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Results for “Poly(A) selection”

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PubMed1977

Messenger RNA for renal phosphoenolpyruvate carboxykinase (GTP). Its translation in a heterologous cell-free system and its regulation by glucocorticoids and by changes in acid-base balance.

A translational assay was used to measure the level of mRNA coding for phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) in the rat kidney in various conditions in which the enzyme is induced. RNA extracted from whole kidneys was chromatographed on oligo(dT)-cellulose to select poly(A)-containing RNA. This crude mRNA preparation was able to stimulate amino acid incorporation into protein in a cell-free system containing an extract of wheat germ. Phosphoenolpyruvate carboxykinase could be detected among the polypeptides synthesized and quantitated by immunoprecipitation with a monospecific antibody followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The amount of enzyme synthesized was proportional to the quantity of RNA added. The level of mRNA coding for phosphoenolpyruvate carboxykinase is increased 3-fold 6 h after triamcinolone injection. Translatable enzyme mRNA also increases 3-fold within 6 h of the onset of metabolic acidosis caused by an ammonium chloride load. In both cases, the increase in functional mRNA is commensurate with the stimulation of enzyme synthesis measured in vivo. Glucocorticoid administration and acidosis cause additive increases in the level of translatable phosphoenolpyruvate carboxykinase mRNA. The inductive effect of acidosis is preserved in the absence of the adrenals, hypophysis, thyroid, and parathyroids.

Acid-Base Equilibrium↗
PubMed1998

Developmental regulation of elongation factor-1 delta in sea urchin suggests appearance of a mechanism for alternative poly(A) site selection in gastrulae.

Elongation factor-1 delta gene expression was analyzed during sea urchin development. EF-1 delta mRNA is present as a single 2.7-kb transcript in unfertilized eggs and in rapidly dividing cleavage stage embryos. It decreases rapidly 6 h after fertilization and then reappears at the gastrula stage as two transcripts of 2.7 and 2.0 kb. cDNA clones encoding the 2.7- and 2.0-kb transcripts were isolated from a sea urchin embryos library. The two cDNAs originate from alternative poly(A) site selection from a unique precursor. Both cDNAs are terminated by a poly(A) tail and were shown to encode for the same protein identified as EF-1 delta. Thus, EF-1 delta gene expression undergoes developmental regulation in early embryos leading to the presence of two poly(A) forms of the transcript. Since the 2.0-kb polyadenylated form of the EF-1 delta transcript appears at gastrula stage, our results suggest that a mechanism for alternative poly(A) site selection of the EF-1 delta transcript appears during embryonic development.

Amino Acid Sequence↗
PubMed2006

Ion selectivity of a poly(3-pentylmethoxythiophene) LB-layer modified carbon-fiber microelectrode as a consequence of the second order filtering in voltcoulometry.

Ion selective properties of poly(3-pentylmethoxythiophene) Langmuir-Blodgett film modified carbon-fiber microelectrode are described. The study of the electrode behavior indicates that important features occur if two electrochemical methods, one of them being kinetics sensitive, are used. While in case of the typical steady-state voltammetry the electrode remains sensitive to both the cations and anions, the kinetics-sensitive properties of voltcoulometry based on the second-order filtering scheme disable the observation of anions. As a model system a mixture of copper and dopamine ions is used.

Carbon↗
PubMed1989

Sequences upstream of AAUAAA influence poly(A) site selection in a complex transcription unit.

The adenovirus major late transcription unit (MLTU) encodes five colinear mRNA families, L1 through L5, each distinguished by a unique poly(A) site. Site selection is regulated during the course of infection, predominating early at the L1 site and late at the L2 through L5 sites. Two general mechanisms can be invoked to explain predominant usage of the L1 site early in infection. MLTU site selection may proceed in a first-come, first-serve manner whereby the L1 site is used most frequently because it is closest to the promoter. Alternatively, specific sequences flanking the L1 site may control predominant L1 site usage in a position-independent manner. To distinguish between these mechanisms, we constructed deletions in the L1 flanking sequences and inserted the mutated sites into either simple transcription units or mini-MLTUs encoding two poly(A) sites. The pattern of site selection for each construct was then quantitated by S1 nuclease analysis after transfection into 293 cells. The results indicated that L1 sequences upstream of AAUAAA define a novel selector element that can cause predominant L1 site usage at either position of a tandem transcription unit. The element did not significantly affect the stability or nucleocytoplasmic transport of L1 transcripts and was not required for efficient 3'-end processing in simple transcription units. Predominant L1 site usage required physical linkage of the processing signals and was independent of the major late promoter.

Adenoviridae↗
PubMed1998

Alterations in human lymphocyte DNA caused by sulfur mustard can be mitigated by selective inhibitors of poly(ADP-ribose) polymerase.

Changes in genomic DNA caused by exposure to the cytotoxic alkylating agent, 2,2'-dichlorodiethyl sulfide (sulfur mustard; HD), alone or in combination with selective inhibitors of poly(ADP-ribose) polymerase (PARP), were analyzed as a function of HD concentration and post-exposure time. Preparations of human peripheral blood lymphocytes were exposed to HD (1x10(-8) M-1x10(-3) M), and incubated at 37 degrees C for 0-24 h. Total genomic DNA was extracted from these cells and compared with DNA from control cells of the same donor using agarose gel electrophoresis. The effects of HD on genomic DNA depended on the HD concentration and the length of the post-exposure time interval. DNA fragmentation was detected as early as 2 h after exposure to 3x10(-4) M HD, or at 24 h after exposure to 6x10(-6) M HD. The qualitative DNA pattern, as well as the extent of DNA fragmentation, changed with post-exposure time. Exposure to HD caused a time-dependent shift in the DNA cleavage pattern from an oligonucleosome-sized 'DNA ladder' characteristic of apoptotic cell death, to a 'broad band' pattern characteristic of necrotic cell death. DNA fragmentation was not observed if cells were killed with heat or with Lewisite. Treatment of cells with selective PARP inhibitors consistently altered the DNA fragmentation caused by HD exposure. The inhibitors arrested DNA fragmentation at the DNA ladder stage. This effect only was observed if the PARP inhibitors were applied within 8 h of HD exposure. We conclude that early inhibition of PARP activity can induce a switch in the mechanism of cell death caused by HD. Such a switch may be useful therapeutically to convert a lytic, pro-inflammatory cell death that includes the disintegration of dying cells (necrosis), into a slower, programmed cell death that includes absorption of dying cells (apoptosis).

Apoptosis↗
PubMed1995

Poly(A) site selection in the HIV-1 provirus: inhibition of promoter-proximal polyadenylation by the downstream major splice donor site.

In common with all retroviruses, the human immunodeficiency virus type 1 (HIV-1) contains duplicated long terminal repeat (LTR) sequences flanking the proviral genome. These LTRs contain identical poly(A) signals, which are both transcribed into RNA. Therefore, to allow efficient viral expression, a mechanism must exist to either restrict promoter-proximal poly(A) site use or enhance the activity of the promoter-distal poly(A) site. We have examined the use of both poly(A) sites using proviral clones. Mutation of the previously defined upstream activatory sequences of the 3' LTR poly(A) site decreases the efficiency of polyadenylation when placed in competition with an efficient downstream processing signal. However, in the absence of competition, these mutations have no effect on HIV-1 polyadenylation. In addition, the 5' LTR poly(A) site is inactive, whereas a heterologous poly(A) site positioned in its place is utilized efficiently. Furthermore, transcription initiating from the 3' LTR promoter utilizes the 3' LTR poly(A) signal efficiently. Therefore, the main determinant of the differential poly(A) site use appears to be neither proximity to a promoter element in the 5' LTR nor the presence of upstream activating sequences at the 3' LTR. Instead, we show that the major splice donor site that is immediately downstream of the 5' LTR inhibits cleavage and polyadenylation at the promoter-proximal site. The fact that this poly(A) site is active in a proviral clone when the major splice donor site is mutated suggests that the selective use of poly(A) signals in HIV-1 is mediated by a direct inhibition of the HIV-1 poly(A) site by downstream splicing events or factors involved in splicing.

Base Sequence↗
PubMed1996

Sequences regulating poly(A) site selection within the adenovirus major late transcription unit influence the interaction of constitutive processing factors with the pre-mRNA.

The adenovirus major late transcription unit (MLTU) encodes five families of mRNAs, L1 to L5, each distinguished by a unique poly(A) site. Use of the promoter-proximal L1 poly(A) site predominates during early infection, whereas poly(A) site choice shifts to the promoter-distal sites during late infection. A mini-MLTU containing only the L1 and L3 poly(A) sites has been shown to reproduce this processing switch. In vivo analysis has revealed that sequences extending 5' and 3' of the L1 core poly(A) site are required for efficient processing as well as for regulated expression. By replacement of the L1 core poly(A) site with that of the ground squirrel hepatitis virus poly(A) site, we now demonstrate that the L1 flanking sequences can enhance the processing of a heterologous poly(A). Upon recombination of the chimeric L1-ground squirrel hepatitis virus poly(A) site onto the viral chromosome, the L1 flanking sequences were also found to be sufficient to reproduce the processing switch during the course of viral infection. Subsequent in vitro analysis has shown that the L1 flanking sequences function to enhance the stability of binding of cleavage and polyadenylation specificity factor to the core poly(A) site. The impact of L1 flanking sequences on the binding of cleavage and polyadenylation specificity factor suggests that the regulation of the MLTU poly(A) site selection is mediated by the interaction of constitutive processing factors.

Adenoviruses, Human↗
PubMed2005

Poly(ethylene glycol) micro-patterns as environmentally sensitive template for selective or non-selective adsorption.

Poly(ethylene glycol) (PEG), a hydrophilic and repulsive polymer to non-specific adsorption, was stamped onto carboxylic acid-enriched polymer surfaces using the micro-contact printing technique. The patterns are stabilized via hydrogen bonds. Areas printed with PEG were then shown to be non-adsorbed with fluorescein isothiocyanate (FITC)-labeled dextran, while the poly(methacrylic acid) (PMAA) regions could via hydrogen bonding. Due to this contrast, well defined dextran patterns were obtained. Tuned with pH and temperature, the PEG molecules could be detached from the surfaces, erasing the template. Moreover, ionization of PMAA at higher pH induced an abrupt transition to an extended conformation, weakening the interactions between PMAA and dextran. Not only the dextran patterns lose their spatial selectivity, but also the overall adsorption amount is much lower. The pH sensitivity was in a quite narrow range, i.e. around pH 5. As the hydrogen bonds are also temperature sensitive, the attach points of PEG molecules on the surfaces disappeared at higher temperature. For poly(acrylic acid) (PAA) photografted surfaces, the pH sensitivity was more complicated due to the formation of the compact complexes of PEG and PAA molecules.

Adsorption↗
PubMed1994

Poly(A) site selection in the yeast Ty retroelement requires an upstream region and sequence-specific titratable factor(s) in vitro.

In the Ty retrotransposon of Saccharomyces cerevisiae, as in most retroelements, the polyadenylation site of the 5' long terminal repeat (LTR) is ignored and the one in the 3' LTR is efficiently used. We examine here the contribution to this poly(A) site selection of the region termed 'U3', corresponding to the upstream non-transcribed portion of the 5' LTR. Using an established assay in vitro, we find that 3' processing is accurate and efficient with an RNA substrate corresponding to most of the LTR, whereas none is detectable with a shorter transcript lacking the U3 region, thus explaining why the 5' poly(A) site is ignored in genomic Ty mRNA. When HIS4 coding RNA, representing 'non-specific' sequence, replaces the U3 region, the Ty polyadenylation site is activated to 50% of the wild-type level. Within one specific region (TS1) in U3, 90-95 nt upstream of the poly(A) site, the change of UAGUAU to UCGCAU reduces processing efficiency by half, to the non-specific level provided by other sequences or by a deletion of the TS1 region. Another region (TS2) near the poly(A) site appears to be independently responsible for the remaining half of the processing activity. Alteration of both TS1 and TS2 eliminates processing entirely. In competition assays, excess unlabeled U3, but not its mutated counterparts, reduces the processing of radiolabeled Ty mRNA, suggesting the involvement of some sequence-specific titratable factor(s) in the whole cell extract for U3-specific activation.(ABSTRACT TRUNCATED AT 250 WORDS)

Binding, Competitive↗
PubMed1998

Repression of phosphoenolpyruvate carboxykinase gene activity by insulin is blocked by 3-aminobenzamide but not by PD128763, a selective inhibitor of poly(ADP-ribose) polymerase.

Expression of the phosphoenolpyruvate carboxykinase (PEPCK) gene is induced by 3-aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase. Synthesis of PEPCK mRNA is repressed by insulin, but remains detectable in H4IIE hepatoma cells exposed simultaneously to both 3-aminobenzamide and insulin. This capability of 3-aminobenzamide to block the inhibitory actions of insulin suggests that ADP-ribosylation is required for the regulation of PEPCK gene expression by insulin. Furthermore, neither changes in chromatin condensation nor cell growth status were linked to these events. The inability of 3,4-dihydro-5-methylisoquinolinone (PD128763), a selective inhibitor of poly(ADP-ribose) polymerase, to impede insulin-dependent repression of PEPCK gene expression, however, indicated that 3-aminobenzamide does not operate by inhibiting poly(ADP-ribosyl)ation. The potential involvement of mono(ADP-ribosyl)ation, a process that is also inhibited by 3-aminobenzamide, in the regulation of PEPCK gene activity was then evaluated. Analysis of poly(ADP-ribose) polymerase activity and poly(ADP-ribosyl)ation confirmed that there were no significant changes in response to insulin, while microsomal mono(ADP-ribosyl)transferase activity was elevated approximately fourfold. An increase in protein hydroxylamine-sensitive mono(ADP-ribosyl)ation was observed following insulin treatment. The sensitivity of the mono(ADP-ribosyl)transferase activity to 3-aminobenzamide but not PD128763 makes it plausible that mono(ADP-ribosyl)ation rather than poly(ADP-ribosyl)ation contributes to the regulation of PEPCK gene expression.

ADP Ribose Transferases↗
PubMedDate not supplied

Patterning poly(organophosphazenes) for selective cell adhesion applications.

Five polyphosphazenes with different hydrophilicites were synthesized and screened in vitro. The purpose was to identify unique types of polymeric substrates that distinctly favored or markedly prevented cellular adhesion. The SK-N-BE(2c) human neuroblastoma cell line, utilized for its electrogenic responses, was used to test this differential adhesion. In particular, the objective was to specifically culture this cell line in a highly selective pattern. Each candidate polymer was cast into films and plated with neuroblastoma cells for 3 days. The polyphosphazene materials which showed negative cellular adhesive properties (-CAPs) were poly[bis(trifluoroethoxy)phosphazene] (TFE) and poly[bis(methoxyethoxyethoxy)phosphazene] (MEEP). The polyphosphazenes which showed positive cellular adhesive properties (+CAPs) were poly[(methoxyethoxyethoxy)(1.0)(carboxylatophenoxy)(1.0)phosphazene] (PMCPP), poly[(methoxyethoxyethoxy)(1.0)(cinnamyloxy)(1.0)phosphazene] (PMCP), and poly[(methoxyethoxyethoxy)(1.0)(p-methylphenoxy)(1.0)phosphazene] (PMMP). To test cellular selectivity, films of -CAP and +CAP were copatterned onto glass substrates. The micropatterned films were plated with SK-N-BE(2c) neuroblastoma cells for one week. The results showed that neuroblastoma cells adhere selectively (over 60%) to the +CAP microfeatures. We also showed that multiple properties can be achieved with a single material and that we can use TFE as both a -CAP and an insulation layer and PMCP as a conductive +CAP layer.

Adhesives↗
PubMed1996

Plasticizer-level study of poly(vinyl chloride) ion-selective membranes.

Highly plasticized poly(vinyl chloride) (PVC) membranes (200 per hundred resin [phr]) form the basis of one class of ion-selective electrodes (ISEs). In previous work on the mechanical properties of membranes, the optimal ratio of plasticizer level employed to minimal level required for complete plasticization (phr(exp)/phrmin) was found to be 2.0. The current study was designed to determine whether this ratio is necessary or sufficient for proper ISE function. Dynamic mechanical analysis (DMA) was used to examine the effects of five plasticizers on the dynamic mechanical properties of membranes at three frequencies (110, 11.0, and 1.1 Hz) as a function of temperature (-100 degrees C to +100 degrees C); dioctyl sebacate (DOS), epoxidized propylene glycol dioleate (PGDO), ortho-nitrophenyl octyl ether (o-NPOE), epoxidized soybean oil (ESO), and epoxidized linseed oil (ELO). The glass transition temperature of PVC, which was found to be +77.1 degrees C at 11.0 Hz, was depressed by the addition of 200 phr of each plasticizer from a high of -1.4 degrees C (PGDO at 110 Hz) to a low of -70.2 degrees C (DOS at 1.1 Hz). DMA and electromotive-force (EMF) measurements on membranes plasticized with o-NPOE through a range of phr(exp)/phrmin from 0.5 to 9.3 indicated that a "transition window" occurs between phr(exp)/phrmin of 2.0 and 3.3 in which the membranes change from minimally plasticized polymer films to predictable ion-selective membranes, coinciding with the optimal mechanical properties observed previously. Based on dynamic mechanical properties and EMF response data, the optimal phr(exp)/phrmin++ ratios for membranes as a function of plasticizer were proposed: 0.8 for ESO and ELO, 1.3 for PGDO, 1.7 for DOS, and 3.0 for o-NPOE.

Elasticity↗
PubMed1997

Ribavirin conjugated with lactosaminated poly-L-lysine: selective delivery to the liver and increased antiviral activity in mice with viral hepatitis.

Ribavirin (RIBV) is a useful drug in the treatment of chronic type C hepatitis but displays a toxicity for red blood cells (RBC), which limits its dosage and necessitates withdrawal in some patients. Selective concentration of RIBV in liver should improve therapeutic results. Liver targeting can be achieved by coupling the drug to galactosyl-terminating peptides, which specifically enter hepatocytes. In the present work, we conjugated RIBV to lactosaminated poly-L-lysine (L-Poly(Lys)), a hepatotropic carrier enabling intramuscular (IM) administration of conjugates. The L-Poly(Lys)-RIBV conjugate had a heavy drug load (312-327 microg of RIBV in 1 mg of conjugate) and was very soluble in 0.9% NaCl (200 mg/mL). The conjugate was devoid of acute toxicity in mouse. When incubated with human or mouse blood, it did not release the drug. After IM administration to mice, the conjugate was selectively taken up by the liver, where the drug was released in a pharmacologically active form. This was demonstrated using mice infected with a strain of murine hepatitis virus (MHV) sensitive to RIBV. Coupled RIBV, IM injected, inhibited MHV replication in liver at a daily dose two to three times lower than that of the free drug. In mice IM injected with a conjugate tritiated in the RIBV moiety, the ratios between the levels of radioactivity in liver and RBC were two times higher than in animals injected with free tritiated RIBV. In conclusion, the present results support the possibility that the chemotherapeutic index of RIBV in chronic type C hepatitis can be increased by conjugation with L-Poly(Lys).

Amino Sugars↗
PubMed2004

The therapeutic effects of PJ34 [N-(6-oxo-5,6-dihydrophenanthridin-2-yl)-N,N-dimethylacetamide.HCl], a selective inhibitor of poly(ADP-ribose) polymerase, in experimental allergic encephalomyelitis are associated with immunomodulation.

Poly(ADP-ribose) polymerase (PARP) activity has been implicated in the pathogenesis of several central nervous system (CNS) disorders. For example, the presence of extensive poly(ADP)ribosylation in CNS tissues from animals with experimental allergic encephalomyelitis (EAE) indicates that PARP activity may be involved in this inflammatory disease process. Using PJ34 [N-(6-oxo-5,6-dihydrophenanthridin-2-yl)-N, N-dimethylacetamide.HCl], a selective PARP inhibitor, we studied the mechanisms through which PARP activity may contribute to the onset of acute EAE. PLSJL mice immunized with myelin antigens were treated with PJ34, and the effects on the progression of EAE and several other parameters relevant to the disease process were assessed. PJ34 exerted therapeutic effects at the onset of EAE that were associated with reduced CNS inflammation and the maintenance of neurovascular integrity. Expression of genes encoding the intercellular adhesion molecule-1 (ICAM-1) and the inflammatory mediators interferon-gamma, tumor necrosis factor-alpha, and inducible nitric-oxide synthase were decreased in CNS tissues from drug-treated animals. Administration of PJ34 biased the class of myelin basic protein (MBP)-specific antibodies elicited from IgG2a to IgG1 and IgG2b and modulated antigen-specific T-cell reactivity. Therefore, the mode of action of PJ34 at the onset of EAE is likely mediated by a shift in the MBP-specific immune response from a proinflammatory Th1 toward an anti-inflammatory Th2 phenotype.

Adjuvants, Immunologic↗
PubMed1989

Regulation of poly(A) site selection in adenovirus.

We have investigated the mechanisms involved in the early-to-late RNA-processing switch which regulates the mRNA species generated from the adenovirus major late transcription unit (MLTU). In particular, polyadenylation choice mechanisms were characterized by using a reconstructed adenovirus E1A gene as a site for insertion of MLTU poly(A) regulation signals (L1 and L3). Adenovirus constructs containing the variant poly(A) recognition elements were used to compare E1A poly(A) signal utilization with wild-type MLTU (L1 to L5) utilization. In both early and late stages of infection, either polyadenylation site (L1 or L3) is capable of being utilized when presented as the only operational poly(A) site. In an early infection, a virus which contains multiple elements presented in tandem (L13) uses the first poly(A) site, L1, preferentially (ratio of L1 to L3, 8:1) in both E1A and MLTU loci. Transcription termination is not involved in restricting the utilization of the downstream L3 site. In a late infection, when each of the five MLTU poly(A) sites is used, a switch also occurs for the E1AL13 construct, with utilization of both the L1 and L3 poly(A) sites. The switch from early to late was not the result of altered processing factors in the late infection, as demonstrated by superinfecting the E1AL13 construct into cells which had already entered a late stage of infection. The superinfecting virus gave an L1-only phenotype; therefore, a cis mechanism is involved in adenovirus poly(A) regulation.

Adenoviridae↗
PubMed1997

Alternative poly(A) site selection in complex transcription units: means to an end?

Many genes have been described and characterized which result in alternative polyadenylation site use at the 3'-end of their mRNAs based on the cellular environment. In this survey and summary article 95 genes are discussed in which alternative polyadenylation is a consequence of tandem arrays of poly(A) signals within a single 3'-untranslated region. An additional 31 genes are described in which polyadenylation at a promoter-proximal site competes with a splicing reaction to influence expression of multiple mRNAs. Some have a composite internal/terminal exon which can be differentially processed. Others contain alternative 3'-terminal exons, the first of which can be skipped in some cells. In some cases the mRNAs formed from these three classes of genes are differentially processed from the primary transcript during the cell cycle or in a tissue-specific or developmentally specific pattern. Immunoglobulin heavy chain genes have composite exons; regulated production of two different Ig mRNAs has been shown to involve B cell stage-specific changes in trans -acting factors involved in formation of the active polyadenylation complex. Changes in the activity of some of these same factors occur during viral infection and take-over of the cellular machinery, suggesting the potential applicability of at least some aspects of the Ig model. The differential expression of a number of genes that undergo alternative poly(A) site choice or polyadenylation/splicing competition could be regulated at the level of amounts and activities of either generic or tissue-specific polyadenylation factors and/or splicing factors.

Alternative Splicing↗
PubMed2004

Selection of poly-alpha 2,8-sialic acid mimotopes from a random phage peptide library and analysis of their bioactivity.

Poly-alpha 2-8 sialic acid (PSA), attached to the neural cell adhesion molecule, is a permissive determinant for numerous morphogenetic and neural plasticity processes, making it a potential therapeutic target. Here, using a monoclonal antibody specific for PSA, we screened a phage-display library and identified two cyclic nine-amino acid peptides (p1, p2) that are PSA epitope analogues. We evaluated their bioactivity in vitro and in vivo. In culture, micromolar concentrations of the peptides promoted axon growth, defasciculation, and migration of neural progenitors. When injected into developing chicken retina, the peptides modified the trajectory of retinal ganglion cell axons. Moreover, they enhanced migration of grafted neuroblasts in mouse brain. These effects were selective and dependent upon the presence of PSA on transplanted cells. Our results demonstrate the feasibility and therapeutic potential of enhancing PSA biological activity.

Animals↗