Antisense RNA

Non-coding RNAs and neuroinflammation: implications for neurological disorders

Neuroinflammation is considered a balanced inflammatory response important in the intrinsic repair process after injury or infection. Under chronic states of disease, injury, or infection, persistent neuroinflammation results in a heightened presence of cytokines, chemokines, and reactive oxygen species that result in tissue damage. In the CNS, the surrounding microglia normally contain macrophages and other innate immune cells that perform active immune surveillance. The resulting cytokines produced by these macrophages affect the growth, development, and responsiveness of the microglia present in both white and gray matter regions of the CNS. Controlling the levels of these cytokines ultimately improves neurocognitive function and results in the repair of lesions associated with neurologic disease. MicroRNAs (miRNAs) are master regulators of the genome and subsequently control the activity of inflammatory responses crucial in sustaining a robust and acute immunological response towards an acute infection while dampening pathways that result in heightened levels of cytokines and chemokines associated with chronic neuroinflammation. Numerous reports have directly implicated miRNAs in controlling the abundance and activity of interleukins, TGF-B, NF-kB, and toll-like receptor-signaling intrinsically linked with the development of neurological disorders such as Parkinson's, ALS, epilepsy, Alzheimer's, and neuromuscular degeneration. This review is focused on discussing the role miRNAs play in regulating or initiating these chronic neurological states, many of which maintain the level and/or activity of neuron-specific secondary messengers. Dysregulated miRNAs present in the microglia, astrocytes, oligodendrocytes, and epididymal cells, contribute to an overall glial-specific inflammatory niche that impacts the activity of neuronal conductivity, signaling action potentials, neurotransmitter robustness, neuron-neuron specific communication, and neuron-muscular connections. Understanding which miRNAs regulate microglial activation is a crucial step forward in developing non-coding RNA-based therapeutics to treat and potentially correct the behavioral and cognitive deficits typically found in patients suffering from chronic neuroinflammation.

Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.

Towards Gene-Inhibition Therapy: A Review of Progress and Prospects in the Field of Antiviral Antisense Nucleic Acids and Ribozymes

Antisense RNA and its derivatives may provide the basis for highly selective gene inhibition therapies of virus infections. In this review, I concentrate on advances made in the study of antisense RNA and ribozymes during the last five years and their implications for the development of such therapies. It appears that antisense RNAs synthesized at realistic levels within the cell can be much more effective inhibitors than originally supposed. Looking at those experiments that enable comparisons to be made, it seems that inhibitory antisense RNAs are not those that are complementary to particular sites within mRNAs but those that are able to make stable duplexes with their targets, perhaps by virtue of their secondary structure and length. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them in vitro and possibly in cells, thereby offering the possibility of markedly increasing their therapeutic potential. The varieties of natural ribozyme and their adaptation as artificial catalysts are reviewed. The implications of these developments for antiviral therapy are discussed.

Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference

In RNA-mediated interference (RNAi), externally provided mixtures of sense and antisense RNA trigger concerted degradation of homologous cellular RNAs. We show that RNAi requires duplex formation between the two trigger strands, that the duplex must include a region of identity between trigger and target RNAs, and that duplexes as short as 26 bp can trigger RNAi. Consistent with in vitro observations, a fraction of input dsRNA is converted in vivo to short segments of approximately 25 nt. Interference assays with modified dsRNAs indicate precise chemical requirements for both bases and backbone of the RNA trigger. Strikingly, certain modifications are well tolerated on the sense, but not the antisense, strand, indicating that the two trigger strands have distinct roles in the interference process.

Different isoforms of fasciclin II play distinct roles in the guidance of neuronal migration during insect embryogenesis

During the formation of the enteric nervous system (ENS) of the moth Manduca sexta, identified populations of neurons and glial cells participate in precisely timed waves of migration. The cell adhesion receptor fasciclin II is expressed in the developing ENS and is required for normal migration. Previously, we identified two isoforms of Manduca fasciclin II (MFas II), a glycosyl phosphatidylinositol-linked isoform (GPI-MFas II) and a transmembrane isoform (TM-MFas II). Using RNA and antibody probes, we found that these two isoforms were expressed in cell type-specific patterns: GPI-MFas II was expressed by glial cells and newly generated neurons, while TM-MFas II was confined to differentiating neurons. The expression of each isoform also corresponded to the motile state of the different cell types: GPI-MFas II was detected on tightly adherent or slowly spreading cells, while TM-MFas II was expressed by actively migrating neurons and was localized to their most motile regions. Manipulations of each isoform in embryo culture showed that they played distinct roles: whereas GPI-MFas II acted strictly as an adhesion molecule, TM-MFas II promoted the motility of the EP cells as well as maintaining fasciculation with their pathways. These results indicate that precisely regulated patterns of isoform expression govern the functions of fasciclin II within the developing nervous system.

Applying in vivo expression technology (IVET) to the fungal pathogen Histoplasma capsulatum

Understanding how pathogens survive within the host cell is of paramount importance in the development of vaccines and therapeutic agents. This task has been particularly daunting in the study of fungal pathogens due to the lack of easily manipulated genetic systems. In recent years several molecular genetic reporter systems have been developed to identify genes expressed during the infection process and potential virulence determinants. The development of one method in particular, in vivo expression technology (IVET), has led to the discovery of several genes from various bacterial pathogens necessary for survival during infection. The recent development of molecular genetic tools for Histoplasma capsulatum has enabled us to adapt the IVET technology for this pathogenic fungus utilizing the URA5 gene, which is essential for H. capsulatum survival in mice and in cultured macrophages, as a reporter of in vivo gene expression. We report the first successful application of IVET screening of a fungal pathogen for genes expressed exclusively during infection.

Targeted inhibition of osteopontin expression in the mammary gland causes abnormal morphogenesis and lactation deficiency

Osteopontin (OPN) is a sialic acid-rich, adhesive, extracellular matrix (ECM) protein with Arg-Gly-Asp cell-binding sequence that interacts with several integrins, including alpha(v)beta(3). Since the ECM is a key regulator of mammary gland morphogenesis, and mammary epithelial cells express OPN at elevated levels, we sought to determine whether this protein plays a role in the postnatal mammary gland development. By generating transgenic mice that express OPN antisense-RNA (AS-OPN mice) in the mammary epithelia we achieved suppression of OPN production in this organ. The pregnant AS-OPN mice displayed a lack of mammary alveolar structures, a drastic reduction in the synthesis of beta-casein, whey acidic milk protein, and lactation deficiency. In agreement with these findings, we uncovered that a mammary cell line, NMuMG, which undergoes both structural and functional differentiation on ECM-coated plates, when transfected with an antisense OPN-cDNA construct, failed to undergo such differentiation. Furthermore, the results of gel-invasion assays demonstrated that these cells manifest elevated matrix metalloproteinase (MMP) activity when OPN expression is significantly reduced. The identity of this proteinase as MMP-2 is confirmed by Western blotting, zymography, and inhibition of its activity by a specific inhibitor, TIMP-2. Taken together, our results demonstrate, for the first time, an essential role of OPN in mammary gland differentiation and that the molecular mechanism(s) of its action, at least in part, involves down-regulation of MMP-2.

A novel TNF-inducible message with putative growth suppressor function

We report the nucleotide sequence of a novel cDNA and TNF-induced expression of the corresponding message (mRNA) in human fibroblast cells. This message is also expressed in certain human tumor cell lines and is over-expressed in a colon cancer cell line (HT-29). NIH3T3 cells transfected with the antisense construct of the 5'-region of this novel cDNA formed 20-fold more colonies in culture compared to cells transfected with a sense construct of the same region or the sense and the antisense constructs of the central region of this cDNA. This observation suggests a possible growth suppressor function for the gene represented by this cDNA.

Enhancing therapeutic glycoprotein production in Chinese hamster ovary cells by metabolic engineering endogenous gene control with antisense DNA and gene targeting

Recombinant glycoprotein therapeutics have proven to be invaluable pharmaceuticals for the treatment of chronic and life-threatening diseases. Although these molecules are extraordinarily efficacious, many diseases have high dosage requirements of several hundred milligrams of protein for each administration. Multiple doses at this level are often required for treatment. One of the major challenges currently facing the biotechnology industry is the development of large-scale, cost-effective production and manufacturing processes of these biologically synthesized molecules. Metabolic engineering of animal cell expression hosts promises to address this challenge by substantially enhancing recombinant protein quality, productivity, and biological activity. In this report, we describe a novel approach to metabolic engineering in Chinese hamster ovary cells by control of endogenous gene expression. Analysis of the advantages and limitations of using antisense DNA and gene targeting as a means of control are discussed and several gene candidates for regulation with these techniques are identified. Practical considerations for using these technologies to reduce the levels of the CHO cell sialidase (Warner et al., Glycobiology, 3, 455-463, 1993) as a model gene system for regulation are also presented.

An antisense RNA in IS30 regulates the translational expression of the transposase

Two functional promoters had previously been identified in the mobile genetic element IS30 of Escherichia coli. One, P30A, controls the transcription of ORF-A, whose product is the transposase; the other, located within the ORF-A sequence but on the opposite strand, is called P30C, but the nature and function of its product had remained unknown. We identified this product as an RNA about 150 nucleotides long (called RNA-C) that functions as an untranslated antisense transcript. Indeed, biochemical evidence indicates that ORF-C, which is completely contained on RNA-C, is not translated at detectable levels. Mutational analysis of P30C revealed that overproduction of RNA-C resulted in a decrease of IS30 transposition, while a reduction in the promoter strength resulted in an increase of transposition, as measured by the rate of cointegrate formation. We showed that the translation of ORF-A, but not transcription, is negatively affected by the presence of antisense RNA-C. In contrast to other antisense RNAs acting inhibitorily on translation, RNA-C does not seem to affect translation initiation. Most likely its hybridization to the transposase mRNA in the complementary region located in the central part of ORF-A inhibits the ribosomes in their progression, thus reducing the number of completely translated transposase molecules.

Mechanisms of inhibition of in vitro dimerization of HIV type I RNA by sense and antisense oligonucleotides

Retroviruses display a strong selective pressure to maintain the dimeric nature of their genomic RNAs, suggesting that dimerization is essential for viral replication. Recently, we identified the cis-element required for initiation of human immunodeficiency virus type I (HIV-I) RNA dimerization in vitro. The dimerization initiation site (DIS) is a hairpin structure containing a self-complementary sequence in the loop. We proposed that dimerization is initiated by a loop-loop kissing interaction involving the self-complementary sequence present in each monomer. We tested the ability of sense and antisense oligonucleotides targeted against the DIS to interfere with a preformed viral RNA dimer. Self-dimerization and inhibition properties of the tested oligonucleotides are dictated by the nature of the loop. An RNA loop is absolutely required in the case of sense oligonucleotides, whereas the nature and the sequence of the stem is not important. They form reversible loop-loop interactions and act as competitive inhibitors. Antisense oligonucleotides are less efficient in self-dimerization and are more potent inhibitors than sense oligonucleotides. They are less sensitive to the nature of the loop than the antisense oligonucleotides. Antisense hairpins with either RNA or DNA stems are able to form highly stable and irreversible complexes with viral RNA, resulting from complete extension of base pairing initiated by loop-loop interaction.

Inhibition of HIV replication by sense and antisense rev response elements in HIV-based retroviral vectors

The life cycle of human immunodeficiency virus type 1 (HIV-1) is critically dependent on the transregulatory proteins Tat and Rev. Tat increases the production of HIV-specific mRNAs by direct binding to the transactivation response (TAR) element located at the 5' end of all HIV transcripts. In contrast, Rev uses a complex RNA stem loop structure, the Rev response element (RRE), which is found in full-length and singly spliced HIV transcripts. Rev is required for the cytoplasmic expression of full-length mRNAs encoding Gag, Pol, and Env structural proteins. The complex intracellular interactions between Tat, Rev, host cell factors, and their respective RNA response elements should be susceptible to interdiction by genetic therapies designed to introduce and express novel genetic information. We show that the expression of antisense RREs inhibited the cytoplasmic expression of RRE containing HIV-1 transcripts. HIV-based retroviral vectors containing either the antisense (-) or sense (+) RREs inhibited HIV replication in transient transfections. The production of full-length HIV mRNA was also decreased significantly by the expression of RREs in either orientation. Interestingly, there was a paradoxic increase in HIV p24 gag production at low levels of inhibitor; this effect may have been the result of encapsidation of RRE-containing HIV-based retroviral vectors. The data suggest that the introduction and inducible expression of RRE-containing, HIV-based retroviral vectors may have therapeutic value in HIV infection.

Cardiovascular gene therapy: current concepts

Gene therapy techniques are under development for many areas of medicine, including cardiovascular disease. Identifying appropriate gene targets will require more detailed knowledge of the molecular pathophysiology of these disorders, and choosing appropriate vectors and delivery systems will contribute significantly to the challenge of developing this approach for clinical use. The concepts of toxicology and therapeutic drug monitoring will need to be broadened to account for the unique chemical, biological, and genetic characteristics of gene therapeutic agents. This review will provide an overview of strategy development, currently available vectors, and examples of their application to cardiovascular gene transfer. Considerations of the potential toxicities associated with particular vectors and delivery systems, as well as the types of genetic modifications possible, will provide some guidelines regarding appropriate monitoring of their clinical application.

Fractals for multicyclic synthesis conditions of biopolymers. Examples of oligonucleotide synthesis measured by high-performance capillary electrophoresis and ion-exchange high-performance liquid chromatography

We have developed models of patterns for nucleotide chain growth. These patterns are measurable by high-performance capillary electrophoresis and ion-exchange high-performance liquid chromatography in crude products of solid-phase synthesized 30mer and 65mer oligodeoxyribonucleotide target sequences N. We introduce mathematical methods for finding characteristic values d(o) and p(o) for constant chemical modes of growth as well as d and p for non-constant chemical modes of growth (d = probability of propagation, p = probability of termination). These methods are employed by presenting the accompanying computer software developed by us in C code, Mathematica R languages, and Fortran. Characteristic values of the parameters d, p, and the target nucleotide length N describe the complete composition of the crude product. From this we have developed the relation 2 - [N/(N - 1)]/Da, measurable(N,d) as a universal quantitative measure for multicyclic synthesis conditions (D, fractal dimension and similarity exponent, respectively). We use this mathematical treatment to compare the efficiency of oligodeoxyribonucleotide syntheses of different target length N on polymer support materials. Further, we analyze selected syntheses of short and long oligodeoxyribonucleotides as well as single-stranded DNA sequences by well-known empirical autocorrelation, fast Fourier transformation, and embedding dimension techniques.

Targeting RNA structures by antisense oligonucleotides

The presence of folded regions in RNA competes with the binding of a complementary oligonucleotide, resulting in a weak antisense effect. Due to the key role played by a number of RNA structures in the natural regulation of gene expression it might be of interest to design antisense sequences able to selectively interact with such motifs in order to interfere with the biological processes they mediate. Different possibilities have been explored. A high affinity oligomer will disrupt the structure; if the target structure is solved one can take advantage of unpaired bases (bulges, loops) to minimize the thermodynamic cost of the binding. Alternatively, the folded structure can be accommodated within the complex via the formation of a local triple helix. Oligomers able to adapt to the RNA structure (aptamers) can be extracted by in vitro selection from randomly synthesized libraries comprising several billions of sequences.

Central administration of antisense oligodeoxynucleotides to neuropeptide Y (NPY) mRNA reveals the critical role of newly synthesized NPY in regulation of LHRH release

Compelling evidence shows that the episodic and cyclic secretion of hypothalamic luteinizing hormone releasing hormone (LHRH), the primary stimulator of pituitary LH release, is subject to regulation by neuropeptide Y (NPY). We have reported earlier that sequential treatment of ovariectomized (ovx) rats with estrogen and progesterone to stimulate a preovulatory-type LH surge elevated the levels of both NPY and preproNPY mRNA levels in the hypothalamus concomitant with dynamic changes in LHRH activity. The present study was designed to determine whether these elevations in NPY content and gene expression represent new synthesis of NPY that is crucial to elicit LHRH discharge. Ovx, steroid-primed rats received intracerebroventricular injections of an unmodified 20-mer oligodeoxynucleotide (oligo) complementary to the NPY mRNA sequence. Control rats were injected similarly with either saline or the sense or missense oligos. Results showed that control rats displayed a characteristic surge-type elevation in plasma LH levels that was not affected by the administration of missense or sense oligos. However, in rats injected with the antisense oligo, the steroid-induced LH surge was completely blocked. In an additional experiment, NPY peptide levels were measured in microdissected hypothalamic sites following the injection of antisense or missense oligos. NPY antisense oligo administration blocked the significant increases in NPY levels in the median eminence-arcuate area, the medial preoptic area and lateral preoptic area seen in control rats. These results suggest that sequential ovarian steroid treatment augments NPY synthesis in the hypothalamus and this newly synthesized NPY is critical for induction of the LHRH and LH surge.

A role for a small stable RNA in modulating the activity of DNA-binding proteins

The 10Sa RNA, encoded by the E. coli ssrA gene, appears to modulate action of some DNA-binding proteins. When ssrA is inactivated, lacZ expression from the lac operon, as well as galK from a gal operon fused to a phage lambda promoter, is reduced from that observed in bacteria wild-type for ssrA. These differences are not observed if the relevant repressor is inactive, suggesting that in the absence of 10Sa RNA binding of LacI and lambda cI repressors is enhanced. Gel mobility shifts show that 10Sa RNA binds these repressors and that an excess of 10Sa RNA competes for binding of lambda cI with a DNA fragment containing the OR2 repressor-binding sequence. Similar observations were made in studies of the E. coli LexA repressor and phage P22 C1 transcription activator proteins. These results suggest that direct interaction with 10Sa RNA may explain this modulation of protein-DNA interactions.

Effects of dexamethasone, heat shock, and serum responses on the inhibition of Hsc70 synthesis by antisense RNA in NIH 3T3 cells

A dexamethasone (Dex)-inducible antisense RNA expression vector was constructed that contains the 5'-untranslated region and one third of the coding sequence for the bovine hsc70 protein. This vector was used to transfect NIH 3T3 cells from which clonal cell lines expressing hsc70 antisense RNA were developed. Quantitative Northern blot analysis with strand-specific probes was used to demonstrate the Dex-inducible accumulation of hsc70 antisense RNA in proliferating cell cultures and the inhibition of hsc70 RNA levels. Surprisingly, antisense RNA was either much less effective in reducing the amounts of hsc70 RNA in Dex-treated cultures than in untreated controls or cells compensated by producing more hsc70 RNA in response to increasing amounts of antisense RNA. Hsc70 protein synthesis did not decrease in either Dex-treated or untreated cultures: it actually increased, again suggesting the activation of a compensatory response. In Dex-treated cultures subjected to heat shock, hsc70 antisense RNA blocked the induction of hsp70, indicating that newly synthesized RNA was targeted effectively before it became translationally active. To test this hypothesis further, Dex-treated cultures were made quiescent by serum deprivation and then restimulated with serum, which causes a burst of RNA and protein synthesis. Consistent with this hypothesis, increased synthesis of hsc70 was blocked in serum-stimulated cultures expressing antisense RNA.

Regulation of angR, a gene with regulatory and biosynthetic functions in the pJM1 plasmid-mediated iron uptake system of Vibrio anguillarum

AngR and the product(s) encoded in the trans-acting factor (TAF) region are necessary for the full expression of the pJM1 plasmid-mediated anguibactin iron-uptake system in Vibrio anguillarum (Va). In this report, we analyzed the factors that affect the expression of the angR gene. Northern blot analysis showed that angR encodes a 3.1-kb transcript which is expressed only under iron-limiting conditions. Measurement of steady-state RNA levels show that, under iron-limiting conditions, angR is positively regulated at the transcriptional level by product(s) of the Va TAF region. However, this enhancement of angR expression by TAF does not occur at high levels of the AngR protein, as assessed by using an angR::lacZ fusion in the presence of a construct containing angR under the control of ptac. We also report that repression of angR by iron could possibly be mediated by an endogenous Va antisense RNA beta, which contains a stem-loop structure complementary to the stem-loop structure located at the 5' end of angR.

Transgenes and gene suppression: telling us something new?

Transgenes provide unique opportunities to assess the relationship between genotype and phenotype in an organism. In most cases, introduction and subsequent expression of a transgene will increase (with a sense RNA) or decrease (with an antisense RNA) the steady-state level of a specific gene product. However, a number of surprising observations have been made in the course of many transgenic studies. We develop a hypothesis that suggests that many examples of endogenous gene suppression by either antisense or sense transcripts are mediated by the same cellular mechanism.

Polyadenylation of c-mos mRNA as a control point in Xenopus meiotic maturation

c-mos protein, encoded by a proto-oncogene, is essential for the meiotic maturation of frog oocytes. Polyadenylation of c-mos messenger RNA is shown here to be a pivotal regulatory step in meiotic maturation. Maturation is prevented by selective amputation of polyadenylation signals from c-mos mRNA. Injection of a prosthetic RNA, which restores c-mos polyadenylation signals by base pairing to the amputated mRNA, rescues maturation and can stimulate translation in trans. Prosthetic RNAs may provide a general strategy by which to alter patterns of mRNA expression in vivo.

Naturally occurring antisense transcripts are present in chick embryo chondrocytes simultaneously with the down-regulation of the alpha 1 (I) collagen gene

It has previously been shown that very low steady state levels of alpha 1 (I) collagen mRNA are present in chick embryo sternal chondrocytes (Askew, G. R., Wang, S., and Lukens, L. N. (1991) J. Biol. Chem. 266, 16834-16841), yet nuclear run-on experiments with double-stranded cDNA probes indicated a high transcription rate at this locus. These findings were investigated in this study using single-stranded probes, where nuclear run-on experiments showed that antisense transcription of the alpha 1 (I) collagen gene was occurring in chondrocytes, while sense strand transcription was down-regulated. Treatment of these chondrocytes with 5-bromo-2'-deoxyuridine (BrdU), which causes the cells to resemble their mesenchymal precursors, resulted in an antiparallel situation, where antisense transcription was lost, and instead, sense strand transcription was acquired, suggesting that the reverse switch from sense to antisense transcription occurs during chondrogenesis. Very large (> 10 kilobases) and heterogeneous antisense transcripts of moderate stability were shown to span both ends of the gene in chondrocytes, while their absence was shown in BrdU-treated chondrocytes, chick embryo fibroblasts, and a variety of other tissues. The function of these antisense transcripts is so far unknown, but their unusual chondrocyte-specific appearance, concurrent with little or no sense strand transcription, suggests a possible functional role in the down-regulation of the alpha 1 (I) collagen gene.

Antisense suppression of skeletal muscle myosin light chain-1 biosynthesis impairs myofibrillogenesis in cultured myotubes

Although the alkali or essential light chains of skeletal muscle myosin are not required for actin-activated myosin ATPase activity, these myosin subunits are necessary for force transmission with in vitro actin motility assays and are believed to stabilize the alpha-helical neck region of myosin subfragment-1. To probe the functions of the essential light chains during myofibril assembly, we used recombinant DNA procedures to deplete this light chain in cultured muscle. Retroviral expression vectors were constructed which encoded the exon-1 sequence of the myosin light chain-1 gene in antisense orientation. These vectors were applied to myogenic cells from embryonic chick and quail pectoralis muscle. Colonies expressing antisense RNA were selected in growth medium containing the neomycin analogue G-418, plus 5-bromo-2'-deoxyuridine (BrdU) and triggered to differentiate by removal of the latter. Expression of antisense myosin light chain-1 mRNA impaired muscle development. In the antisense cultures there were more mononucleated cells, fewer and smaller myotubes which had poorly developed myofibrils and high levels of diffusely staining myosin heavy chain, not apparent in control myotubes. Protein synthesis in the myotube cultures was analyzed by 35S-methionine labelling and two-dimensional gel electrophoresis. Except for a suppression of approximately 80% of myosin light chain-1f synthesis, the overall pattern of protein synthesis was not altered significantly. These studies suggest that retardation of myosin light chain-1f accumulation inhibits or delays myofibrillogenesis.

Murine transcription factor alpha A-crystallin binding protein I. Complete sequence, gene structure, expression, and functional inhibition via antisense RNA

alpha A-crystallin binding protein I (alpha A-CRYBP1) is a ubiquitously expressed DNA binding protein that was previously identified by its ability to interact with a functionally important sequence in the mouse alpha A-crystallin gene promoter. Here, we have cloned a single copy gene with 10 exons spanning greater than 70 kb of genomic DNA that encodes alpha A-CRYBP1. The mouse alpha A-CRYBP1 gene specifies a 2,688-amino acid protein with 72% amino acid identity to its human homologue, PRDII-BF1. Both the human and the mouse proteins contain two sets of consensus C2H2 zinc fingers at each end as well a central nonconsensus zinc finger. The alpha A-CRYBP1 gene produces a 9.5-kb transcript in 11 different tissues as well as a testis-specific, 7.7-kb transcript. alpha A-CRYBP1 cDNA clones were isolated from adult mouse brain and testis as well as from cell lines derived from mouse lens (alpha TN4-1) and muscle (C2C12). A single clone isolated from the muscle C2C12 library contains an additional exon near the 5'-end that would prevent production of a functional protein if the normal translation start site were utilized; however, there is another potential initiation codon located downstream that is in frame with the rest of the coding region. In addition, we identified multiple cDNAs from the testis in which the final intron is still present. Finally, we used an antisense expression construct derived from an alpha A-CRYBP1 cDNA clone to provide the first functional evidence that alpha A-CRYBP1 regulates gene expression. When introduced into the alpha TN4-1 mouse lens cell line, the antisense construct significantly inhibited expression from a heterologous promoter that utilized the alpha A-CRYBP1 binding site as an enhancer.

Transient transfection assays to examine the requirement of putative cell death genes

In conclusion, this chapter provides a convenient and efficient method for the detection and analysis of transiently transfected cells. Such strategies allow a fast and simple analysis of the requirement for particular genes that have been identified as being induced during apoptosis. Our experience has been that, when screening for "cell death genes," it is easy to isolate genes induced during apoptosis but far more difficult to determine the requirement for any given gene. These protocols have rendered such determinations much simpler to perform.

Antisense RNA-mediated inhibition of mouse hepatitis virus replication in L2 cells

We have successfully used antisense RNA to inhibit replication of the mouse hepatitis virus (MHV) in a cell culture system. MHV is a single-stranded RNA virus of positive polarity. Mouse L2 cells were stably transfected with an antisense construct that targets regions of genes 5 and 6 of the virus. High levels of expression from this construct, which is under control of the human elongation factor 1 alpha promoter, were found. After infection of the antisense cell lines with MHV, replication of the virus was significantly reduced compared with control cells. In a viral plaque assay, smaller plaques were found in the antisense cell lines. In addition, up to a 92% inhibition in the number of viral particles produced in one antisense cell line could be seen. This inhibitory effect decreased at longer (> 16 hour) infection times. It was possible to both increase the amount of inhibition and prolong the inhibitory effect by reducing the multiplicity of infection. Our results suggest that antisense RNA may be an effective tool to slow down progression of MHV infection in mice.

Effects of antisense DNA on POMC mRNA and ACTH levels in cultured human corticotroph adenoma cells

Antisense oligonucleotides have been investigated in recent years as potential new therapeutic agents because of their ability to shut off gene expression. Antisense DNA and RNA oligomers can bind specifically to mRNA preventing protein translation. We have studied the ability of an antisense POMC oligomer to reduce the expression of POMC in human ACTH-secreting pituitary adenoma cells cultured from 2 uncommon ACTH-secreting macroadenomas. In separate experiments, tumor tissue was enzymatically dispersed, cultured for 4 days, and treated with and without an antisense POMC oligonucleotide for 18 hours. In addition, cells from one tumor were treated with dexamethasone and cells from the other tumor were treated with an unrelated oligomer as controls. RNA was prepared from cultured cells and POMC mRNA was quantitated in a RNase protection assay using a human POMC RNA probe. ACTH in the media was quantitated by RIA. Tumor cells responded to 250 nmol/L dexamethasone with diminished POMC mRNA and ACTH levels 18 hours after treatment (decreased by 28% and 67% of control respectively). In both tumors, a POMC antisense oligomer at a concentration of 50 mumol/L lowered POMC mRNA levels and detectable ACTH levels in the media 18 hours after treatment, with mRNA levels decreased by 76% and 62% of control and ACTH levels decreased by 58% and 48% of control. Conversely, tumor cells treated with an unrelated oligomer at a 50 mumol/L concentration showed minimal effect on POMC mRNA and ACTH levels 18 hours after treatment (decreased by 2.3% and 1.5% of control respectively).(ABSTRACT TRUNCATED AT 250 WORDS)

Specific inhibition of aphthovirus infection by RNAs transcribed from both the 5' and the 3' noncoding regions

RNA molecules containing the 3' terminal region of foot-and-mouth disease virus (FMDV) RNA in both antisense and sense orientations were able to inhibit viral FMDV translation and infective particle formation in BHK-21 cells following comicroinjection or cotransfection with infectious viral RNA. Antisense, but not sense, transcripts from the 5' noncoding region including the proximal element of the internal ribosome entry site and the two functional initiation AUGs were also inhibitory, both in in vitro translation and in vivo in comicroinjected or cotransfected BHK-21 cells. This effect was not observed with nonrelated RNA transcripts from lambda phage. The inhibitions found were permanent, sequence specific, and dose dependent; an inverse correlation between the length of the transcript and the extent of the antiviral effect was seen. In all cases, the extent of inhibition increased when viral RNAs and transcripts were allowed to reanneal before transfection, concomitant with a decrease in the doses required. The antiviral effect was specific for FMDV, since transcripts failed to inhibit infective particle formation by other picornavirus, such as encephalomyocarditis virus. These results indicate that the ability of RNA transcripts to inhibit viral multiplication depends on their efficient hybridization with target regions on the viral genome. Furthermore, cells transfected with the 5'1as transcript, which is complementary to the 5' noncoding region, showed a significant reduction of plaque-forming ability during the course of a natural infection. RNA 5'1as was able to inhibit FMDV RNA translation in vitro, suggesting that the inhibitions observed are mediated by a blockage of the viral translation initiation. Conversely, hybridization of short sequences of both sense and antisense transcripts from the 3' end induces distortion of predicted highly ordered structural motifs, which could be required for the synthesis of negative-stranded viral RNA, and correlates with inhibition of viral propagation.

Nuclear antisense RNA. An efficient new method to inhibit gene expression

We describe an efficient new antisense RNA method to inhibit gene expression. Antisense RNAs that are retained in the nucleus bind to target transcripts and appear to lead to the degradation of their targets. Antisense RNAs can be expressed and accumulated specifically in the nucleus if they are not polyadenylated at their 3' ends. In antisense expression vectors we use a cis-acting ribozyme to generate 3'-ends independently of the polyadenylation machinery and thereby inhibit transport of RNA molecules from the nucleus to the cytoplasm. We have evaluated this method in the mouse polyoma virus model system, where nuclear antisense transcripts to the viral early transcription region efficiently reduced the level of viral early-strand RNAs. Nonspecific antisense RNA had no effects on viral gene expression. In comparative studies, nuclear antisense RNAs were significantly more effective in downregulating polyoma virus early RNAs than were conventional antisense molecules, which were processed by polyadenylation.

Destabilization of rbcS sense transcripts by antisense RNA

Steady-state rbcS mRNA levels are drastically reduced in transgenic tobacco plants that express rbcS antisense RNAs. We have found that these reductions are not due to an effect of the antisense RNA at the level of rbcS transcription; rather, the sense mRNAs are more actively degraded in the mutant than wild-type plants. We have examined the kinetics of this turnover process by inhibiting transcription with cordycepin, and have found that rbcS sense mRNA decay is accelerated about five-fold in the antisense plants. This provides direct evidence that antisense RNAs can serve to destabilize sense transcripts in plants.

Targeted nuclear antisense RNA mimics natural antisense-induced degradation of polyoma virus early RNA

We describe a general antisense strategy to inhibit target gene expression. The substitution of a cis-acting ribozyme for a polyadenylylation signal in an antisense expression vector results in the nuclear retention of RNAs and the efficient degradation of their targets. We demonstrate the utility of this system in polyoma virus, where early-strand RNA levels are downregulated in the nucleus by antisense late-strand counterparts. We show that mutations destabilizing these naturally occurring antisense transcripts lead to increased levels of early-strand RNAs. Furthermore, expression in trans of nuclear antisense transcripts lowers early-strand RNA levels and quantitatively mimics the natural regulation.

The BCMA gene, preferentially expressed during B lymphoid maturation, is bidirectionally transcribed

In a previous study of a t(4;16)(q26;p13) translocation, found in a human malignant T-cell lymphoma the BCMA gene, located on chromosome band 16p13.1, has been characterized. In this study we show that the BCMA gene is organized into three exons and its major initiation transcription site is located 69 nucleotides downstream of a TATA box. RNase protection assays demonstrated that the BCMA gene is preferentially expressed in mature B cells, suggesting a role for this gene in the B-cell developmental process. A cDNA complementary to the BCMA cDNA was cloned and sequenced and its presence was assessed by RNase protection assay and anchor-PCR amplification. This antisense-BCMA RNA is transcribed from the same locus as BCMA, and exhibits mRNA characteristic features, e.g. polyadenylation and splicing. It also contains an ORF encoding a putative 115 aa polypeptide, presenting no homology with already known sequences. RNase protection assays demonstrated the simultaneous expression of natural sense and antisense-BCMA transcripts in the majority of human B-cell lines tested.

Temporal regulation of a complex and unconventional promoter by viral products

The DNA polymerase (dnapol) gene of Autographa californica nuclear polyhedrosis virus presents a complex promoter organization. It lacks the usual TATA box and start site, and its RNA accumulation initially increases and then decreases dramatically during infection. We investigated dnapol temporal regulation. Transiently expressed dnapol gene was transcribed at a low level from minor start sites. Coexpression with ie0 and/or ie1 immediate-early genes dramatically enhanced dnapol transcription, specifically from a new start site. Moreover, the ie1 transactivation required little or no information in front of this nonconventional proximal promoter. We showed that IE0 and IE1 proteins were stably expressed during infection and that the dnapol mRNA level decrease was not a consequence of the disappearance of these proteins. The dnapol promoter region contains a putative overlapping open reading frame (ORF) in the opposite direction. We showed that ORF-2 was indeed highly expressed late, when the dnapol mRNA level decreased, and that during that time, dnapol mRNA stability was not significantly altered, excluding a destabilizing antisense effect. Additionally, we showed that the dnapol promoter was inhibited late but not early during the infection of cells transiently expressing constructs carrying either the intact or the altered ORF-2 promoter. Therefore, ORF-2 initiation of transcription and dnapol promoter inhibition are two coincidental nonrelated phenomena. Finally, we showed that both IE1 transactivation and late inhibition occurred in the same limited region around the dnapol promoter.

The role of the 5' untranslated region of eukaryotic messenger RNAs in translation and its investigation using antisense technologies

This chapter discusses the recent advances in the field of translational control and the possibility of applying the powerful antisense technology to investigate some of the unanswered questions, especially those pertaining to the role of the 5’untranslated region ( UTR) on translation initiation. Translational regulation is predominantly exerted during the initiation phase that is considered to be the rate-limiting step. Two types of translational regulation can be distinguished: global, in which the initiation rate of (nearly) all cellular messenger RNA (mRNA) is controlled and selective, in which the translation rate of specific mRNAs varies in response to the biological stimuli. In most cases of global regulation, control is exerted via the phosphorylation state of certain initiation factors, whereas only a few examples of selective regulation have been characterized well enough to define the underlying molecular events. Interestingly, cis-acting regulatory sequences, affecting translation initiation, have been found not only in the 5’UTRs of selectively regulated mRNAs, but also in the 3’UTRs. Thus, in addition to the protein encoding open reading frames, both the 5’ and 3’UTRs of mRNAs must be considered for their effect on translation.

Conditional inhibition of beta-glucuronidase expression by antisense gene fragments in petunia protoplasts

Antisense RNA-mediated inhibition of gene expression is a valuable tool to induce mutant phenotypes. We are interested in the application of antisense gene fragments with the aim to improve the efficiency of inhibition and to be able to selectively suppress gene family members in plants. Protoplasts may provide a rapid system to screen the efficiency of antisense gene segments. As a first step, we set up a transient expression system for leaf protoplasts of Petunia hybrida and used as a model system the inhibition of beta-glucuronidase (uidA) expression by uidA antisense gene segments. Both GUS enzyme activities and uidA RNA levels were measured. Co-introducing equal amounts of a full-length uidA antisense gene and a uidA sense gene reduced GUS activity by 60-70%. Various uidA antisense fragments also inhibited expression although with different efficiencies and we show that strong antisense fragments can be retrieved from weak antisense gene fragments. A promoter-less antisense gene did not reduce uidA expression indicating that the inhibition is mediated by antisense transcripts. Using quantitative PCR on first-strand cDNA we show that expression of functional antisense genes lead to reduced levels of uidA mRNA. This suggests that the mechanism of antisense RNA inhibition in protoplasts is similar to that in transgenic plants and that the protoplast system in combination with PCR can be used to preselect antisense fragments of any gene.

Expression of transforming growth factor alpha antisense mRNA inhibits the estrogen-induced production of TGF alpha and estrogen-induced proliferation of estrogen-responsive human breast cancer cells

To ascertain if 17 beta-estradiol (E2)-induced proliferation could be attenuated by blocking the expression of endogenous transforming growth factor alpha (TGF alpha), estrogen receptor (ER)-positive, estrogen-responsive MCF-7 or ZR-75-1 cells and ER-negative, estrogen-nonresponsive MDA-MB-468 or HS-578T cells were infected with a recombinant amphotropic, replication-defective retroviral expression vector containing a 435 base pair (bp) Apa1-Eco R1 coding fragment of the human TGF alpha cDNA oriented in the 3' to 5' direction and under the transcriptional control of an internal heavy metal-inducible mouse metallothionein (MT-1) promoter and containing the neomycin (neo) resistance gene. E2-stimulated expression of endogenous TGF alpha mRNA was inhibited by 4-5-fold, and the production of TGF alpha protein was inhibited by 50-80% when M-1 mass-infected MCF-7 or MZ-1 mass-infected ZR-75-1 cells were treated with 0.75-1 microM CdCl2, whereas in comparably treated parental MCF-7 or ZR-75-1 cells there was no significant effect upon these parameters. E2-stimulated anchorage-dependent growth (ADG) and anchorage-independent growth (AIG) of the M-1 or MZ-1 cells was inhibited by 60-90% following CdCl2 treatment. In contrast, neither the ADG nor AIG of the parental noninfected MCF-7 or ZR-75-1 cells that were maintained in the absence or presence of E2 was affected by comparable concentrations of CdCl2. The ADG and AIG of TGF alpha antisense MD-1 mass-infected MDA-MB-468 cells that express high levels of endogenous TGF alpha mRNA were also inhibited by 1 microM CdCl2, whereas the ADG and AIG of MH-1 mass-infected HS-578T cells, a TGF alpha-negative cell line, were unaffected by CdCl2 treatment. These results suggest that TGF alpha may be one important autocrine intermediary in regulating estrogen-induced cell proliferation.

Inhibition of viral growth by an alpha-oligonucleotide directed to the splice junction of herpes simplex virus type-1 immediate-early pre-mRNA species 22 and 47

A 13-residue alpha-anomeric oligonucleotide [alpha-5'-d(GGGCGTCCTCCTT)3'], 5'-substituted with a psoralen derivative, Pso-alpha-13 psoralen linked to the 5' end of an alpha-anomeric n-residue oligonucleotide, was targeted to the acceptor splice junction of Herpes simplex virus type-1 immediate-early pre-mRNA species 22 and 47. Inhibition of viral growth was observed upon irradiation of Vero cells infected with Herpes simplex virus type-1 and treatment with Pso-alpha-13. The virus titer was decreased by 80% at an oligonucleotide concentration of 0.5 microM and at a multiplicity of infection of 0.1 plaque-forming units/cell. The 13-residue oligonucleotide did not induce any cytotoxic effect after irradiation and the inhibition of viral growth was clearly sequence specific. A non-specific 5' Pso-alpha-15 did not inhibit Herpes simplex virus type-1 growth. The 5' Pso-alpha-13 targeted to the acceptor splice junction of Herpes simplex virus type 1, contained five mismatches with respect to the corresponding sequence of Herpes simplex virus type 2, and did not exhibit any inhibitory effects on Herpes simplex virus type-2 growth. These results show that alpha-oligonucleotides can exhibit a sequence-specific antiviral effect and suggest that they may inhibit splicing reactions and be useful in targeting specific nucleic acid sequences within the cell nucleus.

Infection with a transforming growth factor alpha anti-sense retroviral expression vector reduces the in vitro growth and transformation of a human colon cancer cell line

Transforming growth factor alpha (TGF alpha) is a growth factor produced by colon cancer cells which may function as an autocrine growth regulator. Therefore, the proliferation and transformation of colon cancer cells might be attenuated by blocking the production of endogenous TGF alpha. GEO cells, from a human colon carcinoma cell line that expresses TGF alpha and functional epidermal growth factor (EGF) receptors, were infected with a replication-defective, recombinant amphotropic retroviral expression vector containing the neomycin-resistance gene and a 435-bp ApaI-EcoRI coding fragment of the human TGF alpha cDNA oriented in the 3' to 5' direction under the transcriptional control of the heavy-metal-inducible mouse metallothionein I promoter. Following antibiotic selection, G418-resistant colonies were pooled and expanded into a cell line (GEO TGF alpha AS cells). A 50 to 70% inhibition in the production of secreted and cell-associated TGF alpha protein was observed in GEO TGF alpha AS cells that had been maintained in CdCl2-supplemented medium. Moreover, a growth inhibition of 70% and 50% was observed in CdCl2-treated GEO TGF alpha AS cells under anchorage-dependent and anchorage-independent culture conditions, respectively. In contrast, CdCl2 treatment of parental GEO cells had no significant effect upon these parameters. Our results suggest that TGF alpha may be involved in modulating the in vitro cell growth and transformation of human colon cancer cells that express both this growth factor and its cognate receptor.

Incorporation of the catalytic domain of a hammerhead ribozyme into antisense RNA enhances its inhibitory effect on the replication of human immunodeficiency virus type 1

The catalytic domain of a hammerhead ribozyme was incorporated into a 413 nucleotides long antisense RNA directed against the 5'-leader/gag region of the human immunodeficiency virus type 1 (HIV-1) (pos. +222 to +634). The resulting catalytic antisense RNA was shown to cleave its target RNA in vitro specifically at physiological ion strength and temperature. We compared the antiviral effectiveness of this catalytic antisense RNA with that of the corresponding unmodified antisense RNA and with a mutated catalytic antisense RNA, which did not cleave the substrate RNA in vitro. Each of these RNAs was co-transfected into human SW480 cells together with infectious complete proviral HIV-1 DNA, followed by analysis of HIV-1 replication. The presence of the catalytically active domain resulted in 4 to 7 fold stronger inhibition of HIV-1 replication as compared to the parental antisense RNA and the inactive mutant. Kinetic and structural studies performed in vitro indicated that the ability for double strand formation was not changed in catalytic antisense RNA versus parental antisense RNA. Together, these data suggest that the ability to cleave target RNA is a crucial prerequisite for the observed increase of inhibition of the replication of HIV-1.

Isolation of genetic suppressor elements, inducing resistance to topoisomerase II-interactive cytotoxic drugs, from human topoisomerase II cDNA

Many cytotoxic anticancer drugs act at topoisomerase II (topo II) by stabilizing cleavable complexes with DNA formed by this enzyme. Several cell lines, selected for resistance to topo II-interactive drugs, show decreased expression or activity of topo II, suggesting that such a decrease may be responsible for drug resistance. In the present study, etoposide resistance was used as the selection strategy to isolate genetic suppressor elements (GSEs) from a retroviral library expressing random fragments of human topo II (alpha form) cDNA. Twelve GSEs were isolated, encoding either peptides corresponding to short segments of the topo II alpha molecule (2.4-6.5% of the protein) or 163- to 220-bp-long antisense RNA sequences. Expression of a GSE encoding antisense RNA led to decreased cellular expression of the topo II alpha protein. Both types of GSE induced resistance to several topo II poisons but not to drugs that do not act at topo II. These results provide direct evidence that inhibition of topo II results in resistance to topo II-interactive drugs, indicate structural domains of topo II capable of independent functional interactions, and demonstrate that expression selection of random fragments constitutes an efficient approach to the generation of GSEs in mammalian cells.

In vitro selection of fast-hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1

The rate of double strand formation between procaryotic antisense RNA and complementary RNA in vitro is known to correlate with the effectiveness of antisense RNA in vivo. In this work, an in vitro assay for determining the hybridization rates of a large number of antisense RNA species was developed. A set of HIV-1-directed antisense RNAs with the same 5'-end but successively shortened 3'-ends was produced by alkaline hydrolysis of a 150 nt HIV-1-directed antisense transcript. This mixture was used to determine hybridization rates for individual chain lengths with a complementary HIV-1-derived RNA in vitro. The second order binding rate constants of individual antisense RNA species differed by more than a factor of 100, although in some cases, slow-hybridizing and fast-hybridizing antisense RNAs differed by only two or three 3'-terminally-located nucleotides. The results indicated that there was not a trivial dependence of binding rates on the chain length of antisense RNAs. Further, the binding rate constants determined in vitro for individual antisense RNA species correlated with the extent of inhibition of HIV-1 replication in vivo.

Regulation of the expression of bacterial iron transport genes: possible role of an antisense RNA as a repressor

Expression of the iron transport gene, fatB and fatA, in the bacterium Vibrio anguillarum 775 is negatively regulated by the iron concentration in the medium. Here, we show that iron represses fatB and fatA mRNA levels and concomitantly induces the synthesis of an antisense RNA (RNA alpha). The presence of RNA alpha correlates with the inhibition of FatA protein synthesis and thus may play a role in the iron repression of fatA expression. Since the 5' end of RNA alpha maps 125 nucleotides upstream from the start codon of fatA and this RNA also extends into the coding region of fatB, it may also be involved in the iron regulation of fatB expression. RNA alpha may thus constitute a novel component of the bacterial iron regulatory circuit.

Evaluation of the use of antisense tRNA(met) as an inhibitor for eukaryotic protein synthesis

We attempted to explore the use of antisense RNAs against tRNA as an inhibitor of eukaryotic protein synthesis. For this purpose, antisense RNA against the 5'-end half of the initiator tRNA of wheat germ was synthesized, and its effect on translation of the Brome mosaic virus mRNA was investigated in a wheat germ cell-free system. When the antisense RNA against the 5'-end half of the initiator tRNA including the anticodon sequence was added at the concentration of 8 microM to the cell-free system, protein synthesis was completely inhibited. This inhibitory effect could be suppressed by the addition of wheat germ tRNA. In contrast, sense and control RNA showed slight inhibitory effects, which were not, however, suppressed by wheat germ tRNA. The antisense tRNA formed a double-stranded RNA duplex with the target methionine tRNA in the wheat germ extract which became resistant to ribonuclease treatment. These experiments suggest that antisense tRNA could be utilized for control of tRNA functions and to block protein synthesis.