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R Chalkley

Publications and source records attributed to R Chalkley.

At least 37 records · Page 2Linked to original sources
PubMed1990

Identification and purification of a yeast transcriptional trans-activator. The yeast homolog of the Rous sarcoma virus internal enhancer binding factor.

A cis-acting transcriptional activation sequence (IES2) from the Rous sarcoma virus internal enhancer was found to stimulate transcription of a heterologous gene in Saccharomyces cerevisiae. A hamster protein (termed IBF) which binds to IES2 and stimulates transcription in vitro has previously been purified and was found to have a subunit molecular mass of 40,000 (Karnitz, L., Poon, D., Weil, P.A., and Chalkley, R. (1989) Mol. Cell. Biol. 9, 1929-1939). The identification and purification of the yeast homolog of IBF (yIBF) is reported here. Purified yIBF has a subunit molecular mass of 92,000. This protein functions as a trans-activator of transcription in a heterologous HeLa transcription extract in a cis-element sequence-dependent manner in vitro.

Animals↗
PubMed1990

The structure and assembly of active chromatin.

Much effort has been expended towards understanding the details of how nucleosomes are established on newly replicated DNA. More recently it has begun to be possible to study the binding of both trans-acting factors and histones to DNA. This review is concerned with an assessment of the current status of this work. In addition, we discuss some of the questions that still need to be addressed in order to understand how trans-acting factors can establish extensive interactions with the DNA of active genes while they are excluded from inactive genes.

Chromatin↗
PubMed1990

Transcription factor requirements for in vitro formation of transcriptionally competent 5S rRNA gene chromatin.

The Saccharomyces cerevisiae 5S rRNA gene was used as a model system to study the requirements for assembling transcriptionally active chromatin in vitro with purified components. When a plasmid containing yeast 5S rDNA was assembled into chromatin with purified core histones, the gene was inaccessible to the yeast class III gene transcription machinery. Preformation of a 5S rRNA gene-TFIIIA complex was not sufficient for the formation of active chromatin in this in vitro system. Instead, a complete transcription factor complex consisting of TFIIIA, TFIIIB, and TFIIIC needed to be formed before the addition of histones in order for the 5S chromatin to subsequently be transcribed by RNA polymerase III. Various 5S rRNA maxigenes were constructed and used for chromatin assembly studies. In vitro transcription from these assembled 5S maxigenes revealed that RNA polymerase III was readily able to transcribe through one, two, or four nucleosomes. However, we found that RNA polymerase III was not able to efficiently transcribe a chromatin template containing a more extended array of nucleosomes. In vivo expression experiments indicated that all in vitro-constructed maxigenes were transcriptionally competent. Analyses of protein-DNA interactions formed on these maxigenes in vivo by indirect end labeling indicated that there are extensive interactions throughout the length of these maxigenes. The patterns of protein-DNA interactions formed on these genes are consistent with these DNAs being assembled into extensive nucleosomal arrays.

Chromatin↗
PubMed1990

Interaction of a liver-specific factor with an enhancer 4.8 kilobases upstream of the phosphoenolpyruvate carboxykinase gene.

We have previously identified a series of five DNase-I hypersensitive (HS) sites within and around the rat phosphoenolpyruvate carboxykinase (PEPCK) gene. The far upstream region has now been sequenced, and the tissue-specific HS site has been mapped more precisely at 4,800 base pairs upstream of the transcription start site of the PEPCK gene. DNA fragments that include the HS site were cloned upstream of various promoters to test whether these regions modulate transcription of the chloramphenicol acetyltransferase reporter gene. Chloramphenicol acetyltransferase activity was enhanced when the DNA fragment encompassing the upstream HS site was linked to various lengths of the PEPCK promoter or to the heterologous simian virus 40 promoter. This upstream region in conjunction with the proximal promoter, which may contain a tissue-specific element, conferred maximum activation in H4IIE hepatoma cells, which express the endogenous PEPCK gene. When these experiments were performed in XC cells, in which the gene is not expressed, transcriptional activation by the upstream element was still significant. Evidence of a specific protein-DNA interaction, using DNA mobility shift and DNase I footprinting assays, was obtained only when using H4IIE cell nuclear extracts. Competition assay showed that the interacting factor may be similar or identical to the liver-specific factor HNF3. We suggest that this protein factor binds to DNA within the HS site and interacts with the proximal promoter region to control tissue-specific high-level expression of the PEPCK gene.

Animals↗
PubMed1990

Extinction of phosphoenolpyruvate carboxykinase gene expression is associated with loss of a specific chromatin-binding protein from a far upstream domain.

We have analyzed the chromatin structure of the phosphoenolpyruvate carboxykinase (PEPCK) gene in hepatoma x fibroblast hybrids with different extinction phenotypes. These hybrids included a karyotypically complete hybrid in which all liver gene activity was extinguished, a microcell hybrid that contained a single mouse chromosome 11 and in which PEPCK gene activity was decreased but inducible by cyclic AMP, and a segregant line that had lost all mouse chromosomes and in which the PEPCK gene was reexpressed. We found that only in the completely extinguished hybrid was PEPCK chromatin structure radically different from that in the parental hepatoma cells. In this hybrid, there was no evidence of any factors binding to the promoter or to the upstream hypersensitive site at -4800 base pairs. In the other cell lines, even when PEPCK gene transcription was low, the PEPCK chromatin showed characteristic structures typical of a transcriptionally competent gene, with hypersensitive sites at positions previously described. Loss of the upstream hypersensitive site was also shown to be correlated with the absence of a liver-specific protein factor that binds specifically to the upstream region.

Animals↗
PubMed1989

Hormonal regulation of phosphoenolpyruvate carboxykinase gene expression is mediated through modulation of an already disrupted chromatin structure.

We used indirect end labeling to identify a series of five hypersensitive (HS) sites in the phosphoenolpyruvate carboxykinase (PEPCK) gene in H4IIE rat hepatoma cells. These sites were found at -4800 base pairs (bp) (site A), at -1300 bp (site B), over a broad domain between -400 and -30 bp (site C), at +4650 bp (site D), and at +6200 bp (site E). Sites A to D were detected only in cells capable of expressing the PEPCK gene, whereas site E was present in all of the cells examined thus far. The HS sites were present in H4IIE cells even when transcriptional activity was reduced to a minimum by treatment with insulin. Stimulation of transcription by a cyclic AMP analog to a 40-fold increase over the insulin-repressed level did not affect the main features of the HS sites. Furthermore, increased transcription did not disrupt the nucleosomal arrangement of the coding region of the gene, nor did it affect the immediate 5' region (site C), which is always nucleosome-free. In HTC cells, a rat hepatoma line that is hormonally responsive but unable to synthesize PEPCK mRNA, the four expression-specific HS sites were totally absent. Our experimental results also showed that, although there is a general correlation between lack of DNA methylation and transcriptional competence of the PEPCK gene, the role, if any, of methylation in the regulation of PEPCK gene activity is likely to be exerted at very specific sites.

Animals↗
PubMed1989

Purification and properties of the Rous sarcoma virus internal enhancer binding factor.

The internal enhancer binding factor (IBF) that specifically binds sequences within the gag gene internal enhancer of Rous sarcoma virus Schmidt-Ruppin A was purified to near homogeneity from BHK cells. The polypeptides that constituted IBF DNA-binding activity were identified by sodium dodecyl sulfate-polyacrylamide gel analysis. As isolated from BHK cells, IBF consisted of two different but related polypeptides. One (IBF alpha) had a molecular weight of 40,000; the other (IBF beta) had a molecular weight of 20,000 and appeared to be a proteolytic product of IBF alpha. The site within the gag gene to which IBF bounds in vitro (internal enhancer site 2; nucleotides 856 to 878 of the Rous sarcoma virus genome) were demonstrated to function as a cis-acting transcriptional stimulatory element both in vivo and in vitro. By using HeLa cell nuclear transcription extracts, purified IBF was found to function as a trans-acting transcription factor that stimulated transcription in vitro. Purified IBF was also demonstrated to be very similar to EBP20 (K. Carlberg, T. A. Ryden, and K. Beemon, J. Virol. 62:1617-1624, 1988), and it may well belong to the same family of DNA-binding proteins.

Animals↗
PubMed1988

The separation of transcriptionally engaged genes.

We have developed a method for the separation of transcriptionally engaged chromatin from inactive genes as well as from active genes which are not being transcribed. This approach is dependent upon the integrity of the growing transcript and is reflected in a significant decrease in the density of the chromatin during transcription. The decrease in density appears to be due to an association between the growing transcript and a large zone of lower density, possibly the nuclear matrix. These interactions are preserved after fixation of the nuclear material with formaldehyde. Hormonal induction of transcriptional activity causes a shift of the genetic material for the stimulated gene from the high density domain to the low density region. The vast majority of the polymerase II which is engaged with the chromosomal material is also found in this lower density zone. We find that most of the fast form of histone acetylation occurs on those histones which are associated with the active chromatin, further supporting the idea that this modification is involved in some way with the transcriptional process. The merits of this approach are discussed, as are the possibilities for its further exploitation.

Animals↗
PubMed1987

Purification of a novel, nucleoplasmin-like protein from somatic nuclei.

We have purified a nucleoplasmin-like protein from the nuclei of somatic Xenopus laevis cells. This protein possesses a number of the distinctive features of nucleoplasmin isolated from oocytes or unfertilized eggs. The protein is recognized by both monoclonal and polyclonal antisera raised against egg nucleoplasmin. The protein has an oligomeric structure, which must be heated in SDS to completely dissociate, is acidic, phosphorylated and efficiently promotes the in vitro formation of chromatin. We have partially characterized this novel protein and because of its resemblance to nucleoplasmin isolated from oocytes or unfertilized eggs we have named this protein nucleoplasmin S.

Amino Acids↗
PubMed1987

Specific nuclear proteins interact with the Rous sarcoma virus internal enhancer and share a common element with the enhancer located in the long terminal repeat of the virus.

We have documented that the Rous sarcoma virus (RSV) internal enhancer functions in the nontransformed Baby Hamster Kidney (BHK) cell line. The sequences within this region were assayed for their ability to bind to specific factors present in BHK nuclear extracts using the gel retardation assay and DNAse I footprinting. At least two sequences within the internal enhancer which can specifically bind nuclear factors in vitro have been identified. These regions are located between nucleotides 813-850 and 856-877. These sites map within the overall region of the internal enhancer which has been shown to be essential for enhancer activity and within the specific region which can function as an orientation independent enhancer. Using the DNase I footprinting and binding data to design an oligonucleotide, we have demonstrated that an oligonucleotide extending from nucleotides 804-877 will substitute efficiently as an enhancer. We also demonstrate that the SV40 enhancer does not compete for the factors which bind to the RSV internal enhancer, whereas an oligonucleotide to the binding site for EFII in the LTR can compete for factor binding to the internal enhancer.

Animals↗
PubMed1987

DNA denatures upon drying after ethanol precipitation.

We have observed that ethanol precipitation and subsequent drying of small (less than 400 bp) radiolabelled DNA fragments is able to induce a transition to a form that migrates aberrantly on acrylamide gels. This unusual form has increased sensitivity to S1 nuclease, decreased sensitivity to restriction enzymes, and a concentration dependence for the reversion to the duplex form. Apparently, DNA denatures upon dehydration so that redissolving at low dilution will allow the collapse of DNA fragments into single-stranded hairpin structures. These structures are stable enough at low dilution to prevent complete reannealing of single stranded species. These single stranded species show strong binding to unidentified proteins present in nuclear extracts. This may give rise to misleading interpretations of mobility shift assays, especially if the single-stranded conformers have a similar mobility to the duplex fragment, which can occur in fragments that are 50-100 bp long. Evidence is presented that DNA, in general, denatures upon dehydration, but that hindrances to rotation in the solid state may prevent long fragments from dissociating.

Chemical Precipitation↗
PubMed1987

Novobiocin inhibits interactions required for yeast TFIIIB sequestration during stable transcription complex formation in vitro.

Novobiocin concentrations normally used to inhibit a putative eukaryotic DNA gyrase have been found to inhibit transcription of a yeast 5S rRNA gene using an in vitro yeast transcription system. Purified RNA polymerase III and three yeast transcription factors (chromatographically separated, partially purified and free of any detectable gyrase activity) were used. Novobiocin prevents specific transcription if added to the in vitro system immediately prior to the addition of transcription factors and RNA polymerase. If a stable transcription factor complex is allowed to form prior to the addition of novobiocin, concentrations of novobiocin as high as 1000 micrograms/ml have no effect on in vitro transcription. Transcription factors TFIIIA and TFIIIC are able to be stably sequestered onto 5SrDNA-cellulose, but factor TFIIIB is not able to associate with the 5SrDNA-TFIIIA-TFIIIC complex in the presence of novobiocin. Although novobiocin is able to precipitate other basic proteins, it does not appear to precipitate any of these class III gene transcription factors, but instead appears to act by disrupting specific factor-factor interactions.

Genes, Fungal↗
PubMed1987

At least two nuclear proteins bind specifically to the Rous sarcoma virus long terminal repeat enhancer.

We used the sensitive gel electrophoresis DNA-binding assay and DNase I footprinting to detect at least two protein factors (EFI and EFII) that bound specifically to the Rous sarcoma virus (RSV) enhancer in vitro. These factors were differentially extracted from quail cell nuclei, recognized different nucleotide sequences in the U3 region of the RSV long terminal repeat, and appeared to bind preferentially to opposite DNA strands as monitored by the DNase I protection assay. The EFI- and EFII-protected regions within U3 corresponded closely to sequences previously demonstrated by deletion mutagenesis to be required for enhancer activity, strongly suggesting a functional significance for these proteins. Only weak homologies between other enhancer consensus sequence motifs and the EFI and EFII recognition sites were observed, and other viral enhancers from simian virus 40 and Moloney murine sarcoma virus did not compete effectively with the RSV enhancer for binding either factor.

Avian Sarcoma Viruses↗
PubMed1987

Bleomycin-induced DNA cleavage: studies in vitro and in intact cells.

Bleomycin, an important chemotherapeutic agent useful in the treatment of testicular carcinoma, can cause lung parenchymal injury. Prior studies showing that different cell types have different susceptibilities to bleomycin suggest that intracellular conditions for bleomycin-DNA interactions vary. The purpose of the present studies was to test the effects of therapeutic concentrations of bleomycin on DNA in vitro, and then to study the effects of these levels of bleomycin on intracellular DNA. In the absence of ferrous ion (Fe+2), bleomycin caused no DNA strand scission at any concentration tested. The addition of as little as 100 nmol/L Fe+2 resulted in DNA strand scission at concentrations of bleomycin greater than or equal to 10 nmol/L. Glutathione dramatically augmented the DNA strand breakage. With use of a viral minichromosome replicating in cultured cells, bleomycin caused DNA strand scission at levels equivalent to therapeutic serum concentrations. These studies reveal that bleomycin causes dose-dependent DNA damage at therapeutic serum concentrations in vitro and in intact cells. The observation that in vitro DNA damage is dependent on the availability of ferrous ion and is augmented by glutathione suggests that different cells, which may differ in their intracellular levels of Fe+2 and reducing capacity, may vary in their sensitivity to bleomycin-induced DNA strand scission.

Animals↗
PubMed1986

Novobiocin inhibits passive chromatin assembly in vitro.

Novobiocin, an inhibitor of prokaryotic DNA gyrase and eukaryotic type II topoisomerase enzymes, interferes with in vitro chromatin assembly using purified histones, DNA and nucleoplasmin. The target of inhibition is not topoisomerase II; this energy-independent assembly system lacks any ATP and Mg2+-dependent type II topoisomerase or gyrase activities. Rather, novobiocin interacts with histones, disrupting histone-histone associations required for octamer formation, and causing histones to precipitate from both nucleoplasmin-histone and histone-DNA complexes. Thus, novobiocin is able to generate 'dynamic' chromatin in vitro in the absence of ATP and Mg2+ by removing histones from previously assembled static chromatin, so that the DNA supercoils, previously constrained by conventional nucleosomes, become susceptible to removal by topoisomerase I.

Animals↗
PubMed1986

Massive phosphorylation distinguishes Xenopus laevis nucleoplasmin isolated from oocytes or unfertilized eggs.

Nucleoplasmin isolated from unfertilized Xenopus laevis eggs possesses an in vitro chromatin assembly activity which is superior to nucleoplasmin isolated from oocytes. It is demonstrated here that the two forms of the protein differ in the amount of attached phosphate, with the egg protein possessing nearly 20 phosphate groups per protein monomer and the oocyte protein possessing less than 10 phosphate groups per monomer. A kinase preparation from unfertilized eggs is shown to be capable of modifying oocyte nucleoplasmin so that it displays the electrophoretic heterogeneity of egg nucleoplasmin. Furthermore, when the egg protein is treated with phosphatase and repurified, the chromatin assembly activity deteriorates to the level of the oocyte protein.

Animals↗
PubMed1986

Xenopus nucleoplasmin: egg vs. oocyte.

Nucleoplasmin has been purified from either oocytes or unfertilized eggs of the frog, Xenopus laevis. We find that the pentameric form of egg nucleoplasmin exhibits an apparent molecular mass approximately 15 000 daltons larger than its oocyte counterpart upon sodium dodecyl sulfate (SDS)-acrylamide gel electrophoresis. Egg nucleoplasmin monomers are more heterogeneous, substantially more acidic, and overall larger in apparent molecular weight than oocyte nucleoplasmin monomers when analyzed by isoelectric focusing or SDS gel electrophoresis. Protease digestions indicate that the structural differences between egg and oocyte nucleoplasmin are primarily confined to the N-terminal halves of the proteins. The structural diversity observed is accompanied by a difference in the ability of nucleoplasmin from the two sources to act as a nucleosome assembly agent in vitro. Egg nucleoplasmin efficiently promotes the formation of nucleosomes onto circular pBR322 DNA in vitro at physiological ionic strength and at physiological histone:DNA ratios, while oocyte nucleoplasmin is markedly deficient in serving as an in vitro chromatin assembly agent under all conditions which we have tested. Treatment of egg nucleoplasmin in vitro with alkaline phosphatase demonstrates that the structural diversity between egg and oocyte nucleoplasmin results primarily from extensive additional phosphorylation of the egg protein. The relevance of nucleoplasmin phosphorylation in leading to differences in the chromatin assembly activity of this protein both in vitro and in vivo is considered.

Animals↗