Preferential distribution of active RNA polymerase II molecules in the nuclear periphery

We have combined immunogold labeling with the Miller spreading technique in order to localize proteins at the electron microscope (EM) level in whole mount nuclei from mouse and human fibroblasts. Anti-histone H1 antibody labels nuclei uniformly, indicating that the nuclear interior is accessible to both antibodies and gold conjugates. Anti-topoisomerase I antibody labels nucleoli intensely, in agreement with previous immunofluorescent and biochemical data. Two different antibodies against the large subunit of RNA polymerase II (pol II) show preferential labeling of the nuclear periphery, as do antibodies against lamin, a known peripheral nuclear protein. Treatment of cells with alpha-amanitin results in loss of virtually all RNA polymerase II staining, supporting the specificity of labeling. Finally, when nuclei are incubated in the presence of biotin-UTP (bio-UTP) under run-off transcription conditions, incorporation is preferentially located at the nuclear periphery. These results support the conclusions that transcriptionally active pol II molecules are non-uniformly distributed in fibroblast nuclei, and that their differential distribution mirrors that of total pol II.

Crystallographic structures of the ligand-binding domains of the androgen receptor and its T877A mutant complexed with the natural agonist dihydrotestosterone

The structures of the ligand-binding domains (LBD) of the wild-type androgen receptor (AR) and the T877A mutant corresponding to that in LNCaP cells, both bound to dihydrotestosterone, have been refined at 2.0 A resolution. In contrast to the homodimer seen in the retinoid-X receptor and estrogen receptor LBD structures, the AR LBD is monomeric, possibly because of the extended C terminus of AR, which lies in a groove at the dimerization interface. Binding of the natural ligand dihydrotestosterone by the mutant LBD involves interactions with the same residues as in the wild-type receptor, with the exception of the side chain of threonine 877, which is an alanine residue in the mutant. This structural difference in the binding pocket can explain the ability of the mutant AR found in LNCaP cells (T877A) to accommodate progesterone and other ligands that the wild-type receptor cannot.

Transforming region of 243R E1A contains two overlapping but distinct transactivation domains

Conserved regions 1 and 2 as well as the amino terminus of E1A are required for the transforming activity of the E1A oncoprotein. We show here that the amino terminus of 243R E1A has transactivation activity when brought to a promoter in yeast. Recruitment to a specific promoter is essential. Mutagenesis studies correlated the transactivation function with the extreme amino terminus and the conserved region 1 of E1A. Cotransfection assays in rodent cells confirmed that two overlapping but distinguishable domains, amino acids 1-65 and 37-80, can transactivate independently when targeted to a promoter. We also observed that when recruited to the proliferating cell nuclear antigen (PCNA) promoter, the amino-terminal region was sufficient to transactivate the PCNA promoter. On the other hand, deletion of the amino terminus of E1A resulted in failure to induce PCNA expression. Fusion of VP16 with the amino-terminal-deleted E1A mutant was able to restore the ability to induce the PCNA promoter. We further show that the amino-terminal region also is required for 243R E1A to repress the transactivation mediated by a universal transactivator DBD.VP16 and DBD.E1A. This repression could be specifically relieved by overexpression of TBP but not TFIIB. In addition, we show that the amino terminus of E1A is involved in in vitro interaction with the TATA binding protein (TBP). Thus the amino-terminal transforming region of E1A may regulate cellular gene expression in species that are distant in evolution via a common mechanism, functionally targeting TBP.

Interaction of human immunodeficiency virus type 1 Tat with a unique site of TFIID inhibits negative cofactor Dr1 and stabilizes the TFIID-TFIIA complex

We have previously reported the direct physical interaction between the human immunodeficiency virus (HIV) type I Tat protein and the basal transcription factor TBP/TFIID. Affinity chromatography demonstrated that wild-type Tat, but not a transactivation mutant of Tat, was capable of depleting TBP/TFIID from cell extracts. These experiments represented the first demonstration of a basal transcription factor that binds, in an activation-dependent manner, to Tat. We now report that the Tat-TBP interaction can be detected in HIV type 1-infected cells. The domain of TBP interacting with Tat has been mapped from amino acids 163 to 196 by using deletion and site-specific mutants of TBP. This domain of TBP, which includes the HI and S2 domains, is distinct from the H2 binding site for other activator proteins, such as E1A. The interaction of Tat with TFIID regulates the binding of accessory proteins to TFIID. Tat stabilizes the interaction of TFIID with TFIIA in a gel shift assay. In addition, Tat competes for Dr1 interaction with TBP. Our results suggest that the basal transcription factor TBP/TFIID represents an important regulatory molecule in HIV transcription.

Farnesyltransferase inhibitors are inhibitors of Ras but not R-Ras2/TC21, transformation

Recent results from several laboratories including ours strongly suggest that farnesyltransferase (FT) inhibitors belonging to distinct chemical classes block growth of oncogenic Ras transformed cells at concentrations that do not affect the growth and viability of normal cells. This is despite blocking the farnesylation and thus the membrane association of Ras in both cell types. This is a paradox given the requirement for Ras function in normal cell growth. Recent evidence that R-Ras2/TC21 utilizes components of Ras signal transduction pathways to trigger cellular transformation (Graham et al., MCB 14, 4108-4115, 1994) prompted us to consider the possibility that R-Ras2/TC21 is involved in some aspects of the growth regulation of normal cells. If so, R-Ras2/TC21 may be compensating for Ras function in untransformed cells treated with FT inhibitors. In this study, we demonstrated that a cell active bisubstrate analog FT inhibitor, BMS-186511, completely blocked the function of oncogenic Ras, but did not affect the function of oncogenic R-Ras2/TC21, as determined by several criteria including inhibition of anchorage dependent and independent growth, reversal of transformed morphology and restoration of actin cytoskeleton. While it is known that TC21 protein becomes prenylated, it is not known whether it is farnesylated or geranylgeranylated. Our in vitro prenylation experiments indicate that R-Ras2/TC21 protein serves as a good substrate for FT as well as geranylgeranyltransferase I (GGTI) and thus provide the apparent molecular basis for these differences. Overall, these results, coupled with the ubiquitous expression of R-Ras2/TC21 in many cells including untransformed NIH3T3 cells, are consistent with the possibility that R-Ras2/TC21 may be one of the factors that render normal cells insensitive to the growth inhibitory action of FT inhibitors.

Adenovirus E1A proteins interact with the cellular YY1 transcription factor

The adenovirus 12S and 13S E1A proteins have been shown to relieve repression mediated by the cellular transcription factor YY1. The 13S E1A protein not only relieves repression but also activates transcription through YY1 binding sites. In this study, using a variety of in vivo and in vitro assays, we demonstrate that both E1A proteins can bind to YY1, although the 13S E1A protein binds more efficiently than the 12S E1A protein. Two domains on the E1A proteins interact with YY1: an amino-terminal sequence (residues 15 to 35) that is present in both E1A proteins and a domain that includes at least a portion of conserved region 3 (residues 140 to 188) that is present in the 13S but not the 12S E1A protein. Two domains on YY1 interact with E1A proteins: one is contained within residues 54 to 260, and the other is contained within the carboxy-terminal domain of YY1 (residues 332 to 414). Cotransfection of a plasmid expressing carboxy-terminal amino acids 332 to 414 of YY1 fused to the GAL4 DNA-binding domain can inhibit expression from a reporter construct with GAL4 DNA binding sites in its promoter, and inclusion of a third plasmid expressing E1A proteins can relieve the repression. Thus, we find a correlation between the ability of E1A to interact with the carboxy-terminal domain of YY1 and its ability to relieve repression caused by the carboxy-terminal domain of YY1. We propose that E1A proteins normally relieve YY1-mediated transcriptional repression by binding directly to the cellular transcription factor.

Two domains of p53 interact with the TATA-binding protein, and the adenovirus 13S E1A protein disrupts the association, relieving p53-mediated transcriptional repression

The tumor suppressor gene product p53 can activate and repress transcription. Both transcriptional activation and repression are thought to involve the direct interaction of p53 with the basal transcriptional machinery. Previous work has demonstrated an in vitro interaction between p53 and the TATA-binding protein that requires amino acids 20 to 57 of p53 and amino acids 220 to 271 of the TATA-binding protein. The present results show that a 75-amino-acid segment from the carboxy terminus of p53 also can bind to the TATA-binding protein in vitro, and this interaction requires amino acids 217 to 268 of the TATA-binding protein, essentially the same domain that is required for interaction with the amino-terminal domain of p53. A carboxy-terminal segment of p53 can mediate repression when bound to DNA as a GAL4-p53 fusion protein. The amino- and carboxy-terminal p53 interactions occur within the domain on the TATA-binding protein to which the adenovirus 13S E1A oncoprotein has previously been shown to bind. The 13S E1A oncoprotein can dissociate the complex formed between the carboxy-terminal domain of p53 and the TATA-binding protein and relieve p53-mediated transcriptional repression. These results demonstrate that two independent domains of p53 can potentially interact with the TATA-binding protein, and they define a mechanism--relief of repression--by which the 13S E1A oncoprotein can activate transcription through the TATA motif.

DNA-binding proteins that interact with the 19-base pair (CRE-like) element from the HCMV major immediate early promoter in differentiating human embryonal carcinoma cells

The pluripotent human embryonal carcinoma (EC) cell line NTERA-2 provides a useful tool for investigating cell differentiation in a way that is pertinent to the development of the early human embryo. The major immediate early (MIE) gene of human cytomegalovirus (HCMV), which is not transcribed in undifferentiated NTERA-2 EC cells but is transcribed in their differentiated derivatives, offers a model with which to study the developmental regulation of gene activity during the differentiation of these cells. We have investigated the regulatory activity of the cAMP response elements (CRE) and the activation protein (AP1) site found within several repeated 19-base-pair (bp) elements from the HCMV MIE promoter, and the developmental regulation of nuclear DNA-binding factors that interact with these sites. The 19-bp CRE but not the AP1 site is responsive to cAMP in undifferentiated NTERA-2 EC and its activity is enhanced upon differentiation. Nuclear proteins of the CREB, Fos, and Jun families bind to these sites, but, surprisingly, their levels only show limited regulation during NTERA-2 differentiation. This contrasts with results obtained with murine EC cells. However, additional and apparently novel proteins with molecular weights between 80,000 and 90,000, and binding specificities for both CRE and AP1 sites, were detected in undifferentiated EC cells. The activity of these proteins decreased markedly after differentiation, indicating their involvement in negative regulation of the CRE/AP1-like site in undifferentiated EC cells. This suggests novel members able to interact via leucine zippers with other members of the Jun-Fos-CREB family of DNA binding proteins that are also involved in this regulation.

Characterization of hypoxia-responsive enhancer in the human erythropoietin gene shows presence of hypoxia-inducible 120-Kd nuclear DNA-binding protein in erythropoietin-producing and nonproducing cells

Erythropoietin (Epo) production in response to hypoxia or cobalt is primarily mediated by activation of transcription of the Epo gene. Recently an hypoxia responsive enhancer was identified in the 3' flanking region of the mouse and human Epo genes. Using functional analysis in Hep 3B cells we define here the minimal enhancer element as a 29-bp segment starting at the Apa1 site in the 3' flanking region of the human Epo gene. Mutagenesis studies of the minimal element identified three different areas that are necessary for full enhancer activity. Electrophoretic mobility shift assays show the presence of hypoxia- and/or cobalt-inducible nuclear DNA-binding proteins that bind to one of the active sites of the enhancer. Induction of hypoxia-binding activity was abolished by Anisomycin, a potent protein synthesis inhibitor, suggesting that de novo protein synthesis is necessary for the activation process. Further characterization of DNA-binding proteins by use of UV light crosslinking identified a protein of molecular weight of approximately 120-Kd that was present only in hypoxic extracts. This protein was found to be present in hypoxic nuclear extracts from both Epo-producing and non-Epo-producing cells, suggesting that it may be involved in a more generalized mechanism of cellular response to hypoxia.

Analysis of transcription factors binding to the duplicated PEA1 and PEA3 sites that are required for polyomavirus mutant expression in PCC4 embryonic carcinoma cells

Embryonic carcinoma (EC) cell lines, representative of early embryonic undifferentiated cells, are nonpermissive for polyomavirus (PyV) infection as a result of a blockade of viral DNA early transcription and replication. All enhancers of PyV mutants (Py EC-PCC4), selected for the ability to grow on PCC4 EC cells, display a duplication of PEA1 and PEA3 binding sites (sites 1 and 3). However, the Py EC-PCC4 rearrangement is complex and results in variable mutant enhancer activities. We demonstrate here that duplication of sites 1 and 3 is absolutely required for a cooperative cis activation of early Py EC-PCC4 mutant transcription in PCC4 EC cells. In addition, we detect in PCC4 EC cells significant amounts of site 1- and 3-binding proteins, which we characterize as related to the Fos/Jun and Ets protein families, respectively. Wild-type PyV restriction in PCC4 EC cells may be relieved by a cooperation between site 2- and 3-binding proteins that would thereby be activated. Since site 1- or 3-binding factors could be derepressed, we improved the analysis of UV cross-linked DNA-protein complexes and were able to detect a novel factor, called PEA1/2 (for PyV enhancer A site 1- and 2-binding factor). Its DNA binding sequence overlaps sites 1 and 2 (PEA2 binding site) and is not duplicated in the M1 mutant, which exhibits the highest Py EC-PCC4 enhancer activity. he suggest that PEA1/2 is also involved in the regulation of PyV enhancer activity by repressing the site 1-binding activity.

Wild-type p53 binds to the TATA-binding protein and represses transcription

p53 activates transcription of genes with a p53 response element, and it can repress genes lacking the element. Here we demonstrate that wild-type but not mutant p53 inhibits transcription in a HeLa nuclear extract from minimal promoters. Wild-type but not mutant p53 binds to human TATA-binding protein (TBP). p53 does not bind to yeast TBP, and it cannot inhibit transcription in a HeLa extract where yeast TBP substitutes for human TBP. These results suggest a model in which p53 binds to TBP and interferes with transcriptional initiation.

Negative regulation of the major histocompatibility complex class I enhancer in adenovirus type 12-transformed cells via a retinoic acid response element

In cells transformed by the highly oncogenic adenovirus type 12 (Ad12), the viral E1A proteins mediate transcriptional repression of the major histocompatibility class I genes. In contrast, class I transcription is not reduced in cells transformed by the nononcogenic Ad5. The decreased rate of class I transcription is, at least in part, the result of a reduced major histocompatibility complex class I enhancer activity in Ad12-transformed cells and correlates with an increase in the levels of a DNA-binding activity to the R2 element of the enhancer (R. Ge, A. Kralli, R. Weinmann, and R. P. Ricciardi, J. Virol. 66:6969-6978, 1992). Employing transient transfection assays, we now provide direct evidence that the R2 element can confer repression in Ad12- but not Ad5-transformed cells. Repression by R2 was observed only in the presence of the positive enhancer element R1 and was dependent on (i) the number of the R2 elements and (ii) the relative arrangement of R2 and R1 elements. The putative R2-binding repressor protein, R2BF, was similar in molecular weight and binding specificity to members of the thyroid hormone/retinoic acid (RA) receptor family. RA treatment abrogated the R2-mediated repression in Ad12-transformed cells and had no effect on the activity of R2/R1-containing promoters in Ad5-transformed cells. These results are consistent with the presence of an R2-binding repressor in Ad12-transformed cells. In the absence of RA, the repressor compromises enhancer activity by interfering with the activity of the positive cis element R1. RA treatment of Ad12-transformed cells may render the repressor inactive.

Down-regulation of the major histocompatibility complex class I enhancer in adenovirus type 12-transformed cells is accompanied by an increase in factor binding

In transformed cells, the E1A gene of adenovirus type 12 (Ad12) represses transcription of class I genes of the major histocompatibility complex. The tumorigenic potential of Ad12-transformed cells correlates with this diminished class I expression. In contrast, the E1A gene of the nontumorigenic Ad5 does not affect class I expression. We show here that a transfected reporter chloramphenicol acetyltransferase plasmid driven by an H-2K promoter (-1049 bp) was expressed at much lower levels in Ad12- than in Ad5-transformed mouse cells. Analysis of mutant constructs revealed that only 83 bp of H-2 DNA, consisting of the enhancer juxtaposed to the basal promoter, was sufficient for this differential expression. Whereas the H-2 basal promoter alone was somewhat less active in Ad12-transformed cells, the H-2 TATA box itself did not appear to be important. The H-2 enhancer proved to be the principal element in Ad12 E1A-mediated repression, since (i) substitution of the H-2 enhancer by simian virus 40 enhancers overcame the repression, and (ii) when juxtaposed to either its native or heterologous basal promoters, the H-2 enhancer was functional in Ad5- but not Ad12-transformed cells. Mobility shift assays showed that there is a DNA-binding activity to the 5' site (R2 element) of the enhancer that is significantly higher in Ad12- than in Ad5-transformed cells. These results suggest that decreased class I enhancer activity in Ad12-transformed cells may, at least in part, be due to the higher levels of an enhancer-specific factor, possibly acting as a repressor.

A DNA element that regulates expression of an endogenous retrovirus during F9 cell differentiation is E1A dependent

The retinoic acid-induced differentiation of F9 cells into parietal endoderm-like cells activates transcription of the endogenous mouse retrovirus, the intracisternal A-particle (IAP). To investigate the elements that control IAP gene differentiation-specific expression, we used methylation interference, Southwestern (DNA-protein), and transient-transfection assays and identified the IAP-proximal enhancer (IPE) element that directs differentiation-specific expression. We find that the IPE is inactive in undifferentiated F9 cells and active in differentiated parietal endoderm-like PYS-2 cells. Three proteins of 40, 60, and 68 kDa bind to the sequence GAGTAGAC located between nucleotides -53 and -47 within the IPE. The 40- and 68-kDa proteins from both the undifferentiated and differentiated cells exhibit similar DNA-binding activities. However, the 60-kDa protein from differentiated cells has greater binding activity than that from undifferentiated cells, suggesting a role for this protein in F9 differentiation-specific expression of the IAP gene. The IAP gene is negatively regulated by the adenovirus E1A proteins, and the E1A sequence responsible for repression is located at the N terminus, between amino acids 2 and 67. The DNA sequence that is the target of E1A repression also maps to the IPE element. Colocalization of the differentiation-specific and E1A-sensitive elements to the same protein-binding site within the IPE suggests that the E1A-like activity functions in F9 cells to repress IAP gene expression. Activation of the IAP gene may result when the E1A-like activity is lost or inactivated during F9 cell differentiation, followed by binding of the 60-kDa positive regulatory protein to the enhancer element.

The basic RNA polymerase II transcriptional machinery

All genes encoding proteins in eukaryotes are transcribed by RNA polymerase II. The first step in analyzing transcriptional regulation requires understanding the general mechanisms of RNA polymerase II-specific gene transcription. The basal promoter, a template containing a TATA box devoid of upstream regulatory sequences, has been used to identify and characterize the factors which, together with RNA polymerase II, govern transcription in mammalian systems: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG, TFIIH, and TFIIJ. Interactions between regulatory transcription factors and basal elements of the transcriptional machinery affect the transcriptional rate in a positive or negative fashion. As these multiple proteins are purified, and their coding sequences are isolated, we come closer to reproducing these processes in vitro with pure components, and thus to elucidating the complex interactions among them.

The nonphosphorylated form of RNA polymerase II preferentially associates with the preinitiation complex

The two forms of RNA polymerase II that exist in vivo, phosphorylated (IIO) and nonphosphorylated (IIA), were purified to apparent homogeneity from HeLa cells. The nonphosphorylated form preferentially binds to the preinitiation complex. RNA polymerase II in the complex was converted by a cellular protein kinase to the phosphorylated form.

Enhancer element at the 3'-flanking region controls transcriptional response to hypoxia in the human erythropoietin gene

Erythropoietin gene expression is greatly stimulated under conditions of hypoxia. The activation of the erythropoietin gene appears regulated primarily at the level of gene transcription. To study cis-acting elements involved in the response to hypoxia a mini-gene was constructed by an internal deletion from exon II to V of the human erythropoietin gene and used in transient transfection assays in the erythropoietin producing Hep 3B cell line. It was initially found that hypoxia responsiveness was present in an erythropoietin fragment containing 400 base pairs (bp) of 5'-flanking and 600 bp of 3'-flanking regions. Deletion analysis showed no significant effect on the response to hypoxia when highly conserved regions of 5'-flanking sequence, exon and intron I, and exon V were removed from the mini-gene construct. However, removal of a fragment containing the 3' end of the gene and 3'-flanking sequences completely eliminated hypoxia responsiveness. Reinsertion of the above fragment upstream of the 5' end of the mini-gene restored the response to hypoxia. Further analysis using hybrid erythropoietin-chloramphenicol-acetyltransferase constructs allowed the localization of enhancer-like element(s) in the 3'-flanking region, approximately 120 bp downstream of the polyadenylation site of the human erythropoietin gene. Activation by these sequences were position- and orientation-independent and stimulated 15-fold transcription of the erythropoietin gene in response to hypoxia.

Interactions between adenovirus E1A and members of the AP-1 family of cellular transcription factors

We have studied interactions between bacterially produced E1A linked to Sepharose and the various DNA-binding proteins present in HeLa cell nuclear extracts (NE). DNA-binding activities and cross-reactive polypeptides recognizing the cAMP-responsive element (CRE) and the activator protein 1 (AP1) sites were bound to the E1A column, whereas nuclear factor 1 (NF1) and the activator protein 2 (AP2) DNA-binding activities were not retained by E1A. The binding activities that were retained belonged to the CRE and JUN protein family, as judged by Western blot analysis. Authentic CRE-BP1, c-Jun and c-Fos proteins produced by in-vitro translation also bound to the E1A column. However, efficient binding of in-vitro-translated CRE-BP1 and c-Fos proteins to E1A required preincubation with NE. We show here that immobilized E1A sequesters several cellular upstream transcription activators, and suggest a role for members of the AP1 family of transcription factors in E1A-mediated gene regulation.

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

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

The retinoblastoma protein copurifies with E2F-I, an E1A-regulated inhibitor of the transcription factor E2F

Recently, we identified an inhibitory protein, E2F-I, that blocks the DNA-binding activity of the transcription factor E2F. We also showed that the adenovirus E1A protein reverses this inhibitory activity of E2F-I, thereby restoring the DNA-binding activity of E2F. We have now further purified this inhibitory activity and show that the most purified preparation of E2F-I contains a 105 kd E1A-binding protein. This 105 kd E1A-binding protein cross-reacts with two different antibodies against the retinoblastoma (RB) gene product. Moreover, the RB gene product copurifies with E2F-I activity. Taken together, we conclude that the product of the RB gene is a part of E2F-I and is involved in the regulation of E2F activity.

Enhancement by hypoxia of human erythropoietin gene transcription in vitro

Erythropoietin (Epo) gene transcription is stimulated in Hep3B cells under hypoxic conditions. We have prepared transcriptionally active nuclear extracts from normal and hypoxia-induced Hep3B cells and shown that the hypoxic extracts produce a consistent increase in the level of Epo transcription in vitro, relative to control Hep3B cells. Hypoxic treated HeLa cells failed to express the endogenous Epo gene in vivo, and extracts prepared from them did not show increased Epo transcription in vitro. The Epo transcript which is induced in vitro is initiated at the same site as Epo RNA synthesized in intact Hep3B cells and in human kidney adenocarcinoma cells. This system will facilitate the purification and analysis of factors and sequences required for Epo gene transcription in response to changes in tissue oxygen tension.

c-fos mediated stimulation of an AP-1 DNA binding activity in undifferentiated teratocarcinoma cell lines

Undifferentiated F9 and PCC4 embryonal carcinoma (EC) cells contain low levels of AP-1 DNA binding activity. Upon differentiation induced by retinoic acid and cyclic AMP or in differentiated cell lines, AP-1 DNA binding activity can be readily detected. Minute amounts of 3T6 cells extracts, that by themselves were unable to show any binding to an AP-1 site, stimulate AP-1 DNA binding activity when added to the EC cell extracts, suggesting that components of the 3T6 extracts stimulate this DNA binding activity in F9 and PCC4 cell extracts. This enhancement of DNA binding activity requires the presence in the donor fraction (3T6 cells) of a thermostable protein(s) that possesses neither protein kinase nor phosphatase activities. The proteins responsible for stimulation in 3T6 extracts can be separated from the ones responsible for AP-1 binding by chromatography. 3T6 c-fos immunodepleted fractions are unable to activate AP-1 DNA binding activity in EC cell extracts, while c-jun depleted fractions activate normally. Moreover, in vitro translated c-fos, but not c-jun proteins, are able to stimulate binding in EC extracts. These data suggest an important role for c-fos protein in activation of a specific DNA binding transcriptional factor during cellular differentiation and provide a convenient in vitro assay for c-fos function.

Modification of an adenovirus major late promoter-binding factor during poliovirus infection

To further characterize the mechanism involved in poliovirus-induced inhibition of HeLa cells mRNA synthesis, in vitro formation of DNA-protein complexes between nuclear upstream stimulatory transcription factor (USF) and the adenovirus type 2 major late promoter upstream promoter element (UPE; located between -45 and -65 base pairs) was studied. Using the gel shift assay, we found differences between the UPE-protein complex formed with partially purified nuclear extracts from poliovirus-infected HeLa cells and that obtained in the presence of mock-infected extracts. Formation of the modified UPE-USF complex coincided with virus-induced inhibition of host cell RNA synthesis in vivo and with a less efficient in vitro transcriptional activity of the nuclear extracts from infected cells. Furthermore, using a cross-linking protocol, we found that the host 46-kilodalton UPE-binding USF factor was severely diminished and that a virus-induced or -modified 50-kilodalton polypeptide appeared to be specifically bound to the UPE template.

Factors involved in specific transcription by mammalian RNA polymerase II. Role of factors IID and MLTF in transcription from the adenovirus major late and IVa2 promoters

The role of the adenovirus major late upstream transcription factor (MLTF) in transcription from the adenovirus major late and the IVa2 promoters was studied. The transcription initiation site of the IVa2 promoter is located 210 nucleotides upstream from the CAP site of the major late promoter. Transcription from these two promoters occurs on different DNA strands. Thus, this divergent transcription suggests that the same factor could simultaneously regulate the expression of two different genes. This was investigated utilizing a reconstituted transcription system in vitro. The addition of MLTF to reaction mixtures containing the purified general transcription factors and the major late promoter resulted in a 10-12-fold stimulation of transcription. This stimulation was because of an increase of the stability of the preinitiation complex. MLTF allowed DNA template molecules to undergo multiple rounds of transcription. MLTF also stimulated transcription from the adenovirus-encoded IVa2 promoter. Surprisingly, reconstitution experiments indicated that transcription from the IVa2 promoter which does not have a TATA sequence required all the previously described general transcription factors, including TFIID, the TATA binding protein. The requirement for TFIID was demonstrated by reconstitution experiments as well as by oligonucleotide competition experiments. The implications of this observation are discussed.

Promoter specificity and modulation of RNA polymerase II transcription

RNA polymerase II is a multisubunit enzyme involved in the transcription of protein encoding genes. Recently acquired knowledge of the transcription process and of the RNA polymerase molecule as well as the isolation of subunit clones have led to a better understanding of the enzyme's functional regulation. Specific transcription initiation occurs at promoter regions located upstream of the gene and requires a minimum of five basic factors in addition to the enzyme. Furthermore, proteins that bind to specific DNA elements within the promoter also regulate transcriptional activity. Additional factors are required for the elongation and, possibly, termination of transcription. Two elongation factors, SII and TFIIF, interact directly with the RNA polymerase II molecule. Functional domains of RNA polymerase II have been determined by analysis of genomic clones for the two largest subunits of the enzyme. For example, the 240-kDa largest subunit contains a highly phosphorylated carboxyl-terminal heptapeptide domain repeated 26-52 times that is absolutely required for transcription in vivo. Analysis of the polymerase molecule and its interaction with basic gene-specific transcription factors will aid in our studies of the control of gene expression.

Stimulation of erythropoietin gene transcription during hypoxia and cobalt exposure

Erythropoietin, a plasma glycoprotein produced primarily by the kidney, is a growth and differentiation factor for erythroid progenitor cells. Production of renal erythropoietin is regulated by modulation of mRNA levels in response to changes in tissue oxygenation. Exposure to cobalt, a nonphysiologic stimulus for erythropoietin production, also acts by inducing mRNA accumulation. To determine whether variations in erythropoietin mRNA levels result from enhanced transcription of the erythropoietin gene, in vitro transcription reactions were performed using isolated rat kidney cell nuclei. Quantitation of specific nuclear RNAs labeled during in vitro transcription revealed active erythropoietin gene transcription in kidney nuclei from anemic-hypoxic and cobalt-treated animals while erythropoietin transcriptional activity was undetectable in normal kidney nuclei. Time course studies showed that stimulation of transcription begins between two and four hours following cobalt treatment and parallels the kinetics of mRNA and plasma erythropoietin accumulation. These results indicate that tissue hypoxia and cobalt exposure specifically enhance erythropoietin gene expression. This increase in erythropoietin production is regulated at least in part at the level of gene transcription.

Purified human factor activates heat shock promoter in a HeLa cell-free transcription system

Heat shock protein (hsp) genes are typically silent and are activated by various stresses including heat. As a first step toward understanding this activation event, a human factor, referred to here as human heat shock transcription factor (human HTF), has been purified approximately 14,000-fold from extracts of heat-treated HeLa cells by means of sequence-specific DNA affinity chromatography. The most highly purified fraction of human HTF binds specifically to the known regulatory sequence element (HSE) of hsp genes as shown by footprinting experiments. Purified human HTF has an apparent molecular mass of 83 kDa. Human HTF is specifically required for activation of an hsp gene promoter in a reconstituted in vitro transcription system from human cells. Activation is dependent on the presence of the HSEs in the transcription template.

Transcription elongation factor SII interacts with a domain of the large subunit of human RNA polymerase II

Genomic sequences for the large subunit of human RNA polymerase II corresponding to a part of the fifth exon were inserted into an expression vector at the carboxy-terminal end of the beta-galactosidase gene. The in-frame construct produced a 125-kilodalton fusion protein, containing approximately 10 kilodaltons of the large subunit of RNA polymerase II and 116 kilodaltons of beta-galactosidase. The purified bacterially produced fusion protein inhibited specific transcription from the adenovirus type 2 major late promoter, while beta-galactosidase had no effect. This effect of the fusion protein was during RNA elongation, not at the level of initiation, resembling the faithfully initiated but incomplete transcripts produced with purified factors in the absence of SII. Similarly, monoclonal antibody 2-7B, which reacts with the RNA polymerase II region represented in the fusion protein, inhibited specific transcription at the level of elongation in a whole-cell extract. Both monoclonal antibody 2-7B and the fusion protein, although unable to inhibit purified RNA polymerase II in a nonspecific transcription assay, selectively blocked the stimulation elicited by transcription elongation factor SII on the activity of the purified enzyme in vitro. This suggests that the fusion protein traps the SII in nonstimulatory interactions and that antibody 2-7B inhibits SII binding to RNA polymerase II. Thus, this suggests that an SII-binding contact required for specific RNA elongation resides within the fifth exon region of the largest RNA polymerase II subunit.

A rapid purification method for calf thymus casein kinase II

We report here the rapid purification to homogeneity of a cyclic nucleotide-independent protein kinase sensitive to 5'6-dichloro-1-beta-D-ribofuranozylbenzimidazole (DRB), identical to the previously described casein kinase II, from lyophilized calf thymus by chromatography on phosphocellulose and Mono-Q FPLC columns.

Genetic profile of the transcriptional signals from the adenovirus major late promoter

Identical functional profiles were obtained for in vivo and in vitro transcription assays of more than 30 site-directed point mutants within the adenovirus major late promoter. The functional limits of the functional regions encompassing upstream promoter element are defined (-51 to -61), as well as a region around the transcription start site (-1 to +1), flanked by regions insensitive to sequence alterations.

Erythropoietin-beta-D-galactosidase. The generation, purification and use of a fusion protein

A human erythropoietin (Epo) cDNA fragment encoding the complete erythropoietin peptide sequence was fused to the 3'-end of the lacZ gene in the polylinker region of the high expression vector, pUR 278. Escherichia coli bacteria were transformed with the recombinant plasmid harboring the hybrid Epo-beta-D-galactosidase gene. After induction with isopropyl-thiogalactoside large amounts of the fusion protein, Epo-beta-D-galactosidase were synthesized in the transformed bacteria. The fusion protein was partially purified and shown to exhibit intact galactosidase enzymatic activity. Although no biological activity of the Epo counterpart of the fusion protein was detected both in an in vivo and in an in vitro bioassay, the fusion protein served as an effective antigen for the production of anti-erythropoietin antibodies. Antifusion protein antibodies raised in rabbits were shown to react with the intact human Epo molecule from erythropoietin producing culture supernatants. The affinity of these anti-fusion protein antibodies was sufficiently high to permit the development of a sensitive radioimmunoassay for human Epo. This fusion protein approach is a relatively straightforward and rapid method of generating antibodies with specificity for any protein encoded by a cloned eukaryotic gene.

Purine triphosphate beta-gamma bond hydrolysis requirements for RNA polymerase II transcription initiation and elongation

RNA polymerase II-specific transcription requires, in addition to auxiliary protein factors, the hydrolysis of the beta-gamma phosphate bond of ATP. The nonhydrolyzable analog of ATP, imidoadenosine triphosphate does not suffice for specific in vitro transcription (Bunick, D., Zandomeni, R., Ackerman, S., and Weinmann, R. (1982) Cell 29, 877-886), although it can be incorporated into RNA. The experiments presented here suggest two energy-dependent steps in RNA polymerase II transcription. One of these steps is required at, or close to, the point of initiation, as determined by 5' end primer extension analysis. In vitro transcription occurs efficiently in vitro when imidoadenosine triphosphate is supplemented with dATP to fulfill the energy requirement. In the presence both of imidoadenosine triphosphate and imidoguanosine triphosphate, the concentration of dATP required for transcription initiation is dramatically increased. This suggests that ATP and GTP are co-substrates in transcription initiation, supporting the role of protein kinase II in this process (Zandomeni, R., Zandomeni, M. C., Shugar, D., and Weinmann, R. (1986) J. Biol. Chem. 261, 3414-3419). The concentration of dATP required for maximal initiation is inadequate for the production of full-length transcripts, suggesting a second energy-dependent step in the RNA elongation process. Since the elongation step is unaffected by the presence of imidoguanosine triphosphate, GTP beta-gamma phosphate bond hydrolysis appears to be required only for initiation.

The phosphorylation of nucleoplasmin by casein kinase-2 is resistant to heparin inhibition

Highly purified preparations of casein kinase-2 from the nuclei of Xenopus laevis oocytes and from calf thymus can phosphorylate in vitro purified nucleoplasmin from X. laevis oocytes and eggs. The phosphorylation of nucleoplasmin by both kinase preparations is quite insensitive to heparin in contrast with casein phosphorylation which is completely abolished by heparin concentrations above 10 micrograms/ml. However, the phosphorylation of nucleoplasmin and casein are inhibited in a very similar fashion by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), a well characterized specific inhibitor of casein kinase-2. Similarly, nucleoplasmin phosphorylation by the oocyte enzyme can be stimulated several-fold by spermine, another characteristic of this enzyme. These findings indicate that the phosphorylation of nucleoplasmin by purified casein kinase-2, while showing typical response to DRB and spermine, exhibits anomalous behavior in its resistance to heparin inhibition. It is possible that the large clusters of acidic amino acids in nucleoplasmin permit this substrate to interact with the enzyme more efficiently than other protein substrates. Heparin is generally considered a potent and specific inhibitor of casein kinase-2. This study, however, questions the validity of utilizing heparin inhibition as a criterion for casein kinase-2 involvement.

Independent regulation of tumor necrosis factor and lymphotoxin production by human peripheral blood lymphocytes

We present evidence that human peripheral blood lymphocytes, free of contaminating monocytes, rapidly produce high levels of tumor necrosis factor (TNF) when stimulated with phorbol diester and calcium ionophore, and lower but significant levels of TNF when stimulated with mitogens. These two types of inducers act preferentially on T cells, both CD4+ and CD8+. NK cells produce TNF only when stimulated with phorbol diester and calcium ionophore, and they do so at a much lower level than T cells. The procedures used in the purification of lymphocytes and the differential ability to respond to various inducers allow us to exclude that monocytes or basophils contaminating the lymphocyte preparation participate in the production of TNF. In particular, LPS, a potent inducer of TNF production from monocytes, is unable to induce significant levels of TNF in the lymphocyte preparations. The TNF produced by lymphocytes has antigenic, physicochemical, and biochemical characteristics identical to those of the TNF produced by myeloid cell lines or monocytes upon stimulation with LPS. LT is also produced by lymphocyte preparations. Production of TNF and LT proteins in response to the different inducers is paralleled by accumulation of cytoplasmic TNF and LT mRNA. Both at mRNA and at protein levels, stimulation of T lymphocytes with phorbol diester and calcium ionophore preferentially induces TNF, whereas mitogen stimulation preferentially induces LT. Our data suggest that the TNF and LT genes, two closely linked genes encoding two partially homologous proteins with almost identical biological functions, are independently regulated in lymphocytes.

Purification and functional characterization of transcription factor SII from calf thymus. Role in RNA polymerase II elongation

SII was purified from calf thymus tissue to apparent homogeneity by a rapid procedure. The 38-kDa protein stimulated RNA synthesis by purified calf thymus RNA polymerase II 4-fold. The calf thymus SII had similar chromatographic properties and molecular size and cross-reacted immunologically with antibodies to mouse SII (Sekimizu, K., Nakanishi, Y., Mizuno, D., and Natori, S. (1979) Biochemistry 18, 1582-1588). We have substituted the purified calf thymus SII for the partially purified HeLa transcription factor IIS fraction in a HeLa (human) transcription system reconstituted with purified factors and RNA polymerase II. The purified protein stimulated specific transcription from the adenovirus 2 major late promoter by increasing the efficiency of the elongation reaction.

The gene encoding the large subunit of human RNA polymerase II is located on the short arm of chromosome 17

We have used chromosomal in situ hybridization and Southern blot analysis of DNA from somatic cell hybrids to determine the chromosomal localization of the subgenomic DNA fragment that encodes part of the large subunit of human RNA polymerase II. The results of our analysis demonstrate localization of the human RNA polymerase II large subunit gene to the short arm of chromosome 17.

Protein factor(s) binding independently to two different regions of the adenovirus 2 major late promoter

The protein factor(s) in a fraction from the HeLa cell nuclear extract required for specific in vitro transcription can specifically bind to adenovirus 2 major late promoter (Ad 2 MLP) DNA. We demonstrate by in vitro footprinting assay that there are two asymmetric protected regions covering the TATA box and the nucleotides upstream from the TATA box. In the coding strand, the DNAse I protected regions span from nucleotides -10 to -50 and from -52 to -68. In the noncoding strand, the protected regions span from nucleotides -10 to -32 and from -45 to -65. Using different Ad 2 MLP point mutants in this assay, we show that the transcriptional down mutants of the TATA box (AC-30 and AC-28) abolish the binding of protein factor(s) to the TATA box but do not affect binding in the upstream region. The new upstream transcriptional down mutant (TA-56) abolishes the binding of protein factor(s) in the upstream region but does not affect binding to the TATA box. The mutants which do not affect transcription efficiency (GA-51 and CG-61) do not modify the binding to either the TATA box or the upstream region. Methylation protection experiments show that the guanosines at -58 and -60 in the coding strand and at -57 (probably also -55) in the noncoding strand are in close contact with protein factor(s). The results indicate that the TATA box and its upstream region of Ad 2 MLP are independently bound by at least two different factors in vitro.

The cap structure of simian hemorrhagic fever virion RNA

The molecular weight of simian hemorrhagic fever virus RNA is 4.19 +/- 0.53 X 10(6) as determined by electron microscopy. Its base composition is 19.5 +/- 0.3 A, 33.3 +/- 0.3 U, 26.7 +/- 0.9 G, and 19.7 +/- 0.3 C per 100 nucleotides. The RNA of simian hemorrhagic fever virus contains a single type I cap per molecule, in the form m7G(5')ppp(5')Am.

Casein kinase type II is involved in the inhibition by 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole of specific RNA polymerase II transcription

We have described a HeLa protein kinase whose activity is inhibited by the nucleotide analogue 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) at concentrations similar to those required to inhibit in vivo and in vitro specific transcription (Zandomeni, R., and Weinmann, R. (1984) J. Biol. Chem. 259, 14804-14822). We have now detected an analogous DRB-sensitive kinase from calf thymus and purified it to homogeneity. Based on the subunit composition of the enzyme and other common biochemical and chromatographic properties, we identified it as casein kinase II. The extent of DRB inhibition of the purified calf thymus enzyme is indistinguishable from that observed for inhibition of in vitro transcription with the HeLa cell extract. The DRB bromo- derivative, 5,6-dibromo-1-beta-D-ribofuranosylbenzimidazole is a more potent inhibitor of in vivo transcription and inhibits purified casein kinase II activity and specific in vitro transcription at 6-10 times lower concentrations than DRB. Moreover, addition of an excess of the purified calf thymus casein kinase II enzyme to a HeLa in vitro transcription reaction inhibited by DRB partially overcomes this inhibition. Thus, we conclude that casein kinase II is involved directly or indirectly in the inhibition by DRB of specific RNA polymerase II-mediated transcription. This demonstrates the participation of a protein kinase in a eukaryotic RNA polymerase II-specific transcription system.

The gene encoding the large subunit of human RNA polymerase II

As a first step to approach the structural and functional analysis of DNA-dependent RNA polymerase II (EC 2.7.7.8), we have isolated genomic sequences for the large subunit of the human enzyme. The sequences homologous to Drosophila RNA polymerase II large subunit sequences are present in the genome as single copy genes, when assayed at high stringency. The polypeptide information is encoded in a mRNA of 7.35 kilobases, as determined by Northern blot analysis. In vitro translation reveals a polypeptide of 220 kDa, similar in electrophoretic mobility to the largest subunit of the enzyme. A fusion-polypeptide synthesized in bacteria contains a region that cross-reacts with anti-RNA polymerase II antiserum. Antiserum directed against the purified fusion protein reacts with the large subunit of RNA polymerase II, whether in the intact IIA (220 kDa) or in the degraded IIB (180 kDa) forms. Moreover, the antifusion protein antibody inhibits not only the purified calf thymus RNA polymerase II activity but also specific RNA polymerase II transcription in a HeLa cell extract. Thus, the DNA fragment isolated contains structural and functional domains of the human RNA polymerase II large subunit.

Actin mRNAs in HeLa cells. Stabilization after adenovirus infection

We have carried out a comparative analysis of the expression of the actin genes in HeLa and adenovirus-infected HeLa cells. The rate of actin gene transcription was examined in these cells by pulse-labeling of the newly synthesized RNA and/or by in vitro transcription in nuclei isolated from uninfected or infected HeLa cells. In addition, accumulation of actin-specific heterogeneous nuclear RNA, and rate of appearance of the actin mRNAs in the cytoplasm were examined by dot and Northern blot analysis. The rate of actin gene transcription remained constant after infection of HeLa cells with adenovirus serotype 2, while the level of the actin precursor in the nuclei was slightly reduced. In the infected cells, newly synthesized actin mRNA enters the cytoplasm at a very reduced rate. The deficiency of transport does not affect the steady-state level of the messages in the cytoplasm. The half-life of cytoplasmic actin mRNAs was analyzed by traditional pulse-chase experiments and by a novel procedure using 5-6-diCl-1-beta-d-ribofuranosylbenzimidazole, which does not rely on labeled RNA. Both procedures gave identical results. Uninfected HeLa cells have actin mRNAs with relatively short half-lives, from less than six to 12 hours. In contrast, the half-lives of the actin-specific mRNAs, in the cytoplasm of adenovirus-infected cells, is greater than 14 to 24 hours. These observations suggest that, although the rate of transport of actin mRNAs to the cytoplasm is reduced upon infection with adenovirus, increased half-lives result in accumulation of actin mRNAs to normal levels in the cytoplasm.