assays. Conversely, mutation of the -70 E-box that impaired the binding of factor U led to a positive CAT activity in nonerythroid cells and thus to the loss of the erythroid-specific expression of the GPB gene. This indicates that, in addition to the Ku70 factor, the extinction of the GPB promoter expression in nonerythroid cells depends also on the repressing effect of the factor U.

Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II

Initiation of transcription of a gene from a core promoter region by RNA polymerase II requires the assembly of several initiation factors to form a preinitiation complex. Assembly of this complex is thought to be nucleated exclusively by the sequence-specific binding of the TFIID transcription factor complex, which is composed of the TATA-binding protein (TBP) and TBP-associated factors (TAF(II)s), to the different promoters. Here we isolate and characterize a new multiprotein complex that does not contain either TBP or a TBP-like factor but is composed of several TAF(II)s and other proteins. This complex can replace TFIID on both TATA-containing and TATA-lacking promoters in in vitro transcription assays. Moreover, an anti-TBP antibody that inhibits TBP- and TFIID-dependent transcription does not inhibit activity of this new complex. These results indicate that TBP-free RNA polymerase II mediated transcription may be able to occur in mammalian cells and that multiple preinitiation complexes may play an important role in regulating gene expression.

Enhancement of transcription factor, USF, binding to the adenovirus major late promoter: effect of dithiothreitol and high mobility group protein-1

Up-stream stimulatory factor (USF)1 is a human transcription factor which binds specifically to the E-box in the Ad MLP located at - 58 from the start site. The nature of USF binding on a Ad MLP DNA fragment was investigated in the presence of DTT and also in the presence of purified HMG-1 using electrophoretic mobility shift assay. We show that the binding capacity of USF for the E-box increases significantly with increasing DTT concentrations. At the higher DTT levels, a second USF-DNA complex is formed in which there is co-occupation of both the E-box and the initiator sequence. The stability of the second complex is largely refractory to an excess of unlabeled oligonucleotide which contains the initiator sequence. These findings indicate a cooperative binding interaction between USF ligands bound simultaneously at the E-box and the Inr sequence. Two models are proposed which are consistent with these data. Furthermore, experiments indicate that the presence of HMG-1, a nuclear protein known to influence transcriptional activity, increases USF binding activity at the E-box by as much as 100%. These findings indicate that both reducing conditions and HMG-1 may act as modulators of USF-regulated transcription.

Fractionation of RNA polymerase II transcription factors from HeLa cell nuclear extracts by affinity chromatography on "DNA-like" phosphorylated polystyrene

It was previously shown that phosphorylated cross-linked polystyrene derivatives specifically interacted with anti-DNA antibodies and anti-phospholipid antibodies present in the sera of systemic lupus erythematosus patients. These resins are potential candidates as stationary phases in affinity chromatography. We wondered whether these biospecific resins might allow the fractionation of DNA binding proteins such as RNA polymerase II transcription factors from HeLa cell nuclear extracts. Indeed, these proteins play a major role in gene regulation in mammalian cells and their purification still requires numerous steps. To study the biospecificity of DNA-like phosphorylated polystyrene derivatives, ethanolamine sulfamide crosslinked polystyrene derivatives were phosphorylated at various rates and HeLa cell nuclear extracts were adsorbed on these resins. Adsorbed proteins were eluted with increasing concentrations of aqueous potassium chloride. Collected fractions were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and the biological activities of the eluted transcription factors were tested by in vitro transcription assay. Results showed that the elution of transcription factors depended on the substitution rate in phosphoester groups of the resins. It appears that specific interactions were developed between the polymers and the transcription factors. Moreover, the eluted transcription factors kept their biological activity. These results lead us to propose the purification of RNA polymerase II transcription factors using the phosphorylated polystyrene resins as stationary phases.

Randomly phosphorylated polystyrene derivatives interact with RNA polymerase II transcription factors: part I

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.

BTF3 is evolutionarily conserved in fission yeast

BTF3 is a protein initially identified in HeLa cells that may be involved in the initiation of transcription. Although its specific role in transcription is unclear, BTF3 can form a stable complex with RNA polymerase II. Recently, BTF3 has also been shown to bind to nascent polypeptide chains. We have cloned a homolog of BTF3 from the fission yeast, Schizosaccharomyces pombe. This homolog, spBTF3, encodes a putative 151 amino acid protein that shares 72% similarity with human BTF3, 73% similarity with the Caenorhabditis elegans homolog and between 52 and 53% similarity with the Saccharomyces cerevisiae homologs, EGD1 and BTT1.

Human TAFII30 is present in a distinct TFIID complex and is required for transcriptional activation by the estrogen receptor

We showed previously that coactivators mediating stimulation by different activators were associated with the TATA-binding protein (TBP) in distinct TFIID complexes. We have characterized a human TBP-associated factor (TAF), hTAFII30, associated with a subset of TFIID complexes. hTAFII30 interacts with the AF-2-containing region E of the human estrogen receptor (ER), but not with ER AF-1 or VP16. An antibody against hTAFII30 inhibited transcriptional stimulation by the ER AF-2 without affecting basal or VP16-activated transcription and allowed the separation of TFIID complex(es) containing hTAFII30 from complexes mediating the activity of VP16. These results directly demonstrate the existence of functionally distinct TFIID populations that share common TAFIIs but differ in specific TAFIIs.

The product of the adenovirus intermediate gene IVa2 is a transcriptional activator of the major late promoter

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. We had previously shown that sequence elements located downstream of the MLP start site were implicated in this late-specific transcriptional activation (DE1, between +85 and +98; DE2, between +100 and +120). Two positive transcription factors involved in this activation have been detected. DEF-A, which specifically binds to DE1 and also to the 3' portion of DE2 (DE2a), and DEF-B, which interacts with the 5' part of DE2 (DE2b). When present together, these two proteins cooperatively assemble onto the DE2 element. We now report the purification of DEF-B and show that it is identical to the product of the adenovirus IVa2 gene product. This conclusion is based on microsequence analysis of DEF-B as well as on the inhibitory effect of antibodies against IVa2 on the DNA-binding activity of DEF-B and also on DE-dependent in vitro transcription. In addition, we show that bacterially synthesized IVa2 protein binds to the DE sequences with the same specificity as DEF-B. Finally, in transfected cells, a recombinant IVa2 protein stimulates MLP activity in a DE-dependent fashion. The physiological implications of these findings are discussed.

Immunochemical quantification of procion red HE-3B used as ligand in affinity chromatography

The quantification of Procion Red HE-3B used as a ligand in affinity chromatography for proteins is reported. It's based on an enzyme-linked immunosorbent assay using antibodies against the dye. Polyclonal antibodies were classically prepared after conjugation of the dye on KLH and injection into rabbits. The development of the assay was based on the competitive inhibition between hemoglobin-dye complex and free dye. The sensitivity of this method was about 1000-times higher than a classical spectrophotometric assay, and was modulated by some chemical substituents attached on the native dye. It was demonstrated that the assay was applicable to the determination of dye traces that may be released from dye affinity sorbents. Moreover, the quantification of the dye was successfully applied to proteins that are being purified from a dye affinity column.

Purification, cloning, and RXR identity of the HeLa cell factor with which RAR or TR heterodimerizes to bind target sequences efficiently

We have purified and cloned a HeLa cell nuclear protein that strongly stimulates binding of retinoic acid and thyroid hormone receptors (RARs and TRs) to response elements. The purified protein is a human retinoid X receptor beta (hRXR beta). Three murine members of the RXR family (mRXR alpha, beta, and gamma) have also been cloned, and their interactions with RARs and TRs have been investigated. Under conditions where RAR, RXR, and TR bound poorly as homodimers to various response elements, strongly cooperative RAR-RXR and TR-RXR binding was observed. The binding efficiency was dependent on the sequence, relative orientation, and spacing of the repeated motifs of response elements. We show also that unstable RAR-RXR heterodimers were formed in solution, and that C-terminal sequences and the DNA-binding domains of both receptors were required for efficient formation of stable heterodimers on response elements. These findings suggest a convergence of the signaling pathways of some members of the nuclear receptor superfamily.

A human binding site for transcription factor USF/MLTF mimics the negative regulatory element of human immunodeficiency virus type 1

Transcriptional regulation of the proviral form of the human immunodeficiency virus type 1 (HIV-1) is exerted by its 5' long terminal repeat (LTR), which contains recognition sites for several cell factors. By gel retardation and DNase I footprinting experiments we have identified a binding site for a human nuclear protein between nucleotides -152 to -174 upstream of transcription start site, in a region previously recognized as a negative regulator of transcription (negative regulatory element, NRE). The recognized sequence contains the dyad symmetry element CACGTG, which represents a binding motif, very conserved through evolution, present in a putative human DNA replication origin (pB48), in the upstream element of the major late promoter (MLP-UE) of adenovirus, and, as transcriptional element, upstream of many eukaryotic genes. Common binding activities exist in human nuclear extracts for pB48, MLP-UE and the HIV-1 LTR; at least three protein species recognize the LTR sequence, of 44 (corresponding to transcription factor USF/MLTF), 70, and 110 kDa, respectively. Chloramphenicol acetyltransferase assays suggest that the USF/MLTF binding site located in the HIV-1 LTR acts as a negative regulator of transcription, and that it contributes to the overall negative function exerted by the NRE. An oligonucleotide corresponding to another characterized human USF/MLTF binding site can functionally replace part of the activity of the NRE. This negative function is exerted both in presence or absence of tat transactivation, in different cell lines, and after PMA stimulation.

Expression in Escherichia coli: purification and properties of the yeast general transcription factor TFIID

A T7 RNA polymerase expression system has been used for the efficient expression of the yeast RNA polymerase general transcription factor TFIID (TFIIDY), the TATA-box factor (previously called BTF1) in Escherichia coli. Expression of the gene was performed at 25 degrees C instead of 37 degrees C to increase the total amount of soluble TFIIDY. Soluble TFIIDY was purified in three chromatographic steps and was eluted from the final column, a heparin-5PW HPLC column, in two peaks at 0.38 M (peak I) and 0.42 M (peak II) KCl in which this protein was 52% and greater than 95% pure, respectively. The protein in both peaks was active in an in vitro transcription assay. However, while TFIIDY from peak II was essentially indistinguishable from the material isolated from yeast, the protein of peak I differed in a number of biochemical characteristics, having a lower specific activity in an in vitro transcription assay and displaying an altered pattern of bands in a DNA band shift assay. Despite these differences, the proteins in both peaks have identical molecular weights on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, have indistinguishable N-terminal amino acid sequences, and apparently exist as monomers under the conditions used for the heparin-5PW chromatography.

The adenovirus major late transcription factor USF is a member of the helix-loop-helix group of regulatory proteins and binds to DNA as a dimer

We isolated full-length cDNAs encoding the 43-kD form of human upstream stimulatory factor (USF), a cellular factor required for efficient transcription of the adenovirus major late (AdML) promoter in vitro. Sequence analysis showed USF to be a member of the c-myc-related family of DNA-binding proteins. Using proteins translated in vitro, we identified a DNA-binding domain near the carboxyl terminus, which includes both a helix-loop-helix motif and a leucine repeat. We show that USF interacts with its target DNA as a dimer. The leucine repeat is required for efficient DNA binding of the intact protein and for interactions between full-length and truncated USF proteins. Interestingly, it is not required for DNA binding of the isolated helix-loop-helix domain. The structure of different cDNA clones indicates that USF RNA is differentially spliced, and alternative exon usage may regulate the levels of functional USF protein.

The mammalian upstream element factor recognizes two sites in the adenovirus type 2 IVa2-major late promoter intergenic region and stimulates both promoters

The adenovirus type 2 major late upstream element factor (UEF) recognizes two similar elements that lie between the major late promoter (MLP) and IVa2 promoter cap sites (the previously characterized MLP-UE from nucleotides -49 to -67 and the IVa2-UE from nucleotides -98 to -122). DNase I footprinting and gel retention assays showed that the UEF has a lower affinity for the IVa2-UE than for the MLP-UE. In vitro transcription experiments demonstrated first that the IVa2 promoter, which lacks a consensus TATA box, may work, as does the MLP, in the absence of its proximal upstream element and second that the IVa2-UE stimulated IVa2 transcription two- to threefold, as MLP-UE did for the MLP. In addition, we demonstrated that the more distal upstream element has a weak stimulatory effect on transcription of both promoters.

Purification of the upstream element factor of the adenovirus-2 major late promoter from HeLa and yeast by sequence-specific DNA affinity chromatography

The purification to homogeneity of the Adenovirus-2 major late promoter (MLP) upstream element factor (UEF), a sequence specific transcription factor, which binds to upstream elements of various class B (II) genes, is reported. The protein was purified from HeLa cells and also from the yeast Saccharomyces cerevisiae, by using sequence-specific DNA affinity chromatography. The human (UEFh, 45,000 dalton) and the yeast (UEFy, 60,000 dalton) proteins protect the same sequences over the MLP-IVa2 intergenic region: the MLP-UE (from nucleotide -49 to -67) and the IVa2-UE (from nucleotide -98 to -122 relative to the MLP initiation site). Both proteins have a higher affinity for the MLP-UE than for the IVa2-UE.

Transcription factor IIA of wheat and human interacts similarly with the adenovirus-2 major late promoter

Transcription factor IIA (TFIIA) is a necessary component of many RNA polymerase II transcription complexes. Assembly of the transcription complex begins when TFIIA interacts with the promoter. We have previously purified wheat germ TFIIA to homogeneity and demonstrated that it substitutes for human TFIIA in a human in vitro transcription system which utilizes the adenovirus-2 major late promoter (Ad-2 MLP). We now show, by gel retardation assays, that wheat TFIIA interacts with the Ad-2 MLP. Extensively purified human (HeLa) TFIIA interacts with the Ad-2 MLP similarly. Both wheat and human TFIIA interact with a DNA fragment comprising the minimal promoter region (-51/+32) but not with upstream or downstream regions. With both TFIIAs multiple complexes form; the fastest wheat TFIIA/DNA complex appears to be larger than the corresponding human TFIIA/DNA complex. Limited point mutation analysis of the Ad-2 MLP demonstrates that changes at -30 (TATAA region), +1, and -1 diminish TFIIA binding, but a change at -40 does not. DNA footprint analysis of this region is not definitive, but does indicate that following TFIIA binding there are changes in the pattern of hypersensitive sites.

Sequencing and expression of complementary DNA for the general transcription factor BTF3

The initiation of transcription of eukaryotic genes involves the ordered assembly of a multiprotein complex on proximal promoter elements such as the TATA box. In addition to RNA polymerase II (otherwise RNA pol II, RNA polymerase B), four general transcription factors are required for initiation of transcription: BTF1 (also referred to as TFIID) which has recently been cloned from yeast, BTF2, BTF3 and STF. The first step in assembly of the initiation complex is the stable binding of BTF1 to the TATA box, which is facilitated by STF. Neither BTF2 nor BTF3 bind directly to the promoter proximal elements, but BTF3 can form a stable complex with RNA pol II. We recently purified BTF3, which is a protein of relative molecular mass 27,000, but further studies have been hampered by its low abundance in cells. On the basis of sequences from peptides of BTF3, we have now cloned two complementary DNAs, one for a protein (BTF3a) with all the characteristics of purified BTF3, and one for a shorter protein (BTF3b) lacking the first 44 residues of BTF3a and which is transcriptionally inactive, despite its ability to bind RNA pol II.

An upstream transcription factor, USF (MLTF), facilitates the formation of preinitiation complexes during in vitro chromatin assembly

During in vitro chromatin assembly the formation of transcription complexes is in direct competition with the assembly of promoter sequences into nucleosomes. Under these conditions the fold stimulation of transcription by an upstream transcription factor (USF) was greater than that observed in the absence of nucleosome assembly. Function of USF during nucleosome assembly required the simultaneous presence of the TATA box binding protein TFIID. Unlike TFIID, USF alone was unable to prevent repression of the promoter during nucleosome assembly. Furthermore, USF displayed reduced or no transcriptional stimulatory activity when added to previously assembled minichromosomes. Under conditions of nucleosome assembly, USF increased the number of assembled minichromosomes which contained stable preinitiation complexes. Subsequent to assembly, the rate at which preformed complexes initiated transcription appeared to be independent of the presence of USF. Thus USF potentiated the subsequent transcriptional activity of the promoter indirectly, apparently by increasing the rate or stability of TFIID binding. This activity resulted in the promoter becoming resistant to nucleosome mediated repression. These observations suggest that some ubiquitous upstream factors, e.g. USF, may play an important role in establishing the transcriptional potential of cellular genes during chromatin assembly.

In vitro transcription from cauliflower mosaic virus promoters by a cell-free extract from tobacco cells

We have studied transcription from the cauliflower mosaic virus 19S and 35S promoters in a cell-free system derived from tobacco cells in suspension culture. While a whole-cell extract is incapable of detectable transcription from these promoters, successive purification by column chromatography allows the preparation of two fractions which contain all factors necessary for transcription from the 19S promoter. In contrast, transcription from the 35S promoter leads to the accumulation of short RNAs. This accumulation can only be partially alleviated by modifying the conditions of transcription.

Early events of RNA polymerase II transcription initiation

We have investigated the earliest stages of assembly of an RNA polymerase II transcription complex. General transcription factors from HeLa cells were partially purified and assayed using the adenovirus-2 major late promoter. Preincubation of either all the transcription factors (TF) with the DNA or only the subset consisting of TFIIA, TFIID, and DNA overcame the 15-20 min lag normally observed. The kinetics demonstrate that TFIIA first interacts with the template over a 5 min. period, and then TFIID interacts with the IIA:DNA complex over a 2 min. period. The remainder of the necessary transcription factors then interact with the IIA:IID:DNA complex. There are apparently interactions between IIA and IID, as a pre-incubation of these factors (without DNA) overcomes the lag period. Both IIA:DNA and IIA:DNA:IID interactions are temperature sensitive, resulting in slower kinetics at 0 degree C. Thus, the kinetics of transcription involve activation processes in addition to DNA binding.

A protein target site in an early replicated human DNA sequence: a highly conserved binding motif

We have previously reported that a human nuclear factor, probably corresponding to the USF/MLTF protein [1,2], is able to bind specifically to a DNA sequence present in DNA replicated at the onset of S-phase [3]. Here we demonstrate that the same factor binds also to several other similar sequences, present in eukaryotic and viral genomes. Mutations or methylation in a CpG dinucleotide, central in the palindromic binding site, completely abolish binding. Furthermore, we present evidence for the existence of at least two other nuclear proteins in human cells with the same DNA binding specificity. The data presented suggest a strong evolutionary conservation, among distantly related organisms, of the binding motif, which is probably the target of a number of nuclear factors that share the same DNA binding specificity albeit in the context of different functions.

Drug inhibitors of RNA polymerase II transcription

Transcription by RNA polymerase II occurs after formation of a transcription complex. This complex is assembled in stages by the interaction of transcription factors with the template and/or with each other. We report on the ability of six drugs to inhibit the assembly of the RNA polymerase II transcription complex. Assembly of the complex on the adenovirus major late promoter requires several transcription factors. The normal assembly process requires that the DNA first interact with TFIIA, then with TFIID, and finally with at least four additional transcription factors (one of which is RNA polymerase II). We observed that streptolydigin (10 micrograms/ml) inhibits association of ILA and IID, and at higher concentrations (100 micrograms/ml) inhibits that IIA/IID complex from binding to DNA. Streptovaricin (100 micrograms/ml) appears to inhibit the IIA/IID interaction with DNA and prevents reinitiation (at 500 micrograms/ml). Adriamycin (1 microgram/ml) inhibits the interaction of TFIID with the IIA/DNA complex and inhibits an additional event immediately prior to, or during, elongation. Daunorubicin may be an elongation inhibitor. Heparin at 10 micrograms/ml inhibits further assembly after the IIA/IID/DNA complex has formed, and at 100 micrograms/ml also inhibits a late event in the assembly process and blocks reinitiation. Rifamycin AF/013 (100 micrograms/ml) inhibits the early events necessary to form the IIA/IID/DNA complex and (at 10 micrograms/ml) an assembly event following formation of the IIA/IID/DNA complex. Therefore, these compounds should be useful as probes for further examination of the assembly process.

Proteins binding to the liver-specific pyruvate kinase gene promoter. A unique combination of known factors

A 183 base-pair fragment of the liver-specific promoter of the L-type puruvate kinase (L-PK) gene has been shown by transfection assay to be sufficient to confer a tissue-specific expression to a reporter gene. The proteins binding in vitro to this fragment have been investigated by a combination of DNase I footprinting, gel retardation of synthetic oligonucleotides and ultraviolet cross-linking. Four proteins from liver nuclear extracts bind to the investigated fragment. They were called, from 3' to 5', L1 to L4 binding factors. The L1 site (nucleotides -95 to -66 with respect to the cap site) binds hepatocyte nuclear factor 1 (HNF1), a liver-specific protein. The L2 site (nucleotides -114 to -97) binds the ubiquitous nuclear factor 1 (NF1), or a related factor. The L3 site (nucleotides -144 to -126) binds liver factor A1 (LF-A1), another liver-specific protein. Finally, the L4 site (nucleotides -168 to -145) binds major late transcription factor (MLTF/USF/UEF), an ubiquitous protein. Each of these proteins has been detected in other liver-specific promoters, but their combination is unique to the liver-specific promoter of the L-PK gene.