Selective alkylation of poly(A) tracts of RNA inside the cell with the derivative of ethyl ester of oligothymidilate bearing 2-chloroethylamino group.
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Alkylating Agents↗
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Results for “Poly(A) selection”
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Maternal PAN2 selectively maintains mRNA Poly(A) tail homeostasis to regulate RNA degradation during oocyte-to-early embryo transition in mice.
In mammals, the precise degradation of maternal mRNAs is essential for oocyte maturation and early embryonic development, as it facilitates the "maternal-to-zygotic transition (MZT)" by eliminating maternal transcripts and enabling zygotic genome activation (ZGA). However, the physiological role of the poly(A)-specific nuclease 2 (PAN2), a deadenylase that initiates cascade degradation of long-tailed transcripts, remains unknown. Here, we generated oocyte-specific Pan2 conditional knockout (cKO) mice to investigate its role. We found that Pan2 cKO females exhibit severe female subfertility despite normal oocyte maturation and ovulation, with embryos arresting at the 2-cell stage. PAIso-seq2 and transcriptome sequencing reveal that PAN2 coordinates maternal mRNA deadenylation and decay. Mechanistically, PAN2 recognizes its substrates through a PAN3-PABPC1 bridging complex, and it preferentially targets transcripts whose poly(A) tails lack guanosine (G) but are enriched for uridine (U). PAN2 deficiency causes poly(A) tail dyshomeostasis, leading to global accumulation of maternal mRNAs, impaired zygotic genome activation, and abnormal protein accumulation in 2-cell embryos. Overexpression of these proteins phenocopies developmental defects. Notably, the PAN2-regulated transcriptome is largely non-overlapping with the LC3B-mediated degradation pathway, highlighting the unique and non-redundant role of PAN2 in maternal mRNA clearance. Our study establishes maternal PAN2 as a critical regulator of poly(A) tail homeostasis, ensuring timely maternal mRNA clearance and proper ZGA, highlighting the stage-specific and tail-composition-dependent functions of the deadenylase cascade during the maternal-to-zygotic transition. These findings offer new perspectives on post-transcriptional regulatory mechanisms in early mammalian embryogenesis.
Deadenylation↗
Selective loss of poly(ADP-ribose) and the 85-kDa fragment of poly(ADP-ribose) polymerase in nucleoli during alkylation-induced apoptosis of HeLa cells.
Alkylation treatment of HeLa cells results in the rapid induction of apoptosis as revealed by DNA laddering and cleavage of poly(ADP-ribose) polymerase (PARP) into the 29-and 85-kDa fragments (Kumari S. R., Mendoza-Alvarez, H. & Alvarez-Gonzalez, R. (1998) Cancer Res. 58, 5075-5078). Here, we performed a time-course analysis of (i) poly(ADP-ribose) synthesis and degradation as well as (ii) the subnuclear localization of PARP and its fragments by using confocal laser scanning immunofluorescence microscopy. PARP was activated within 15 min post-treatment, as revealed by nuclear immunostaining with antibody 10H (recognizing poly(ADP-ribose)). This was followed by a late, time-dependent, progressive decline of 10H signals that coincide with the time of PARP cleavage. Strikingly, nucleolar immunostaining with antibodies 10H and C-II-10 (recognizing the 85-kDa PARP fragment) was lost by 15 min post-treatment, whereas F-I-23 signals (recognizing the 29-kDa fragment) persisted. We hypothesize that the 85-kDa PARP fragment is translocated, along with covalently bound poly(ADP-ribose), from nucleoli to the nucleoplasm, whereas the 29-kDa fragment is retained, because it binds to DNA strand breaks. Our data (i) provide a link between the known time-dependent bifunctional role of PARP in apoptosis and the subcellular localization of PARP fragments and also (ii) add to the evidence for early proteolytic changes in nucleoli during apoptosis.
Alkylation↗
A single point mutation in the yeast TRP4 gene affects efficiency of mRNA 3' end processing and alters selection of the poly(A) site.
The yeast TRP4 mRNA 3' end formation element is a bidirectional element which functions in both orien-tations in an artificial in vivo test system. In this study, the role of 3' end formation was analysed in the context of the entire TRP4 gene. The 3' untranslated region (3'UTR) of TRP4 was altered and changes were analysed for their influence on TRP4 gene expression. The 3'UTR in reverse orientation was fully functional and did not affect TRP4 gene expression. Exchanging the TRP4 3'UTR by the bidirectional ARO4 or the unidirectional GCN4 3' end formation element allowed efficient gene expression. Deletion of the entire TRP4 3'UTR resulted in 70% reduction of TRP4 mRNA and 50% reduced specific Trp4 enzyme activity in comparison to wild-type. A single point mutation within the TRP4 3'UTR caused the same effect on gene expression. This point mutation did not only affect the efficiency of 3' end formation, but also produced new poly(A) sites which were situated upstream of the wild-type poly(A) sites. Therefore this sequence motif in the TRP4 3'UTR acts simultaneously as both an efficiency and positioning element.
3' Untranslated Regions↗
The selective action of poly A:U on the electrophoretic mobility and surface charge of a subpopulation of B cells.
Electrophoretic mobility (E.P.M.) of lymphoid cells has been determined in three species. In chicks, the E.P.M. of bursa cells was 0.47 plus or minus 0.07 and of thymocytes 0.64 plus or minus 0.10 mum/sec/volt/cm. On the basis of the E.P.M. profile of the Ficoll gradient purified lymphocytes from the rat spleen, two populations of cells present in the proportion of 65 and 35% were identifiable. The former had a mobility of 1.06 plus or minus 0.08 and the latter 1.24 plus or minus 0.09. The E.P.M. of lymphocytes prepared from athymic nude mice was 0.86 plus or minus 0.06 with a Gaussian distribution profile. On incubation of these cells with poly adenylate-poly uridylate (poly A:U) for 30 min at 38 degrees C followed by extensive washings, the E.P.M. of thymocytes from the chick and rat as well as the thymus-derived cells in rat spleen remained essentially unchanged. On the other hand, poly A:U increased the E.P.M. of avian bursa cells and of a subpopulation of B cells in rat spleen and of splenocytes from nude mice. The proportion of cells markedly affected by poly A:U was 70 to 83% of the total B cells in these species.
Animals↗
Spectroscopic characterization of poly(amidoamine) dendrimers as selective uptake devices: Phenol blue versus Nile red.
Selectivity of amine-terminated poly(amidoamine) (PAMAM-AT) dendrimers as host molecules for phenol blue and Nile red guests was investigated using absorption and fluorescence spectroscopies. Phenol blue has been known to associate near the core in the PAMAM-AT dendrimers. Nile red has also been shown to associate with this dendrimer family; however, this occurs in the outermost branches. Concentration ratios and generational dependencies were investigated. It was found that phenol blue was sequestered in the PAMAM-AT dendrimers in the presence of the interfering Nile red, and this association appeared to be the same as that of PAMAM-AT with phenol blue alone. As the concentration of Nile red increased relative to the concentration of phenol blue, the desired association of phenol blue became increasingly hindered. While the presence of Nile red did affect association, phenol blue still had considerable association even when Nile red was in ten-fold excess. The association of phenol blue with PAMAM-AT was stable and robust; however, Nile red's association was relatively weak and unstable.
Journal Article↗
Effect of RNA secondary structure on polyadenylation site selection.
Functional polyadenylation [poly(A)] sites consist of two sequence elements, the AAUAAA and G/U box signals, that closely flank the site of mRNA 3'-end formation. In agreement with previous results, random sequence insertions between the AAUAAA and G/U box signals were observed to inhibit poly(A) site function. However, sequence insertions of similar size that were predicted to form RNA stem-loop structures were found to have little effect on the efficiency of polyadenylation and instead induced a 3' shift in the site of polyadenylation that was equal to the length of the inserted stem-loop. The in vivo utilization of a poly(A) site bearing an internal RNA stem-loop structure was inhibited by mutations that destabilized the predicted stem but was restored by compensatory mutations. These results strongly support the hypothesis that the appropriate spacing of the AAUAAA and G/U box signals is critical for poly(A) site function. Sequence insertions that are able to form RNA secondary structures that maintain the correct spacing of these two RNA target sequences are well tolerated, whereas sequence insertions that disturb this spacing inhibit poly(A) site recognition. It is proposed that the effect of sequence insertions on poly(A) site function may be sufficiently predictable to allow the development of an assay for in vivo RNA secondary structure that uses poly(A) site selection as a readout.
Animals↗
Further investigations on a poly(vinyl alcohol)- polyelectrolyte chemically selective optical film.
The ionomer poly(vinylbenzyltrimethylammonium chloride) has been blended with cross-linked poly(vinyl alcohol) to form optically clear composites that can be covalently linked as thin films to oxide surfaces. Films are characterized using spectroscopic ellipsometry with refractive index (n) and extinction coefficient (k) data presented for wavelengths 300 to 1100 nm. A refractive index of 1.54 and average thickness of 709 nm are typical of an air dry film prepared by spin-coating. Dynamic in situ ellipsometry results for films exposed to 0.1 M KNO(3) and 1.0 mM Fe(CN)(6)(-3) are presented. Upon initial exposure to 0.1 M KNO(3), an air dry film expands by about 160% and stabilizes in size and refractive index at about 18 hours. Ion exchange of film cationic groups with ferricyanide is marked by slight film contraction, presumably due to electrostatic cross-linking by the multivalent anion. These films are useful in the spectroelectrochemical sensor with our newly developed fluorescence detection mode, as demonstrated by results of the reversible incorporation of the fluorescent anion fluorescein.
Journal Article↗
[Characteristics of ion selective electrodes with hetero-poly anion sites].
Drug ion-selective electrodes made with hetero-poly anion as exchange site exhibit better performances than the respective electrodes of conventional tetraphenylboron type, yielding low detection limits and fast responses. Functions of propantheline, berberine, dibazol, thiamine, streptomycin, moroxydine, tetracycline, oxytetracycline, doxycycline, erythromycin, carbetapentane, benzydamine, tetramisole and trifluoperazine electrodes are reported. The electrodes can be used in potentiometric determinations of the respective drugs in aqueous solutions, urine and mixture of water and organic solvents.
Berberine↗
Improving the blood compatibility of ion-selective electrodes by employing poly(MPC-co-BMA), a copolymer containing phosphorylcholine, as a membrane coating.
The hydrogelpoly(2-methacryloyloxyethylphosphorylcholine-co-butyl methacrylate), or poly(MPC-co-BMA), was used as a coating for polyurethane- and poly(vinyl chloride)-based membranes to develop ion-selective electrodes (ISEs) with enhanced blood compatibility. Adverse interactions of poly(MPC-co-BMA) with blood were diminished due to the phosphorylcholine functionalities of the hydrogel, which mimic the phospholipid polar groups present on the surface of many cell membranes. As demonstrated by immunostaining, hydrogel-coated PVC membranes soaked in platelet-rich plasma showed less adhesion and activation of platelets than uncoated PVC membranes, indicating an improvement in biocompatibility owing to the hydrogel. Furthermore, little differences in the potentiometric response characteristics, e.g., slope, detection limit, and selectivity, of ISEs employing uncoated and coated membranes were observed.
Animals↗
Methotrexate-poly(lysine) as a selective agent for mutants of Chinese hamster ovary cells defective in endocytosis.
Methotrexate (MTX) covalently linked to poly(L-lysine) [poly(Lys)] enters cells by endocytosis, is degraded in lysosomes and, upon liberation of small molecular methotrexate, is cytocidal to Chinese hamster cells in culture. This drug conjugate was used to select mutants resistant to MTX-poly(Lys), which were examined for defects in endocytosis. Two mutants resistant to MYX-poly(Lys) and sensitive to free MTX, MPL 3-4 and MPL 2-5, internalized the conjugate in normal fashion, but had a decreased ability to degrade it to small molecular drug. The magnitude of this defect in the two mutants correlated with their level of resistance. In addition, both mutants were cross resistant to diphtheria toxin and modeccin and hypersensitive to ricin. While MPL 3-4 internalized MTX-poly(Lys) and inulin normally, it showed decreased endocytosis via the mannose-6-phosphate receptor and decreased uptake of 125I-alpha-2 macroglobulin. Acidification of subcellular fractions was measured using the partitioning of acridine orange. In MPL 3-4, the ATP-driven acidification of the endosome-containing cell fractions was slightly decreased (80% of controls), while acidification of the heavy lysosome-containing fraction was normal. Complementation analysis using hybrids of MPL 3-4 x MPL 2-5 indicated that the mutations occurred at the same gene, but were expressed with different severity. This genotype is identical to that of the End 2 mutants described by Roff et al. (1986). Thus, surprisingly, mutants with identical genotypes were isolated independently by totally different selection procedures.
Animals↗
Conformational transition of the core chain in radiation-modified polysilane micelles formed in selective solvents.
Poly(methyl acrylate)-grafted poly(methyl-n-propylsilane) (PMPrS-g-PMA) and poly(acrylic acid)-grafted PMPrS (PMPrS-g-PAA) were synthesized by gamma-ray-induced graft polymerization, and the association behavior of these graft copolymers was investigated in selective solvents composed of good and poor solvents for the PMPrS main chain. Fluorescence spectroscopy with perylene as a fluorescent probe revealed that PMPrS-g-PAA in a water/THF mixed solvent self-assembles into micelles with a swollen core of PMPrS chains in the water content range of 50-95%. UV spectroscopy demonstrated that a further increase of the water content gives rise to the conformational transition of the PMPrS chains in the micelle core from the random conformation to the conformation that corresponds to that in the solid state at a water content of ca. 95%, independent of the grafting yield. Similar behavior was also observed in DMSO/THF solutions of PMPrS-g-PMA, for which the conformational transition occurred at the constant DMSO content of ca. 95%. These results indicate that solvatochromic behavior of polysilane, which is a characteristic feature of polysilane, proved to provide information on the inner structure of those micelles: PMPrS chains in the core undergo conformational transition as the content of the poor solvents for PMPrS increases, while maintaining the micelle structure.
Journal Article↗
Monolithic capillary-based ion-selective electrodes.
Poly(styrene-co-divinylbenzene)-based monolithic capillaries of an inner diameter of 200 mum and a length of 2-5 mm have been used to construct Ca2+-, Ag+-, and Na+-selective electrodes. The membranes consist of a solution of ionophore and ion exchanger in bis(2-ethylhexyl) sebacate or 2-nitrophenyl octyl ether, which are used as plasticizers in conventional PVC-based membranes. With capillaries of low porosity, the potentiometric responses down to 10(-8)-10(-9) M solutions do not depend on the composition of the internal solution, which indicates a strong suppression of transmembrane ion fluxes. Thus, no tedious optimization of the inner solution is required with monolith ISEs. The lower detection limits of Ag+- and Ca2+-ISEs are comparable to the best ones obtained earlier with optimized inner solutions. Additionally, a monolithic Na+-selective ISE has been obtained exhibiting a lower detection limit of 3 x 10(-8) M Na+. With monolithic capillaries of higher porosity and fused-silica GC capillaries, the transmembrane flux effects are noticeable but still significantly smaller than with conventional PVC membranes.
Calcium↗
Postulation of the mechanism of the selective synthesis of isotactic poly(methyl methacrylate) catalysed by [Zr[(Cp)(Ind)CMe2](Me)(thf)](BPh4): a Hartree-Fock, MP2 and density functional study.
The bridged. C1-symmetric, single-component zirconocene [Zr((Cp)(Ind)CMe2](Me)(thf)](BPh4) (Ind = indenyl, Cp = cyclopentadienyl) polymerises methyl methacrylate (MMA) selectively to isotactic poly(methyl methacrylate) (PMMA) without further cocatalysts or activators. To elucidate the stereoselective steps of the polymerisation of MMA by using this catalyst we studied the propagation steps occurring with the derivative [Zr[(Cp)(Ind)CH2][-O-C(OMe)=C(Me)(Et)](MMA)]+ by ab initio calculations at the Hartree-Fock(HF) level of theory. After the initiation step, which consumes the first two MMA molecules, each new catalytic cycle begins with the stereoselective addition of a new MMA molecule at the indenyl side of the zirconocene fragment. At the same time the enolate ring undergoes a stereoselective in-plane ring shift to the side opposite to the indenyl ring. These findings are used to postulate a mechanism for the polymerisation that explains the stereoselective synthesis of isotactic PMMA.
Journal Article↗
Expression of mRNA of beta 1- and beta 2-adrenergic receptors in Xenopus oocytes results from structurally distinct receptor mRNAs.
Poly(A)+-selected RNA prepared from cells or tissues that express a homogeneous population of either beta 1- or beta 2-adrenergic receptors was isolated and then microinjected into Xenopus laevis oocytes. Following microinjection, the expression of beta-adrenergic receptors was assessed by equilibrium radioligand binding analysis using the antagonist ligand [3H]dihydroalprenolol. The pharmacology of the newly- expressed beta-adrenergic receptors in oocyte membranes was the same as that of the original tissue used as a source of RNA. Hybridization of nick-translated cDNA of hamster beta 2-adrenergic receptor to poly(A)+-selected RNA from tissues containing beta 2-adrenergic receptors was to a mRNA species of 2.2 kilobases. In contrast, hybridization of the cDNA probe to poly(A)+-selected RNA from tissues containing beta 1-adrenergic receptors was to a mRNA species of 2.0 kilobases. A single-stranded fragment of hamster beta 2-adrenergic receptor cDNA corresponding to nucleotides 730-886 was isolated and uniformly radiolabeled. This region of the gene is predicted to encode for the entire second exofacial loop (L4-5), the entire fifth transmembrane-spanning region, and the first 5 amino acid residues of the third cytoplasmic loop (L5-6) of the beta 2-adrenergic receptor. Hybridization at 48 and 56 degrees C of poly(A)+-selected RNA prepared from sources that express either beta 1 or beta 2-adrenergic receptors to the antisense orientation strand of this region of the beta 2-adrenergic receptor cDNA was followed by S1 endonuclease digestion of nonhybridized sequences. At 48 degrees C, S1-resistant hybrids from both sources of RNA protected the probe from S1 endonuclease digestion. At 56 degrees C, however, only the RNA prepared from the source of beta 2-adrenergic receptors protected the probe from S1 endonuclease digestion. These results demonstrate that the mRNAs encoding for the structurally homologous beta 1- and beta 2-adrenergic receptors are distinct in the pharmacological specificity of their translation products and in their size and structure.
Animals↗
Preparation and characterization of polypseudorotaxanes based on block-selected inclusion complexation between poly(propylene oxide)-poly(ethylene oxide)-poly(propylene oxide) triblock copolymers and alpha-cyclodextrin.
A series of new polypseudorotaxanes were synthesized in high yields when the middle poly(ethylene oxide) (PEO) block of poly(propylene oxide)-poly(ethylene oxide)-poly(propylene oxide) (PPO-PEO-PPO) triblock copolymers was selectively recognized and included by alpha-cyclodextrin (alpha-CD) to form crystalline inclusion complexes (ICs), although the middle PEO block was flanked by two thicker PPO blocks, and a PPO chain had been previously thought to be impenetrable to alpha-CD. X-ray diffraction studies demonstrated that the IC domains of the polypseudorotaxanes assumed a channel-type structure similar to the necklace-like ICs formed by alpha-CD and PEO homopolymers. Solid-state CP/MAS (13)C NMR studies showed that the alpha-CD molecules in the polypseudorotaxanes adopted a symmetrical conformation due to the formation of ICs. The compositions and stoichiometry of the polypseudorotaxanes were studied using (1)H NMR, and a 2:1 (ethylene oxide unit to alpha-CD) stoichiometry was found for all polypseudorotaxanes although the PPO-PEO-PPO triblock copolymers had different compositions and block lengths, suggesting that only the PEO block was closely included by alpha-CD molecules, whereas the PPO blocks were uncovered. The hypothesis was further supported by the differential scanning calorimetry (DSC) studies of the polypseudorotaxanes. The glass transitions of the PPO blocks in the polypseudorotaxanes were clearly observed because they were uncovered by alpha-CD and remained amorphous, whereas the glass-transition temperatures increased, because the molecular motion of the PPO blocks was restricted by the hard crystalline phases of the IC domains formed by alpha-CD and the PEO blocks. The thermogravimetric analysis (TGA) revealed that the polypseudorotaxanes had better thermal stability than their free components due to the inclusion complexation. Finally, the kinetics of the threading process of alpha-CD onto the copolymers was also studied. The findings reported in this article suggested interesting possibilities in designing other cyclodextrin ICs and polypseudorotaxanes with block structures.
Cyclodextrins↗
Alternative poly(A) site-selection regulates the production of alternatively spliced vesl-1/homer1 isoforms that encode postsynaptic scaffolding proteins.
The vesl-1/homer1 gene encodes a scaffold protein that interacts with several receptors to modulate synaptic functions. The gene also encodes two shorter forms that counteract the functions of the long form of Vesl. Expression of the shorter forms is driven by neural activities such as long-term potentiation. Here we analyzed the mechanism regulating vesl-1 alternative splicing. Each functional poly(A) site was in a different part of the 3'-terminal exon, with promoter-proximal and promoter-distal sites at the end of exons corresponding to the short and long form Vesl-1, respectively. 3'-End-processing at proximal poly(A) site, specifically at the vesl-1M poly(A) site, was enhanced by extracellular stimuli, thereby switching transcription termination from promoter-distal to -proximal poly(A) site. This switch was not specifically coupled to the vesl-1 promoter and was independent of de novo protein synthesis. Analysis of transcripts from mini-genes that mimic the structure of endogenous vesl-1 revealed that the vesl-1M poly(A) region plays a crucial role in switching to the alternative pre-mRNA splicing that is triggered by extracellular stimuli. Therefore, a 3'-end-processing event regulates the neural activity-dependent alternative splicing of vesl-1. This is the first report of a gene in which alternative poly(A) site-selection regulates alternative splicing in a protein synthesis-independent manner.
Alternative Splicing↗
Strategy for selection of cell variants deficient in poly(ADP-ribose) polymerase.
A selection strategy to obtain cells deficient in poly(ADP-ribose) polymerase was developed based on the fact that treatment with high levels of N-methyl-N'-nitro-N-nitrosoguanidine results in sufficient activation of poly(ADP-ribose) polymerase to cause NAD and ATP depletion leading to cessation of all energy-dependent processes and rapid cell death. In contrast, cells with low levels of poly(ADP-ribose) polymerase should not consume their NAD and might therefore be more likely to survive the DNA damage. Using this approach, we have cloned a number of cell lines containing 37-82% enzyme activity. The apparent decrease in poly(ADP-ribose) polymerase activity is not due to increases in NAD glycohydrolase, poly(ADP-ribose) glycohydrolase, or phosphodiesterase activities. Further characterization of the poly(ADP-ribose) polymerase-deficient cells indicates that they have prolonged generation times and increased rates of spontaneous sister chromatid exchanges.
Adenosine Triphosphate↗