A factor from calf thymus stimulating DNA-dependent RNA polymerase isolated from this tissue

TFIIS binds to mouse RNA polymerase I and stimulates transcript elongation and hydrolytic cleavage of nascent rRNA

Efficient transcription elongation by RNA polymerase I (Pol I) requires a specific Pol I-associated factor, termed TIF-IC. Here we show that TFIIS, a factor that has previously been shown to promote read-through past many types of blocks to elongation by RNA polymerase II, also enhances Pol I-directed transcription elongation. In a reconstituted transcription system containing purified proteins, TFIIS stimulates Pol I transcription by increasing the overall rate of RNA chain elongation. As with Pol II, ternary Pol I complexes cleave the 3' end of the nascent transcripts in response to TFIIS. The truncated RNAs remain bound to the template, are subject to pyrophosphorolysis, and can be chased into longer transcripts. Moreover, we show by immunoprecipitation and specific affinity chromatography that TFIIS physically interacts with Pol I. The results suggest that nascent transcript cleavage by TFIIS or a TFIIS-related factor may be a general mechanism by which both Pol I and Pol II can bypass transcriptional impediments.

Nuclear sialyl cholesterol causes changes in the structure of chromatin and its transcription level followed by the promotion of neuritogenesis

Exogenously added sialyl cholesterol (SC) induced neuritogenesis and accumulated in the nuclear fraction of a mouse neuroblastoma cell line, Neuro2a, as reported elsewhere. To clarify the significance of nuclear SC, we examined the structure of chromatin and its transcriptional level. The chromatin of SC-treated cells exhibits greater circular dichroism amplitude (260-310 nm) than that of nontreated cells. The transcriptional level of chromatin from SC-treated cells was significantly higher than that of nontreated cells. The chromatin structural change has a good correlation to the transcriptional enhancement. On the addition of SC to the chromatin of nontreated cells, the circular dichroism spectra increased in amplitude and the transcriptional level also increased in a concentration-dependent manner. alpha-Amanitin-treated cells did not show SC-dependent neuritogenesis. These results strongly suggest that nuclear SC affects gene expression, which results in promotion of the neuritogenesis of cells.

Class II ribonuclease H comigrates with, but is distinct from, the third largest subunit of calf thymus RNA polymerase I

It has been reported (Iborra et al. (1979) J. Biol. Chem. 254, 10920-10924) that the third and the fifth largest subunit of yeast RNA polymerase I exhibit ribonuclease H activity. The authors suggested that the third largest subunit is identical with the chromatin-associated ribonuclease H49, the putative yeast equivalent of bovine ribonuclease H IIb. Although the third largest subunit of calf thymus RNA polymerase I and ribonuclease H IIb display nearly identical molecular masses under denaturing conditions, serological analysis reveals that, in contrast to their counterparts in yeast, these mammalian proteins are distinct entities. Interestingly, sera from some patients with mixed connective tissue disease which contain antibodies directed against RNA polymerase I, also react with ribonuclease H IIb epitopes. This observation suggests that a protein displaying ribonuclease H IIb antigenicity could be associated with RNA polymerase I. Additional indications supporting this conclusion are discussed.

Small peptides controlling transcription in vitro are bound to chromatin DNA

Low-molecular-weight peptides are linked to the chromatin DNA of several tissues, from which they can be dissociated by alkaline extraction at pH 9.5. The level of the active peptide fraction ranges between 10 and 35 micrograms/mg DNA. The removal of peptides from DNA causes a relevant amplification of DNA template capacity for prokaryotic and eukaryotic RNA polymerases. Gel filtration on Sephadex G-25 or BioGel P4 shows that the chromatin peptide fraction from purified DNA migrates as a sharp peak with an elution volume corresponding to a molecular weight of about 1000. The chromatin peptides are further purified by Sephadex G-10 and high-performance liquid chromatography. Four active fractions are isolated, one of which shows very high inhibition activity on the RNA synthesis in vitro. The amino acid analysis and the inhibition mechanism of the purified peptides are reported.

Native deoxyribonucleic acid transcription by yeast RNA polymerase--P37 complex

The specific activity of yeast RNA polymerases A or B, when complexed with P37 cofactor, compares favorably with that of E. coli RNA polymerase. The stimulation is observed only with double-stranded DNA but does not result from DNase action. The Km for nucleotide substrates and the optimal conditions of transcription are not modified. P37 stimulates RNA synthesis by ternary transcription complexes in the presence of poly(rI) which prevents reinitiations. The RNA chain length, estimated by 5' end labeling or sedimentation, is increased in the presence of P37. On the other hand, the trinucleotide synthesis, which reflects the chain initiation reaction, is not affected. Therefore, the cofactor appears to act at the elongation step of RNA synthesis.

DNA-dependent RNA polymerases from Drosophila melanogaster adults: isolation and partial characterization

In preparation for the isolation and biochemical characterization of putative RNA polymerase mutants, DNA-dependent RNA polymerases of Drosophila melanogaster adults were isolated and partially characterized. Approximately 70% of the female adult RNA polymerase is located in ovaries. Multiple forms of ovarian RNA polymerases I and II are separable by DEAE-Sephadex chromatography. The two forms of RNA polymerase II differ in ammonium sulfate optima. RNA polymerase IIA is more active with double-stranded DNA as template, whereas RNA polymerase IIB transcribes single-stranded DNA most efficiently. Rechromatography of RNA polymerase IIA on DEAE-Sephadex results in the loss of ability of this form to transcribed double-stranded DNA most efficiently. Ovariectomized carcasses have two forms of RNA polymerase I and one form of RNA polymerase II and each transcribes single-stranded DNA most efficiently. As judged by gel filtration chromatography, female adult extracts have forms of RNA polymerase II that differ in molecular weight and template preference.

Incorporation of ribonucleic acid in vitro into dense ribonucleoprotein-like materials by isolated rat liver nuclei

A cell-free system of isolated rat liver nuclei is described which permits an active incorporation of newly synthesized RNA into 'dense' ribonucleoprotein-like materials. The reaction is stimulated with increasing amounts of cytosol protein isolated from rat liver. This indicates that cytosol protein plays an important role in the formation of such material.

Effect of non-histone chromosomal proteins on transcription in vitro in sea-urchin

Non-histone chromosomal proteins prepared from chromosomal material of the sea-urchin Paracentrotus lividus affect RNA synthesis in vitro. 1. The extent of transcription can be radically changed from inhibition to stimulation, depending on the DNA/non-histone chromosomal proteins ratio. 2. A correlation exists between stage of development and influence on transcription. 3. Non-histone chromosomal proteins exert their action by intervening directly on some initiation step of RNA synthesis, as shown by the numbers of initiation events that take place in their presence or absence. 4. Stimulatory activity is observed only in restrictive conditions of ionic strength and temperature. These observations are in agreement with models that predict for non-histone chromosomal proteins a regulatory role on the transcription process exerted through a modulation of promoter availability.

The influence of brain cytosol on RNA synthesis and RNA products of isolated mouse brain nuclei

The incubation of isolated nuclei obtained from 10-day-old mouse brain in the presence of brain cell cytosol resulted in an increase in the synthesis of RNA. Under conditions of saturating concentrations of nucleoside triphosphates, the influence of cytosol could not be duplicated by the addition of cyclic nucleotides. The stimulatory activity of cytosol on brain nuclear RNA synthesis could not be attributed to either alterations in the permeability of the nuclear envelope or an increased uptake of radioactively-labeled precursors. Sucrose gradient analysis demonstrated that the RNA products synthesized by nuclei isolated from 10-day-old and adult mouse brain were of a relatively low molecular weight. However, the addition of cytosol resulted in a significant increase in the size of the RNA transcripts. In contrast to the observations with 10-day-old and adult brain nuclei, the RNA from 2-day-old mouse brain nuclei was larger in size and relatively unaffected by the presence of cytosol. Although cytosol caused an increase in the amounts of poly[A]-RNA in nuclei of 2-day-old and adult animals, no comparable effect could be measured in nuclei from 10-day-old brain tissue.

Functional modification of liver form-B RNA polymerase activity by a protein fraction from rats accustomed to controlled feeding schedules

A protein fraction extracted from the liver of rats accustomed to eating during the first 8 h of a daily 12 h dark period is able to increase homologous form-B RNA polymerase activity. When the protein factor is added to RNA polymerase extracted at the end of the daily fasted period (0.9:OOh) the sensitivity of enzyme to ionic strength is modified, and resembles that of the enzyme extracted during the eating period (15:00 h) either using liver deproteinized DNA or chromatin as template. The chromatin-bound RNA polymerase activity is also modified in the presence of the factor, showing a modification of enzyme sensitivity to ionic strength similar to the one induced by food intake.

Characterization of a protein factor stimulating RNA synthesis by DNA-dependent RNA polymerase II from plant cell cultures

During purification of DNA-dependent RNA polymerase II (or B) from cell cultures of parsley a protein fraction was separated by phosphocellulose chromatography which enhanced RNA synthesis in the presence of native homologous DNA. This 'stimulatory factor' was characterized in respect to some effects on the reaction catalyzed by RNA polymerase II. In the presence of the factor the metal ion requirements as well as the ionic strength for optimal RNA synthesis were markedly changed; addition of the factor to RNA polymerase II purified by cellulose chromatography restored those enzyme properties which had apparently changed upon this purification step. The chain length of the RNA product synthesized is favouring the view that the factor acts mainly by stabilizing the elongation step during transcription. The stimulatory factor was further purified by several steps of column chromatography. As derived from the results of gel electrophoresis under denaturing conditions the factor consists of several small polypeptides. Those of Mr = 26000, 25000 and 14000 apparently have counterparts among the smaller subunits of highly purified RNA polymerase II from parsley cells. Another polypeptide of the factor, with Mr = 30000, was only found in those preparations of RNA polymerase II which had not been subjected to phosphocellulose chromatography.

On the initiation of mammalian RNA polymerase at single-strand breaks in DNA

Mammalian RNA polymerase B is able to initiate at single-strand breaks in the DNA template. A 3'-OH end at a nick is required for initiation whereas the 5'-end may be either -- OH or phosphate. The 3'-OH group does not function as a primer. An appreciable part of the newly synthesized RNA started at a nick remains associated with the DNA in hydrid form. Initiation of exogeneous RNA polymerase B on chromatin exhibits similar requirements.

Evidence for the presence in calf thymus of a peptidic factor controlling DNA transcription in vitro

A thymic factor causes a strong inhibition of the DNA-directed RNA polymerase reaction in vitro. The active factor was isolated from aqueous ultrafiltered thymus extracts and purified by means of chromatography on DEAE-cellulose and then on Dowex 50 WX2. The purified thymic factor was characterized as a peptide of low molecular weight (less than 5000). The biological activity of the thymic factor cannot be attributed to the presence of a nuclease or of a histone fragment. The RNA synthesis is controlled by this factor by means of electrostatic interactions between the peptide compound and DNA. Inhibitory activity on RNA synthesis was absent from kidney extracts.

Nucleolar RNA synthesis in the liver of partially hepatectomized and cortisol-treated rats

RNA synthesis by isolated nucleoli from rat liver is significantly enhanced 12--14 h after partial hepatectomy and 4 h after cortisol administration. The increased RNA synthetic capactiy is demonstrable also in the respective high salt nucleolar extracts and in Biogel A-1.5 filtration fractions of the nucleolar extracts. DNA saturation experiments using nucleoli and Biogel fractions from control and treated animals as RNA polymerase source, have demonstrated, that independent of the extent of RNA synthesis, saturation of transcription is reached at the same concentration of exogenous template. We conclude that the activity and not the amount of nucleolar RNA polymerase is increased as a result of partial hepatectomy or cortisol administration. Parallel to the effects on RNA polymerase, the activity, of RNA-degrading enzymes present in nucleoli is also enhanced by the same treatment.

DNA-dependent RNA polymerases I and II from kidney. Effect of polyamines on the in vitro transcription of DNA and chromatin

DNA-dependent RNA polymerases I and II were purified from pig kidney nuclei by chromatography on DEAE-Sephadex and phosphocellulose. When nonlimiting amounts of double-stranded DNA were used as the template, the in vitro transcription was markedly stimulated by spermidine and spermine. Maximal stimulation of RNA polymerase I occurred at 2-5 mM spermidine and 0.5-2 mM spermine, whereas optimal polyamine concentrations for RNA polymerase II were 5-10 and 1-5 mM for spermidine and spermine, respectively. DNA transcription by polymerase II was stimulated to a greater extent than that of polymerase I. Higher spermine (5-10 mM) concentrations were strong inhibitors of both polymerases under these conditions. The apparent Km of RNA polymerases I and II for UTP was unchanged at optimal polyamine concentration; under the same conditions the maximal reaction velocity was increased two- to three-fold and was essentially due to an increase in the rate of chain elongation. Thus, in a typical experiment the average chain length as determined by the UMP/uridine ratio increased from 570 to 1330 and the chain elongation rate increased from 0.64 to 1.44 nucleotides times sec-1 in the presence of spermine. When limiting quantities of native DNA were employed as the template, both RNA polymerases I and II were inhibited by 1-2 mM spermine. Kidney chromatin could be transcribed by homologous RNA polymerases with an efficiency ranging from 2 to 10% of that with native DNA. When chromatin was used in nonlimiting amounts instead of DNA, RNA polymerase II activity was again stimulated about two-fold at 2 mM spermine. Under these conditions, RNA polymerase I activity was inhibited by spermine. The inhibition of RNA synthesis in vitro at limiting quantities of templates (DNA or chromatin) could be overcome by preincubation of the enzyme with templates before polyamines were added. This inhibition thus appears to be due to a block in the initiation of RNA chains. Similar inhibition of transcription by RNA polymerase II was also observed with limiting quantities of chromatin as the template.

Ribonucleic acid synthesis in isolated rat liver nuclei under conditions of ribonucleic acid processing and transport

A cell-free system is described which permits a significant and prolonged synthesis of RNA in isolated rat liver nuclei, under conditions previously demonstrated to support normal nuclear processing and transport of both rRNA and mRNA. The system contains cytosol but not (NH4)2SO4 or other non-physiological components. Evidence is presented for cytosol factors which stimulate ribosomal, and to a lesser degree, non-ribosomal RNA synthesis.

Activation and inactivation of genes determining hemoglobin types.20s

Globin gene switching in sheep and goats has been used as a model system for examining gene expression in differentiating red blood cells. Sheep and goats switch from the synthesis of hemoglobin A to hemoglobin C in response to erythropoietin. The regulatory mechanism producing this switch in hemoglobin types could occur at the cellular, nuclear, or cytoplasmic level. Evidence is presented which suggests that regulation is occurring, in fact, at the nuclear level. Sheep and goat erythroid colonies have been grown in plasma clot culture in order to study the synthesis of individual globin chains. Erythropoietin is required for colony formation. The switch from hemoglobin A to hemoglobin C synthesis requires not only colony formation but also a higher concentration of erythropoietin than is required just for the production of colonies. A cell-free transcriptional system using bone marrow chromatin and mammalian DNA-dependent RNA polymerase has been developed in order to examine the nuclear control mechanisms in more detail.

Distribution of murine type B and type C viral nucleic acid sequences in template active and template inactive chromatin

Template active chromatin and template inactive chromatin have been fractionated from mouse cells infected with the Moloney strain of murine leukemia virus. In vivo the cells produce abundant Rna homologous to Moloney leukemia virus, but do not produce either globin mRNA or RNA homologous to type B mouse mammary tumor virus. The DNA extracted from the template active chromatin or template inactive chromatin contained equal amounts of sequences homologous to Moloney type C virus, to type B virus, or to globin mRNA. The results are discussed with regard to the in vivo structure of chromatin and the difficulties in fractionating chromatin in vitro.

On the DNA polymerase III of mouse myeloma: partial purification and characterization

A high molecular weight membrane-bound DNA polymerase from the mouse myeloma, MOPC-104E, has been purified extensively, and characterized with regard to physical and reaction properties. This enzyme, which is readily distinguishable from other myeloma enzymes that are analogous to the recognized forms of cellular DNA polymerase, is ddesignated DNA polymerase III. DNA polymerase III activity in whole homogenates from MOPC-104E was solubilized and then prurifed using a series of ion-exchange chromatographic procedures followed by DNA-cellulose chromatography and glycerol gradient centrifugation; the enzyme activity as measured with poly(rA)-(dT)12-18 as template-primer and Mn2+ as divalent cation, was purified as much as 18,000-fold. In the final stages of the pruification, DNA polymerase III possessed no detectable RNA polymerase activity, nucleoside diphosphokinase activity, or nucease activity toward DNA or single- and double-stranded RNA...

Modification of the template capacity of liver chromatin for form-B ribonucleic acid polymerase by food intake in rats under controlled feeding schedules

Nuclei from liver of rats accustomed to eating during the first 8h of a daily 12h dark period demonstrate an increased capacity to synthesize RNA 6H after the beginning of the feeding period. 2. This increase is accompanied by a higher yield of extractable form-B DNA-dependent RNA polymerase activity. 3. The endogenous RNA polymerase activity associated with nuclear chromatin is also stimulated by food intake. Both purified and chromatin-associated form-B enzyme activities exhibit different ionic strength requirements after food intake. 4. The sensitivity of exogenous (added) form-B-enzyme to changes in ionic strength changes after feeding when chromatin is used as template. 5. Chromatin extracted from the liver of fed rats is a better template for form-B-enzyme than chromatin extracted from starved rats.