Addition Of Nuclear Extract Research Articles

Inhibition of DNA replication by fish oil-treated cytoplasm is counteracted by fish oil-treated nuclear extract.

We have recently noted that cells treated with fish oil and n-3-fatty acids show slower DNA replication rates than cells treated with a control emulsion or corn oil only. However, it is not clearly understood how such an effect is induced. Fish oil and its metabolites are known to have several modulating effects on signal transduction pathways. Alternatively, they may influence DNA replication by interacting directly with nuclear components. To investigate this problem in greater detail, we have studied the kinetics of DNA synthesis in a cell-free system derived from HeLa cells. Nuclei and cytosolic extract were isolated from cells synchronized in early S phase after treatment with control emulsion, corn oil, or fish oil, respectively. The nuclei were reconstituted with cytosolic extract and a reaction mixture containing bromodeoxyuridine (BrdU) triphosphate to label newly synthesized DNA. The rate of DNA synthesis was measured by bivariate DNA/BrdU analysis and flow cytometry. We show that fish oil-treated cytosol inhibits the elongation of newly synthesized DNA by ~80% in control nuclei. However, nuclei treated with fish oil escape this inhibitory effect. We also show that addition of nuclear extract from fish oil-treated cells reverses the inhibitory effect seen in the reconstitution system of control nuclei and fish oil-treated cytosol. These results indicate that polyunsaturated fatty acids can modulate DNA synthesis through cytosolic as well as soluble nuclear factors.

Importance of Sp1 consensus motifs in the MYCN promoter

Background.MYCN (N-myc) amplification in neuroblastoma is associated with poor clinical outcome. Factors that regulate MYCN expression have not been elucidated. MYCN is considered a TATA-less promoter, whereas significant promoter activity resides within 160 bp 5′ of the major transcription start site. This region contains two GC-rich motifs and a CT box, regions for potential transcription factor interaction. Methods. To characterize DNA-protein interactions in this region of the MYCN promoter, electrophoretic mobility shift assays, and promoter-reporter were used. Results. A MYCN promoter fragment was incubated with HeLa nuclear extract, with or without competitors. Three major protein/DNA complexes were formed. Formation of 2 complexes could be inhibited by unlabeled Sp1 consensus duplex and by the Sp1 site-specific drug WP631. Purified Sp1 protein produced a complex similar to that formed with HeLa extract. To determine whether these DNA/protein interactions could be blocked in a sequence-specific fashion, a triplex forming oligonucleotide (TFO) was used. This TFO was designed to bind in the major groove of the promoter, covering the CT-box (putative Sp1 binding) motif. When triplex formation was followed by addition of nuclear extract, protein binding was indeed inhibited. Functional significance of this inhibition was tested with pE/Bnmyc-luc, a promoter-reporter plasmid containing the human MYCN promoter driving luciferase expression. Incubation with TFO, but not control oligodeoxynucleotides, completely inhibited luciferase activity. Conclusions. These data suggest that protein binding does occur in regions of the MYCN promoter containing GC and CT box elements and that this interaction is important for MYCN promoter activity. By inference, these data also suggest that the proteins that bind in this region are Sp1 family members. (Surgery 2002;132:232-8.)

Effect of Altered Redox States on Expression and DNA-Binding Activity of Hypoxia-Inducible Factor 1

Hypoxia-inducible factor 1 (HIF-1) is a heterodimeric basic helix-loop-helix (bHLH)-PAS DNA-binding protein tightly regulated by cellular oxygen tension. Cellular redox states are related to hypoxia by changes in the expression of redox regulated genes and the generation of reactive oxygen intermediates. Here, we provide evidence that alteration of cellular redox states by treating cells with H2O2 or dithiothreitol impairs hypoxia signaling mechanisms and the expression of HIF-1α protein in hypoxic cells. In addition, HIF-1 DNA-binding activity in vitro is sensitive to oxidizing reagents diamide and H2O2 and the alkylating agent N-ethylmaleimide. The activity of N-ethylmaleimide-inactivated HIF-1 can be partially restored by addition of nuclear extract from nonhypoxic cells.

The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences.

Steroid hormone receptors are ligand-dependent transcriptional activators that exert their effects by binding as dimers to cis-acting DNA sequences termed hormone response elements. When human progesterone receptor (PR), expressed as a full-length protein in a baculovirus system, was purified to homogeneity, it retained its ability to bind hormonal ligand and to dimerize but exhibited a dramatic loss in DNA binding activity for specific progesterone response elements (PREs). Addition of nuclear extracts from several cellular sources restored DNA binding activity, suggesting that PR requires a ubiquitous accessory protein for efficient interaction with specific DNA sequences. Here we have demonstrated that the high-mobility-group chromatin protein HMG-1, as a highly purified protein, dramatically enhanced binding of purified PR to PREs in gel mobility shift assays. This effect appeared to be highly selective for HMG-1, since a number of other nonspecific proteins failed to enhance PRE binding. Moreover, HMG-1 was effective when added in stoichiometric amounts with receptor, and it was capable of enhancing the DNA binding of both the A and B amino-terminal variants of PR. The presence of HMG-1 measurably increased the binding affinity of purified PR by 10-fold when a synthetic palindromic PRE was the target DNA. The increase in binding affinity for a partial palindromic PRE present in natural target genes was greater than 10-fold. Coimmunoprecipitation assays using anti-PR or anti-HMG-1 antibodies demonstrated that both PR and HMG-1 are present in the enhanced complex with PRE. HMG-1 protein has two conserved DNA binding domains (A and B), which recognize DNA structure rather than specific sequences. The A- or B-box domain expressed and purified from Escherichia coli independently stimulated the binding of PR to PRE, and the B box was able to functionally substitute for HMG-1 in enhancing PR binding. DNA ligase-mediated ring closure assays demonstrated that both the A and B binding domains mediate DNA flexure. It was also demonstrated in competition binding studies that the intact HMG-1 protein binds to tightly curved covalently closed or relaxed DNA sequences in preference to the same sequence in linear form. The finding that enhanced PRE binding was intrinsic to the HMG-1 box, combined with the demonstration that HMG-1 or its DNA binding boxes can flex DNA, suggests that HMG-1 facilitates the binding of PR by inducing a structural change in the target DNA.

The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences.

Steroid hormone receptors are ligand-dependent transcriptional activators that exert their effects by binding as dimers to cis-acting DNA sequences termed hormone response elements. When human progesterone receptor (PR), expressed as a full-length protein in a baculovirus system, was purified to homogeneity, it retained its ability to bind hormonal ligand and to dimerize but exhibited a dramatic loss in DNA binding activity for specific progesterone response elements (PREs). Addition of nuclear extracts from several cellular sources restored DNA binding activity, suggesting that PR requires a ubiquitous accessory protein for efficient interaction with specific DNA sequences. Here we have demonstrated that the high-mobility-group chromatin protein HMG-1, as a highly purified protein, dramatically enhanced binding of purified PR to PREs in gel mobility shift assays. This effect appeared to be highly selective for HMG-1, since a number of other nonspecific proteins failed to enhance PRE binding. Moreover, HMG-1 was effective when added in stoichiometric amounts with receptor, and it was capable of enhancing the DNA binding of both the A and B amino-terminal variants of PR. The presence of HMG-1 measurably increased the binding affinity of purified PR by 10-fold when a synthetic palindromic PRE was the target DNA. The increase in binding affinity for a partial palindromic PRE present in natural target genes was greater than 10-fold. Coimmunoprecipitation assays using anti-PR or anti-HMG-1 antibodies demonstrated that both PR and HMG-1 are present in the enhanced complex with PRE. HMG-1 protein has two conserved DNA binding domains (A and B), which recognize DNA structure rather than specific sequences. The A- or B-box domain expressed and purified from Escherichia coli independently stimulated the binding of PR to PRE, and the B box was able to functionally substitute for HMG-1 in enhancing PR binding. DNA ligase-mediated ring closure assays demonstrated that both the A and B binding domains mediate DNA flexure. It was also demonstrated in competition binding studies that the intact HMG-1 protein binds to tightly curved covalently closed or relaxed DNA sequences in preference to the same sequence in linear form. The finding that enhanced PRE binding was intrinsic to the HMG-1 box, combined with the demonstration that HMG-1 or its DNA binding boxes can flex DNA, suggests that HMG-1 facilitates the binding of PR by inducing a structural change in the target DNA.

Regulation of tissue-specific splicing of the calcitonin/calcitonin gene-related peptide gene by RNA-binding proteins.

Transcripts of the rat calcitonin/calcitonin gene-related peptide (CGRP) gene are alternatively spliced in a tissue-specific manner resulting in the production of calcitonin mRNA and peptide in thyroid C cells and CGRP mRNA and peptide in neurons. Transfection studies using calcitonin and chimaeric human beta-globin/calcitonin exon minigene constructs showed that the splice acceptor and exon specific to calcitonin mRNA are spliced much less efficiently in CGRP-producing cells (F9 teratocarcinomas) than in cells that preferentially make calcitonin (HeLa cells). In vitro splicing of chimaeric human beta-globin/calcitonin transcripts in HeLa nuclear extracts were inhibited by the addition of nuclear extract from CGRP-favoring cells or tissues such as rat brain. This inhibition was specific as splicing of human beta-globin first intron transcripts was not affected by comparable amounts of rat brain extract. Fractionation of rat brain nuclear extracts allowed the partial purification of two brain-specific polypeptides of apparent molecular mass of 43 and 41 kDa which preferentially bind RNA containing the calcitonin-specific splice acceptor. Since these polypeptides cofractionate with the calcitonin mRNA-specific splicing inhibition activity, we suggest that they may mediate the inhibition of splicing observed in vitro and underlie, in part, the inefficient calcitonin mRNA production observed in CGRP-favoring cells in vivo.

Analysis of promoter-specific repression by triple-helical DNA complexes in a eukaryotic cell-free transcription system

A site-specific triple-helical DNA complex has previously been shown to inhibit DNA binding by eukaryotic transcription factor Sp1. To examine the functional consequences of such inhibition, homopurine target sequences for oligonucleotide-directed triple-helix formation were inserted in various configurations relative to Sp1 transcription activator binding sites, upstream of the TATA element of recombinant eukaryotic promoters. The resulting promoters were tested for activity in the presence or absence of recombinant human Sp1 in a Drosophila in vitro transcription system lacking endogenous Sp1. When triple-helical complexes were assembled on the promoters by incubation with specific oligodeoxyribonucleotides, promoter-specific repression of basal transcription was observed in the absence of Sp1. Transcriptional repression required the preassembly of triple-helical complexes before addition of nuclear extract. The degree of basal repression was a function of the number and proximity of triple-helical complexes relative to the basal promoter complex. Repression did not result from triple-helix-induced template degradation. Addition of recombinant Sp1 did not cause derepression. These results suggest that triple-helical complexes can repress transcription primarily by blocking promoter DNA assembly into initiation complexes rather than by occluding Sp1 binding. One of several plausible mechanisms for triple-helix-induced repression involves changes in DNA flexibility. Evidence in favor of this model is provided by a permutation-dependent gel mobility assay in which formation of site-specific triple-helical complexes is shown to stiffen double-helical DNA.

Identification of exon sequences and an exon binding protein involved in alternative RNA splicing of calcitonin/CGRP.

Transcripts derived from the 6 exon CALC I gene are differentially processed in a tissue-specific fashion to include or exclude a calcitonin-specific exon 4. All cell types which transcribe a second calcitonin/CGRP gene, CALC II, exclude exon 4. Substitution of the first 30 nucleotides of CALC I exon 4 with analogous CALC II sequence was sufficient to prevent recognition of exon 4 in in vitro or in vivo RNA splicing systems. UV crosslinking detected a approximately 66 kDa RNA-binding protein in HeLa nuclear extract which interacted with CALC I proximal exon sequence, but not CALC II or mutant sequences. UV crosslinking of this protein was inhibited by addition of nuclear extract from a cell type which normally causes exclusion of exon 4. These results identify an important regulatory element within exon 4 and support a model in which calcitonin production requires protein interaction with this sequence to facilitate exon recognition.

Oligomeric binding of T3 receptor is required for maximal T3 response.

Receptors in the thyroid-steroid hormone superfamily bind preferentially as dimers to palindromic response elements containing two hexameric half-sites. The 23-base pair rat growth hormone (rGH) T3 response element (T3RE), however, contains three hexameric binding domains, all of which are required for maximal T3 response. We examined the binding of purified T3 receptor alpha (T3R alpha), overexpressed in Escherichia coli, to wild-type and up and down mutations of the rGH T3RE to evaluate whether transcriptional potency correlates with changes in T3R binding. T3R binds to the rGH T3RE as a monomer, dimer, or higher order oligomer. Cooperative T3R dimer binding was demonstrated to two hexameric domains of the rGH T3RE arranged as either direct or inverted repeats. Decreased binding was seen with point mutations in each domain as well as with mutations which altered hexamer orientation and spacing within the site. These results demonstrate that all three hexamers of the rGH T3RE are involved in binding T3R. Occupancy of all three hexamers by T3R in the gel shift assay was observed with functional up mutations of the T3RE, increasing receptor concentration or addition of nuclear extract. The transcriptional response potencies of T3RE up or down mutants in a transient transfection assay correlated closely with T3R binding. These results confirm our earlier hypothesis that all three hexamers of the rGH T3RE bind T3R in a novel binding arrangement and provide a model for the interaction of T3R and other nuclear proteins with the DNA sequences of thyroid hormone-regulated genes.

3,5,3′-Triiodothyronine Receptor Auxiliary Protein (TRAP) Enhances Receptor Binding by Interactions within the Thyroid Hormone Response Element

We have previously demonstrated that binding of in vitro synthesized thyroid hormone receptor (TR) to thyroid hormone response elements (TREs) is enhanced by the addition of nuclear extracts from several different cell types, suggesting that binding of TR is partially dependent on a T3 receptor auxiliary protein (TRAP). We have used the avidin-biotin complex DNA-binding assay to discriminate between regions of TREs that bind TR alone and sites that are influenced by interactions with TRAP. Mutations in the TREs from rat GH and glycoprotein hormone alpha-subunit genes show that a specific DNA sequence is required for TRAP-mediated enhancement of TR binding. Mutations in the B half-site of the rat GH TRE or in similar sequences [(T/A)GGGA] in the alpha-subunit TRE ablate the enhancement of TR binding by TRAP. Furthermore, binding of TR to a natural half-site in the TSH beta-subunit gene (bases -16 to 6), which lacks an additional AGGGA-like sequence, is not enhanced by the addition of TRAP. Binding of TR to TREs was also tested at physiological salt concentrations in the avidin-biotin complex DNA-binding assay. Binding of human TR beta to TREs decreases dramatically at 140 mM KCl compared to binding at 50 mM KCl; however, the addition of TRAP enhances the binding to almost 4-fold of basal binding, suggesting that TRAP may be important for stabilization of TR binding to TREs in the cell.

Nucleoids, a subnuclear system capable of chain elongation

Nucleoids, prepared by salt extraction of non-DNase-digested nuclei, have properties similar, but not identical to those of nuclear matrices which are prepared by salt extraction of DNase-digested nuclei. Nuclear matrices, retained less pulse-labelled DNA, slightly less bound DNA polyesterase α and DNA primase, but had greater in vitro DNA synthesis and in vitro priming. Nucleoids contains larger (110 S) DNA chains than nuclear matrices (30 S). Each type of residual nuclear structure could synthesize 4.5 S Okazaki fragments. When extracted with increasing concentrations of salt, DNase-digested nucleo lost the ability for further elonation of the 4.5 S DNA intermediate after 0.1–0.2 M NaCl, whereas undigested nucleo retained this ability up to 0.9 M NaCl. Chain elongation to 28 S DNA chains could be restored to nucleoids, but not to nuclear matrices, by the addition of nuclear extracts.

Nuclear androgen binding sites in the male rat—II. Seminiferous tubules

A nuclear exchange for androgens in the seminiferous tubules of the mature male rat has been established. The exchange, utilizing technology established on the ventral prostate gland described in the previous paper [7], is based upon LH-20 chromatography of salt extract of purified nuclei. The extract is incubated with [ 3H]methyltrienolone (R 1881) or [ 3H]dihydrotestosterone (DHT) at 4°C for 21 h. Bound is separated from free on a hydroxylapatite microcolumn. Nonspecific binding is determined by use of 100-fold molar excess of the unlabeled ligand. Specific binding in an incubation volume of 2ml containing 1.4 nM [ 3H]R 1881 was 5.78 ± 0.57 fmol/mg DNA (mean ± SE). Specific binding was linearly related to protein concentration. Of the steroids studied, only testosterone competed with DHT in suppression of [ 3H]DHT (one-sixth the affinity). in 4 experiments by saturation analysis, specific binding was saturable and of high affinity: K d = 6.1 ± 0.93 × 10 −10, n = 2.2 ± 0.41 pM (3.75 ± 0.77 fmol/mg DNA). A second receptor of low affinity and high capacity was also observed: K d = 3.28 × 10 −7; n = 161 pM (2.46 pmol/mg DNA). in an analysis of specific binding by ultracentrifugation on an 8–34% glycerol density gradient, 2 radioactively labeled peaks were observed, one at 5.6 S, completely suppressed by 100-fold molar excess of unlabeled steroid, and a second larger peak at 3 S, only partially suppressed. The possibility that marginal binding was due to proteolysis could not be confirmed: (1) Addition of nuclear extract from seminiferous tubules to nuclear extract from the ventral prostate enhanced specific binding in the latter; (2) A 4-h delay in processing of seminiferous tubules did not decrease specific binding; (3) A protease inhibitor (PMSF) did not enhance binding. However, sonication of the testes, retaining only late spermatids and spermatozoa, triple specific binding (16.2 ± 0.8 fmol/mg DNA). These results confirm our previous reports in which we observed by radioimmunologic analysis the presence of androgen receptors in seminiferous tubules, and in late spermatids and spermatozoa. It is suggested that the sonicated testis is an ideal model in which to study the role of the androgen receptor in the maintenance of spermatogenesis.