Effects of estrogen on gene expression in the chick oviduct. IV. Initiation of RNA synthesis on DNA and chromatin

Novel CRE-binding proteins of 11-16 kDa bind to the LDH A-gene CRE in a sequence specific and hepatocyte-growth dependent manner in partially hepatectomized rat liver

We examined cAMP response element (CRE)-binding proteins involved in lactate dehydrogenase A (LDHA)-gene transcription in rat liver after partial hepatectomy. Gel retardation and Southwestern blot assays showed that the CRE-binding activity of the 11-16 kDa novel proteins increased in accordance with increases in LDH A-mRNA in regenerating liver tissues, whereas that of the 43 kDa CREB did not. Using CRE-oligonucleotide affinity chromatography and reverse-phase HPLC, we purified four CRE-binding proteins of 11.2, 15.2, 15.8, and 16.3 kDa. N-terminal amino acid sequences of 15.2 and 16.3 kDa proteins revealed a high sequence homology to but were not identical with those of rat histone H2A.1 and H2B, respectively. CRE-bindings of these two proteins were highly specific, while those of histones H2A.1 and H2B were nonspecific as shown by competition-Southwestern blot and DNase I footprinting assays. Taking these data together, we suggest that the novel 11-16 kDa CRE-binding proteins are responsible for the cell growth-dependent inducibility of LDH A-gene transcription during liver regeneration.

The use of competitive affinity chromatography for the isolation of proteins which promote transcription

A method is described for isolating proteins which bind preferentially to specific sequences of DNA and is used to enrich preparations in proteins promoting eukaryotic gene transcription. An ion-exchange fraction which promotes the transcription of the ovalbumin gene in in vitro runoff assays was isolated from the oviducts of diethylstilbesterol-stimulated chicks. This fraction was recirculated between two coupled columns, one containing random sequences of prokaryotic DNA and the other a specific cloned DNA fragment from the 5' region of the ovalbumin gene. Recirculation was performed in the presence of a decreasing salt gradient, after which columns were disconnected and separately eluted. The eluate obtained from the column containing cloned DNA showed a preference for binding to DNA fragments derived from the ovalbumin gene when examined in nitrocellulose filter binding assays. This fraction retained the ability of its precursor to promote gene transcription in a concentration-dependent manner. Active preparations were also examined in assays measuring total RNA synthesis from native DNA templates. Although the fraction isolated from the column of specific DNA had no detectable RNA polymerase activity itself, it enhanced the activity of calf thymus RNA polymerase II. The method presented should find general application in the purification of factors which regulate biological processes by binding to specific sequences of DNA.

Studies on the mechanism of glucocorticoid hormone induced alterations in rat thymic transcription--I. Evidence from reconstituted cross-over transcription assays that sequential increases and decreases in transcription are due to changes in the activity of RNA polymerase II rather than in the activity of chromatin template

In experiments to determine the mechanism of glucocorticoid induced decreases in thymic transcription, adrenalectomized rats were injected with hydrocortisone (50 mg/kg) or vehicle. Thymic nuclei were used to prepare chromatins and soluble nuclear extracts containing RNA polymerase II for cross-over experiments. With calf thymus DNA or rat thymic chromatins as templates limiting RNA polymerase II from rats treated with hydrocortisone 3 h previously had 130% of the [3H]UMP incorporating activity of RNA polymerase II from control vehicle treated rats. In contrast, limiting RNA polymerase II from rats treated with hydrocortisone 12 h previously had 40-50% of the [3H]UMP incorporating activity of RNA polymerase II from controls. When limiting calf thymus DNA or rat thymic chromatins were used in 12 h cross-over experiments. Individual RNA polymerases II produced equal [3H]UMP incorporations, but RNA polymerase II activity from hydrocortisone treated rats was again only 50% of control values. Thus with template saturation, RNA polymerase II from hydrocortisone treated rats could not transcribe rat thymic chromatin templates to the level achieved by RNA polymerase II from control rats. This suggests that the activity, rather than the amount, of RNA polymerase II from hydrocortisone treated rats is reduced. Double reciprocal plots of [3H]UMP incorporation on rat chromatins with increasing concentrations of RNA polymerases II were made at 12 h. The apparent Km for RNA polymerase II from animals treated with hydrocortisone was identical to that of RNA polymerase II from controls, but the Vmax of RNA polymerase II from hydrocortisone treated animals was reduced. These data suggest the presence of an inhibitor of transcription or an RNA polymerase II defective in its capacity to initiate and/or elongate RNA transcripts. Further experiments demonstrated that these effects were not due to steroid induced changes in ribonuclease or protease activities.

Ribonucleic acid precursors are associated with the chick oviduct nuclear matrix

Nuclear matrix was prepared by sequential treatment of oviduct nuclei with Triton X-100, DNase I, and 2 M NaCl. Published procedures were modified such that as many steps as possible were performed at -20 degrees C to minimize endogenous ribonuclease activity. Examination of electron micrographs confirmed the isolation of intact nuclear matrix structures. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the proteins in these structures showed an absence of histones and an enrichment of certain nonhistone proteins. RNA was isolated from the nuclear matrix preparations and subjected to denaturing gel electrophoresis. Gels were analyzed by ethidium bromide staining and by hybridization of Northern blots to cloned DNA probes for ovalbumin, ovomucoid, 5.8S ribosomal RNA, and U1 RNA. All of the precursors to ovalbumin and ovomucoid mRNAs (including various splicing intermediates) and all of the precursors to ribosomal RNA were associated exclusively with the nuclear matrix fraction. By contrast, mature ovalbumin and ovomucoid mRNAs were distributed between matrix and nonmatrix fractions. These observations were further supported by quantitative hybridization analysis of the RNA in nuclear and matrix fractions. It was found that less than 50% of the mature message of intact nuclei was recovered in the matrix, while most significantly, over 95% of the mRNA precursors remained associated with the matrix. Finally, mature ribosomal RNAs and virtually all of the small nuclear RNAs (including U1 RNA) were also distributed between matrix and nonmatrix fractions. Our results suggest that all precursor RNAs (be they precursors to mRNA or rRNA) are exclusively associated with the nuclear matrix and support the notion that the nuclear matrix may be the structural site for RNA processing within the nuclei of eucaryotic cells.

Alterations in ribonucleic acid synthesis by chromium (III)

The effect of Cr(III) on in vitro RNA synthesis directed by DNA and chromatin isolated from mouse liver was investigated in comparison with other inorganic metals. At 1 mM, CrCl3 significantly stimulated RNA synthesis when incubated with DNA or chromatin prior to the addition of Escherichia coli RNA polymerase, while other metals inhibited it. This stimulation by Cr(III) was caused even at 1 muM CrCl3 on either DNA- or chromatin- directed RNA synthesis. The Cr(III)-complexes of DNA and chromatin also showed significantly enhanced template activities. On the other hand, when RNA polymerase was preincubated with Cr(III), a remarkable inhibition was observed in RNA synthesis directed by both DNA and chromatin. In isolated mouse liver nuclei with endogenous RNA polymerases, Cr(III) stimulated Mg2+-activated RNA synthesis but not Mn2r-(NH4)2SO4-activated synthesis. These results suggest that Cr(III) may alter or regulate gene expressions in mammals.

Problems associated with dose response in steroid-hormone activation of structural genes

A typical target cell for a sex steroid hormone contains 10 000--20 000 specific high-affinity receptors for that hormone. However full physiological responses can be achieved with only 2000 of these receptors involved in hormone--receptor complex interaction with the nucleus. The number of nuclear acceptor sites that must be filled before responses occur maybe even less. This implies that multiple occupation of nuclear acceptor sites by hormone--receptor may occur permitting co-operative induction of transcription of selected genes. The numbers of sites of initiation of RNA synthesis seem excessively high (about 70 000 per cell). Although this may be an artifact of the isolation procedures the proportion of initiation sites under hormonal control (equivalent to about 30 000 per cell) is still large. The numbers of mRNA species under hormonal control varies greatly depending on the particular hormone and target tissue. The extent to which these different observations can be incorporated into a unifying theory is discussed.

Chromatin-associated RNA: differential extraction and characterization

Mammalian cells in different states of cytodifferentiation exhibited different RNA-synthesizing and processing patterns that could be used as markers for phenotypic variability. Inherent in these patterns was an RNA class which was differentially extracted from the cellular homogenate by elevating the temperature and pH of the buffer used in the phenol procedure. This class of RNA was initially designated fraction B (chromatin-associated RNA). In the characterization of fraction B, human myeloma cells labeled for 3 and 24 h were fractionated into subcytoplasmic and subnuclear components and the [3H]-RNA was differentially extracted. After 3 and 24 h labeling 84% and 73%, respectively, of the labeled RNA in the chromatin was extracted in fraction B. Only 10-20% of the polysomal RNA was extracted in fraction B with little enrichment in poly(A) RNA. These and other observations suggested that fraction B was a subpopulation of heterogeneous nuclear RNA which was tightly bound to the chromatin complex.

Factors influencing association of glucocorticoid receptor-steroid complexes with nuclei, chromatin, and DNA: interpretation of binding data

Attempts to reconstruct, in a test tube, the steroid-hormone system of a responsive cell are fraught with enumerable difficulties. In this chapter I have attempted to point out some of the factors that affect receptor-steroid complexes and their interactions with acceptors. In most cases there is a quantitative influence of these factors on the level of steroid complex binding to acceptors. In some cases, selected experimental designs that neglect these factors and methods of presenting the observed data may lead to artifactual conclusions. Several of these problems should disappear when the prospect of pure receptor-steroid complexes [127, 147, 150, 181, 247, 248] becomes a common occurrence. Nevertheless much has already been learned about the interactions of complexes with acceptors, which in turn have been used to help formulate models of steroid-hormone action.

Effect of estrogen on gene expression in the chick oviduct. In vitro transcription of the ovalbumin gene

Problems involved in using the Hg-nucleotide technique for in vitro chromatin transcription are 2-fold. First, Escherichia coli RNA polymerase can utilize endogenous RNA as template and synthesize complementary sequences which remain base-paired to the template, thereby allowing it to bind to the SH-Sepharose column and copurify with the newly synthesized Hg-RNA. Second, non-mercurated endogenous RNA can bind to the SH-Sepharose through aggregation with Hg-RNA and thus be retained in the final RNA preparation. These two problems associated with the Hg-nucleotide technique can be minimized by modifying the conditions for RNA synthesis and SH-Sepharose chromatography. Using the modified procedure the Hg-nucleotide and SH-Sepharose technique can remove more than 90% of endogenous RNA contaminants. In order to directly demonstrate that the mRNAov sequences detected in vitro result from de novo transcription of oviduct chromatin, experiments were carried out which show that the hybridizable RNA sequences contain the Hg element and that the synthesis of these RNA sequences is sensitive to low concentrations of actinomycin D. These combined results strongly suggest that the majority of mRNAov sequences detected by hybridization to cDNAov is indeed due to DNA-dependent RNA synthesis by E. coli RNA polymerase and not due to an artifact of endogenous RNA contamination. This observation was further supported by data obtained using a filter hybridization method which measures directly the mRNAov sequences present in [3H]RNA synthesized from chromatin. The 3H-labeled ovalbumin messenger RNA was assayed by hybridization to cloned pOV230 DNA containing the ovalbumin structural gene sequence. With this modified Hg-nucleotide-SH-Sepharose technique and filter hybridization technique, we have restudied the in vitro transcription of the ovalbumin gene from chromatins isolated at different stages of hormone-induced oviduct development. The results are in agreement with our previous findings which suggest that the primary regulation of ovalbumin synthesis by steroid hormones occurs at the transcriptional level.

Transcription of structural and intervening sequences in the ovalbumin gene and identification of potential ovalbumin mRNA precursors

Structural sequences that are extensively separated by nonstructural intervening sequences in the natural ovalbumin gene are coordinately expressed in target and nontarget tissue. The intervening sequences, which consist of unique sequences in the chick genome, are transcribed in their entirety. The amount of nuclear RNA corresponding to these sequences, however, is approximately 10 times less than that observed for structural sequences. The accumulation of RNA corresponding to structural and intervening sequences during acute estrogen stimulation suggests either that there are different rates of transcription for these regions of the ovalbumin gene or that RNA sequences corresponding to the intervening sequences are preferentially processed and degraded. Comparison of the in vitro expression of portions of the ovalbumin gene in nuclei isolated from chronically stimulated oviducts indicates that both structural and intervening sequences are preferentially transcribed in vitro at rates approximately 500 times greater than expected for random transcription of the haploid chick genome. In addition, electrophoresis of oviduct nuclear RNA on agarose gels containing methylmercury hydroxide reveals multiple species of RNA that are from 1.3 to over 4 times larger than ovalbumin mRNA and hybridize to both structural and intervening sequences of the ovalbumin gene. These results are consistent with transcription of the entire ovalbumin gene into a large precursor molecule followed by excision of the intervening sequences and appropriate ligation of the structural sequences to form the mature mRNA.

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.

Progesterone receptors of chick oviduct

The chick oviduct progesterone receptor has been purified to homogeneity by affinity chromatography and its molecular action studied in vitro. The native receptor is a 200,000 MW dimer of two dissimilar 4S subunits with different intranuclear function. The receptors directly regulate RNA chain initiation sites in oviduct chromatin by interactions involving target tissue nuclear acceptor sites. There is a 1:1 correspondence between receptor "acceptor" sites and RNA sites. Only the dimer form of the receptor is active in vitro on chromatin templates. The study suggests a novel model for hormone action which can be tested directly in this system.

Lutropin stimulation of RNA synthesis in corpus luteum chromatin

Lutropin and human choriogonadotropin stimulated the endogenous chromatin-associated polymerase activity in purified chromatin prepared from nuclei of bovine corpus luteum. Chromatin was incubated in two different buffer systems: one that mainly supports the activity of polymerase I, another that supports the activity of polymerase II and is largely alpha-amanitin sensitive. The hormones lutropin and chorigonadotropin stimulated an increase in the rate of incorporation of [14C]ATP or [14C]UTP into RNA in both buffer systems. Follitropin, prolactin and beta-corticotropin had no stimulatory effect. Neither the alpha nor beta subunit of lutropin stimulated RNA synthesis. When premixed, the subunits rapidly formed the active molecule. A maximum response to RNA synthesis was achieved by a 10(-9) M concentration of human choriogonadotropin. Considerable activity was obtained at 10(-11) M human choriogonadotropin. There was no lutropin stimulation to RNA synthesis using calf thymus DNA and Escherichia coli RNA polymerase.

Release of template restriction in chromatin by nuclear 4.5s RNA

The stimulatory mechanism of RNA synthesis of calf-thymus chromatin by nuclear 4.5 S RNA from the homologous tissue was investigated by using exogenously added Escherichia coli RNA polymerase. The RNA synthesis was initiated at low concentration of salt, and then the chain elongation was achieved at high concentration of ammonium sulfate in the presence of polyvinyl sulfate. Under these conditions the number of binding sites of RNA polymerase on chromatin which were capable of initiating RNA chain was increased by the addition of the 4.5 S RNA. This stimulation was presumed to result from the release of template restriction in chromatin. The polyvinyl salt minimized ribonuclease activity without changing the RNA polymerase activity bound to the template. Neither rearrangement nor release of chromatin proteins affected the amount or size of RNA produced. Preliminary analysis suggested that the molecular species of RNA produced upon the addition of the 4.5 S RNA from various tissues seemed to be heterologous.