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PubMed2001

Nanofilms and nanoclusters: energy sources driving fluorophores of biochip bound labels.

Nanoclusters and nanofilms have the potential to amplify fluorescence and thus to enhance the signal of labeled biomolecules on biochip surfaces. Fluorescent molecules are bound at a certain distance to a resonant layer of a metal or a semiconductor or both, resulting in enhanced absorption and emission of the fluorophore within the electromagnetic near-field. This property makes the system highly useful for interaction studies, including those of DNA and proteins. Due to the amount of data, derived from various sequencing projects and from Proteomic interaction studies within the next years, microarrays (or biochips) will represent a central technology in every lab facilitating high-throughput screening and being easily interfaced with computer databases. However, most chips suffer from the disadvantage of insufficient signal-to-noise (background) ratio and are thus limited to molecules of medium-to-high abundance. Novel approaches are needed for identification of, e.g., low copy RNAs or regulatory proteins. Here we present a study, using novel surface enhanced chips in the standard glass-slide-formats. Applying surface-enhanced fluorescence (SEF), the chips turned out to be useful for interaction studies, such as DNA hybridization, thereby strongly enhancing the on-chip-signals. Compared to standard glass-slide-DNA chips, both the fluorescent signals as well as signal-to-noise ratio were considerably higher.

Animals↗
PubMed2004

The tRNA-like structure of Turnip yellow mosaic virus RNA is a 3'-translational enhancer.

Many positive stand RNA viral genomes lack the poly(A) tail that is characteristic of cellular mRNAs and that promotes translation in cis. The 3' untranslated regions (UTRs) of such genomes are expected to provide similar translation-enhancing properties as a poly(A) tail, yet the great variety of 3' sequences suggests that this is accomplished in a range of ways. We have identified a translational enhancer present in the 3' UTR of Turnip yellow mosaic virus (TYMV) RNA using luciferase reporter RNAs with generic 5' sequences transfected into plant cells. The 3' terminal 109 nucleotides comprising the tRNA-like structure (TLS) and an upstream pseudoknot (UPSK) act in synergy with a 5'-cap to enhance translation, with a minor contribution in stabilizing the RNA. Maximum enhancement requires that the RNA be capable of aminoacylation, but either the native valine or engineered methionine is acceptable. Mutations that decrease the affinity for translation elongation factor eEF1A (but also diminish aminoacylation efficiency) strongly decrease translational enhancement, suggesting that eEF1A is mechanistically involved. The UPSK seems to act as an important, though nonspecific, spacer element ensuring proper presentation of a functional TLS. Our studies have uncovered a novel type of translational enhancer and a new role for a plant viral TLS.

3' Untranslated Regions↗
PubMed1995

Regulatory autonomy and molecular characterization of the Drosophila out at first gene.

Our previous work has shown that the expression of the Drosophila decapentaplegic (dpp) gene in imaginal disks is controlled by a 30 kb array of enhancers located 3' of the dpp coding region. Here, we describe the cloning and characterization of out at first (oaf), a gene located near this enhancer region. Transcription of oaf results in three classes of alternatively polyadenylated RNAs whose expression is developmentally regulated. All oaf transcripts contain two adjacent open reading frames separated by a single UGA stop codon. Suppression of the UGA codon during translation, as seen previously in Drosophila, could lead to the production of different proteins from the same RNA. During oogenesis, oaf RNA is expressed in nurse cells of all ages and maternally contributed to the egg. During embryonic development, zygotic transcription of the gene occurs in small clusters of cells in most or all segments at the time of germband extension and subsequently in a segmentally repeated pattern in the developing central nervous system. The gene is also expressed in the embryonic, larval and adult gonads of both sexes. We also characterize an enhancer trap line with its transposon inserted within the oaf gene and use it to generate six recessive oaf mutations. All six cause death near the beginning of the first larval instar, with two characterized lines showing nervous system defects. Last, we discuss our data in light of the observation that the enhancers controlling dpp expression in the imaginal disks have no effect on the relatively nearby oaf gene.

Amino Acid Sequence↗
PubMed2005

Nonviral genetic modification mediates effective transgene expression and functional RNA interference in human mesenchymal stem cells.

BACKGROUND: Human mesenchymal stem cells (hMSC) are increasingly the focus of both basic and clinical research due to their ability to strike a balance between self-renewal and commitment to mesodermal differentiation. However, the promising therapeutic utility of hMSC in regenerative medical approaches requires detailed knowledge about their molecular characteristics. Therefore, genetic modification of hMSC provides a powerful tool to understand their complex molecular regulation mechanisms. METHODS: Here we describe a proof of concept approach of separate and combined gene transfer and gene silencing by nonviral DNA transfection of enhanced green fluorescent protein (EGFP) and EGFP-targeted small interfering RNAs (siRNAs) in hMSC. For optimization of nonviral DNA and siRNA transfer different liposomal-based transfection strategies were validated. RESULTS: The highest fraction of EGFP-expressing hMSC was obtained using Lipofectamine 2000 (50%) which also mediated the highest transfection rates of siRNAs into hMSC (>or=92%). Stably EGFP-expressing hMSC maintained their proliferation capacity paired with the ability to differentiate into different mesodermal lineages (bone, cartilage, and fat) without loss of transgene expression. Based on our nonviral nucleic acid delivery technique we showed efficient, functional, and long-term RNA interference (RNAi) in hMSC by gene specific knock-down of transiently and stably expressed EGFP (88-98%). CONCLUSIONS: This is the first demonstration of efficient nonviral transfer of both nucleic acids (DNA and siRNA) into hMSC, exhibiting the potential of targeted modification of hMSC. In particular, the combination of these techniques represents a powerful gene transfer/silencing strategy, thus facilitating detailed genetic approaches to study regulatory networks in stem cell differentiation processes.

Cell Culture Techniques↗
PubMed1981

Effect of thyrotropin on the properties of messenger RNA from cultured human thyroid cells.

When added to the culture medium of thyroid cells isolated from diffuse nontoxic goiter, thyrotropin increased the poly(adenylic acid) content and the template activity of the unfractionated RNA. This increase was correlated with higher thyroglobulin messenger activity, as demonstrated by specific immunoprecipitation of the labeled peptides synthesized in two heterologous cell-free systems. When RNAs were separated in a sucrose gradient, thyrotropin was shown to enhance the poly(adenylic acid) content and template activity of fractions with sedimentation coefficients of 34, 23 and 15 S. Specific immunoprecipitation showed that a thyroglobulin messenger activity was present in these three fractions. Another way by which thyrotropin regulates the thyroid protein synthesis is suggested by the shift of poly(adenylic acid)-containing RNA to large polysomes when thyroid cells were cultured in the presence of the hormone.

Cells, Cultured↗
PubMedDate not supplied

Evolution of structure in RNA.

Evidence is presented that structures formed by RNA and by RNA in association with protein have evolved from simpler structures by successive unions among them. The progressively more complex molecular structures have conferred selective advantage in evolution by progressively enhancing the specificities of the biochemical reactions. Before each union, the RNAs which joined at the time of union belonged to separate reproducing species. The record of unions in RNA therefore reflects unions among species in the biosphere, tracing the evolution of life from quite simple reproducing molecules up to well developed organisms.

Biological Evolution↗
PubMed2001

Pyrimidine tract binding protein and La autoantigen interact differently with the 5' untranslated regions of lentiviruses and oncoretrovirus mRNAs.

Retrovirus genomic mRNA exhibits a several hundred nucleotides-long untranslated region (5' UTR) which encloses many control elements required for retrovirus replication. In addition, this 5' UTR contains translation regulatory elements, such as internal ribosome entry sites (IRESes) that have been described in oncoretroviruses, as well as in lentiviruses. UV cross-linking experiments suggested that the pyrimidine tract binding protein (PTB), a cellular protein known to regulate the activity of several picornaviral IRESes, binds to human T-cell leukemia virus (HTLV)-I RNA but not to lentiviral human immunodeficiency virus (HIV)-1, HIV-2 or simian immunodeficiency virus RNAs. To calculate the affinity of such RNA-protein interactions, we developed a new method based on the BIAcore technology. The absence of affinity of PTB for lentiviral RNAs was confirmed, whereas its affinity for HTLV-I RNAs was 1000-fold lower than for picornaviral RNAs. The BIAcore technology also revealed a significant affinity of the La autoantigen, previously described for its involvement in translational control of viral mRNAs, for HIV-1 and HTLV-I RNAs. Addition of recombinant PTB to in vitro translation experiments weakly enhanced translation initiation in the presence of HTLV-I IRES, suggesting that such an IRES requires additional trans-acting factors.

5' Untranslated Regions↗
PubMed1997

Induction of ferritin synthesis in ischemic-reperfused rat liver: analysis of the molecular mechanisms.

BACKGROUND & AIMS: Iron may catalyze the production of reactive oxygen species (ROS) during postischemic reoxygenation. Ferritin, a cellular iron storage protein, can either represent a source of iron or perform a cytoprotective action against ROS. The aim of this study was to address the role of ferritin in postischemic reperfusion. METHODS: Transcriptional and posttranscriptional mechanisms controlling ferritin gene expression were studied in reperfused rat livers. RESULTS: Proteolysis reduced ferritin levels 2 hours after reperfusion, but a concomitant increase of synthesis, accompanied by enhanced transcription and accumulation of H and L ferritin subunit messenger RNAs (mRNAs), almost re-established normal ferritin content at 4 hours. Pretreatment with interleukin 1 receptor antagonist (IL-1RA) did not prevent the rise of ferritin mRNAs. RNA bandshift assays showed that the activity of the iron regulatory proteins (IRPs), which control ferritin mRNA translation, declined early after reperfusion and recovered progressively thereafter. Pretreatment with either the antioxidant N-acetyl cysteine or IL-1RA was sufficient to prevent almost completely down-regulation of IRP activity. CONCLUSIONS: Postischemic reperfusion causes degradation of ferritin, possibly increasing iron levels. However, induction of ferritin gene transcription, possibly mediated by ferritin-derived iron and ROS-mediated inactivation of IRP, which allows translation of ferritin mRNAs, counteracts this effect and concurs to reestablish the amount of ferritin, which may thus act to limit reperfusion damage.

Animals↗
PubMed2000

Hypoxia inhibits the Na(+)/Ca(2+) exchanger in pulmonary artery smooth muscle cells.

The cellular mechanisms underlying hypoxic pulmonary vasoconstriction are not fully understood. We examined the effect of hypoxia on Ca(2+) efflux from the cytosol in single Fura-2-loaded pulmonary artery myocytes. During mild hypoxia (pO(2)=50-60 Torr), peak [Ca(2+)](i) was increased and the rate of Ca(2+) removal from the cytosol was markedly slowed after stimuli that elevated [Ca(2+)](i). Removal of extracellular Na(+) potentiated the peak [Ca(2+)](i) rise and slowed the Ca(2+) decay rate in cells recorded under normoxic conditions; it did not further slow the Ca(2+) decay rate or potentiate the [Ca(2+)](i) increase in hypoxic cells. An Na(+)/Ca(2+) exchange current was recorded in isolated pulmonary artery myocytes. Switching from Li(+) to Na(+) (130 mM) revealed an inward current with reversal potential consistent with the Na(+)/Ca(2+) exchange current in cells in which [Ca(2+)](i) was clamped at 1 microM similar currents, although smaller, were observed with normal resting [Ca(2+)](i) using the perforated patch clamp technique. The Na(+)/Ca(2+) exchange current was markedly inhibited in myocytes exposed to mild hypoxia. RT-PCR revealed the expression of specific alternatively spliced RNAs of NCX1 in rat pulmonary arteries. These findings provide an enhanced understanding of the molecular mechanisms underlying hypoxic sensing in pulmonary arteries.

Animals↗
PubMed1984

Localization and analysis of bovine papillomavirus type 1 transforming functions.

Bovine papillomavirus type 1 (BPV-1) or cloned BPV-1 DNA can transform susceptible rodent cells, and the viral DNA remains as a stable extrachromosomal plasmid in the transformed cells. The transforming region of the BPV-1 genome has previously been localized to a specific fragment comprising 69% of the genome, which also contains the elements sufficient for extrachromosomal plasmid maintenance. To define more precisely the viral DNA sequences which are involved in cellular transformation, we have tested the ability of defined deletion mutants of BPV-1 DNA to morphologically transform mouse C127 cells. Cells containing the mutated DNAs have been examined for anchorage independence and tumorigenicity in nude mice. Several distinct regions of the BPV-1 genome were found to influence expression of the viral transformation functions. A transcriptional regulatory region located in the noncoding region 5' to the early open reading frames is essential for transcriptional activity and transformation. A transcriptional enhancer element, located 3' to the polyadenylation site for the viral RNAs expressed in transformed cells, has previously been shown to be essential for transformation (Lusky et al., Mol. Cell. Biol., 3:1108-1122, 1983). Deletion mutants affecting the E2 open reading frame, particularly the NH2 half, are significantly impaired in their ability to transform, suggesting that the E2 gene product is an important transforming protein of BPV-1. Mutants lacking the E6 and E7 open reading frames are still able to induce transformation but at a lowered efficiency, and the transformants have altered characteristics. Mutations localized within the E1 open reading frame do not significantly affect the transforming functions but result in the integration of the viral genome in the transformed cells, implicating the E1 gene product in stable plasmid replication and maintenance.

Animals↗
PubMed2005

Focal adhesion kinase regulates syndecan-2-mediated tumorigenic activity of HT1080 fibrosarcoma cells.

Expression of syndecan-2, a transmembrane heparan sulfate proteoglycan, is crucial for the tumorigenic activity in colon carcinoma cells. However, despite the high-level expression of syndecan-2 in mesenchymal cells, few studies have addressed the function of syndecan-2 in sarcoma cells. In HT1080 fibrosarcoma cells, we found that syndecan-2 regulated migration, invasion into Matrigel, and anchorage-independent growth but not cell-extracellular matrix adhesion or proliferation, suggesting that syndecan-2 plays different functional roles in fibrosarcoma and colon carcinoma cells. Consistent with the increased cell migration/invasion of syndecan-2-overexpressing HT1080 cells, syndecan-2 overexpression increased phosphorylation and interaction of focal adhesion kinase (FAK) and phosphatidylinositol 3-kinase (PI3K), membrane localization of T-lymphoma invasion and metastasis gene-1 (Tiam-1), and activation of Rac. Syndecan-2-mediated cell migration/invasion of HT1080 cells was diminished when (a) cells were cotransfected with nonphosphorylatable mutant FAK Y397F or with other FAK mutants lacking PI3K interactions, (b) cells were treated with a specific PI3K inhibitor, or (c) levels of Tiam-1 were knocked down with small interfering RNAs. Furthermore, expression of several FAK mutants inhibited syndecan-2-mediated enhancement of anchorage-independent growth in HT1080 cells. Taken together, these data suggest that syndecan-2 regulates the tumorigenic activities of HT1080 fibrosarcoma cells and that FAK is a key regulator of syndecan-2-mediated tumorigenic activities.

Cell Line, Tumor↗
PubMed1990

Characterization of enhancer-of-white-apricot in Drosophila melanogaster.

The white-apricot (wa) allele differs from the wild-type white gene by the presence of the retrovirus-like transposable element copia within the transcription unit. Most RNAs derived from wa have 3' termini within this insertion, and only small amounts of structurally normal RNA are produced. The activity of wa is reduced in trans by a semidominant mutation in the gene Enhancer-of-white-apricot (E(wa). Flies that are wa and heterozygous for the enhancer have eyes which are much lighter than the orange-yellow of wa alone while E(wa) homozygotes have white eyes. This semidominant effect on pigmentation is correlated with a corresponding decrease in white RNA having wild type structure, and flies homozygous for E(wa) have increased levels of aberrant RNAs. Three reverant alleles of E(wa) generated by reversion of the dominant enhancer phenotype with gamma radiation are noncomplementing recessive lethals, with death occurring during the larval stage. The effects on wa eye pigmentation of varying doses of the original E(wa) allele, the wild type allele, and the revertant alleles suggest that the original E(wa) allele produces a product that interferes with the activity of the wild type gene and that the revertants are null alleles. We propose that the E(wa) gene product influences the activity of the downstream copia long terminal repeat in 3' end formation.

Alleles↗
PubMed1986

The neuronal identifier element is a cis-acting positive regulator of gene expression.

A middle-repetitive DNA element termed the identifier (ID) sequence, located in introns of postnatal-onset neuronal-specific genes, is transcribed in early postnatal rats by RNA polymerase III (Pol III) specifically in the brain. We show that these Pol III transcripts, although brain specific in vivo, are also expressed in immortalized rodent cell lines in culture. We demonstrate that the ID sequence can act as a positive regulator or enhancer of RNA polymerase II gene expression in cell lines that express these RNAs but not in primary cells in which Pol III transcription of the ID sequence is absent. Thus, ID elements may be positive regulators of postnatal-onset neuronal-specific gene expression.

Animals↗
PubMed1994

P element transformation vectors for studying Drosophila melanogaster oogenesis and early embryogenesis.

We have constructed six new P-element-based Drosophila melanogaster transformation vectors that specifically allow for the high-level accumulation of any RNA of interest in the developing egg and pre-blastoderm embryo. Such specificity results, in part, from the inclusion in the vectors of an enhancer active exclusively in nurse cells, the principal providers of RNA to the egg and early embryo. The nurse cell enhancer was derived from the hsp26 heat-shock (HS) gene, but its activity was neither dependent on nor sensitive to HS. In addition to the nurse cell enhancer, two of the vectors contain sequences from the K10 gene that promote the early transfer of RNAs from nurse cells into the oocyte; RNAs that contain the K10 sequence are transferred into the oocyte during the early to middle stages of oogenesis (i.e., during stages 2-9), while RNAs that lack such sequences are stored in nurse cells until stage 11. All of the vectors contain a tsp and a multiple cloning site (MCS) immediately downstream from the hsp26 nurse cell enhancer. In three of the vectors, the MCS is preceded by an ATG start codon. A wild-type copy of the white gene is included in all of the vectors as a selectable marker for transformation. The specificity of the vectors was demonstrated by the analysis of the expression patterns of lacZ derivatives.

Amino Acid Sequence↗
PubMed2003

Isolation of GnafC, a polysaccharide constituent of Gnaphalium affine, and synergistic effects of GnafC and ascorbate on the phenotypic expression of osteoblastic MC3T3-E1 cells.

After screening extensively factors in plant extracts that increase alkaline phosphatase activity, an osteoblastic differentiation marker protein in mouse calvarial osteoblast MC3T3-E1 cells, GnafC derived from Gnaphalium affine, was found to significantly enhance the alkaline phosphatase (ALPase) activity in a synergistic manner with ascorbate. GnafC was a polysaccharaide with an approximate molecular mass of 10,000 and comprised mannose, xylose, arabinose, galactose and glucose in a molar ratio of 1:2:4.3:2.5:2.7. Expression of the osteoblastic differentiation marker genes was examined by semiquantitative RT-PCR with RNAs prepared from cells at different developmental stages. With ascorbate in the culture, GnafC enhanced the expression of the ALPase and MMP13 genes from the early stage of differentiation, leading to maturation of the collagenous extracellular matrix (ECM), a prerequisite for mineralization.

Alkaline Phosphatase↗
PubMed2000

Replication of lengthened Moloney murine leukemia virus genomes is impaired at multiple stages.

It has been assumed that RNA packaging constraints limit the size of retroviral genomes. This notion of a retroviral "headful" was tested by examining the ability of Moloney murine leukemia virus genomes lengthened by 4, 8, or 11 kb to participate in a single replication cycle. Overall, replication of these lengthened genomes was 5- to 10-fold less efficient than that of native-length genomes. When RNA expression and virion formation, RNA packaging, and early stages of replication were compared, long genomes were found to complete each step less efficiently than did normal-length genomes. To test whether short RNAs might facilitate the packaging of lengthy RNAs by heterodimerization, some experiments involved coexpression of a short packageable RNA. However, enhancement of neither long vector RNA packaging nor long vector DNA synthesis was observed in the presence of the short RNA. Most of the proviruses templated by 12 and 16 kb vectors appeared to be full length. Most products of a 19. 2-kb vector contained deletions, but some integrated proviruses were around twice the native genome length. These results demonstrate that lengthy retroviral genomes can be packaged and that genome length is not strictly limited at any individual replication step. These observations also suggest that the lengthy read-through RNAs postulated to be intermediates in retroviral transduction can be packaged directly without further processing.

3T3 Cells↗
PubMed2025

A long noncoding RNA with enhancer-like function in pig zygotic genome activation.

The zygotic genome activation (ZGA) is crucial for the development of pre-implantation embryos. Long noncoding RNAs (lncRNAs) play significant roles in many biological processes, but the study on their role in the early embryonic development of pigs is limited. In this study, we identify lncFKBPL as an enhancer-type lncRNA essential for pig embryo development. lncFKBPL is expressed from the 4-cell stage to the morula stage in pig embryos, and interference with lncFKBPL leads to a developmental arrest at the 8-cell stage. Mechanistic investigations uncover that lncFKBPL is able to bind to MED8, thereby mediating enhancer activity and regulating FKBPL expression. Additionally, FKBPL interacts with the molecular chaperone protein HSP90AA1, stabilizing CDK9 and boosting its protein-level expression. Elevated CDK9 levels enhance Pol II phosphorylation, facilitating ZGA. Our findings illuminate the role of lncFKBPL as an enhancer lncRNA in pig ZGA regulation and early embryo development, providing a foundation for further exploration in this area.

Animals↗
PubMed2006

Suppression of viral RNA recombination by a host exoribonuclease.

RNA viruses of humans, animals, and plants evolve rapidly due to mutations and RNA recombination. A previous genome-wide screen in Saccharomyces cerevisiae, a model host, identified five host genes, including XRN1, encoding a 5'-3' exoribonuclease, whose absence led to an approximately 10- to 50-fold enhancement of RNA recombination in Tomato bushy stunt virus (E. Serviene, N. Shapka, C. P. Cheng, T. Panavas, B. Phuangrat, J. Baker, and P. D. Nagy, Proc. Natl. Acad. Sci. USA 102:10545-10550, 2005). In this study, we found abundant 5'-truncated viral RNAs in xrn1delta mutant strains but not in the parental yeast strains, suggesting that these RNAs might serve as recombination substrates promoting RNA recombination in xrn1delta mutant yeast. This model is supported by data showing that an enhanced level of viral recombinant accumulation occurred when two different 5'-truncated viral RNAs were expressed in the parental and xrn1delta mutant yeast strains or electroporated into plant protoplasts. Moreover, we demonstrate that purified Xrn1p can degrade the 5'-truncated viral RNAs in vitro. Based on these findings, we propose that Xrn1p can suppress viral RNA recombination by rapidly removing the 5'-truncated RNAs, the substrates of recombination, and thus reducing the chance for recombination to occur in the parental yeast strain. In addition, we show that the 5'-truncated viral RNAs are generated by host endoribonucleases. Accordingly, overexpression of the Ngl2p endoribonuclease led to an increased accumulation of cleaved viral RNAs in vivo and in vitro. Altogether, this paper establishes that host ribonucleases and host-mediated viral RNA turnover play major roles in RNA virus recombination and evolution.

Exoribonucleases↗