On the role of RNA amplification in dsRNA-triggered gene silencing.

We have investigated the role of trigger RNA amplification during RNA interference (RNAi) in Caenorhabditis elegans. Analysis of small interfering RNAs (siRNAs) produced during RNAi in C. elegans revealed a substantial fraction that cannot derive directly from input dsRNA. Instead, a population of siRNAs (termed secondary siRNAs) appeared to derive from the action of a cellular RNA-directed RNA polymerase (RdRP) on mRNAs that are being targeted by the RNAi mechanism. The distribution of secondary siRNAs exhibited a distinct polarity (5'-->3' on the antisense strand), suggesting a cyclic amplification process in which RdRP is primed by existing siRNAs. This amplification mechanism substantially augments the potency of RNAi-based surveillance, while ensuring that the RNAi machinery will focus on expressed mRNAs.     

RNA biosynthesis in the microsomes of splenic cells during the inductive phase of the immunological response]

RNA labeled with 3H-uridine was extracted from the microsomes of the spleen of the intact and antigen-stimulated mice. A study was made of the composition of this RNA by electrophoresis in polyacrylamide gel. Apart from rRNA, there were revealed in the microsome composition up to 10 RNA components in the mol wt range of from 0.4-10(5) to 7-10(5) dalton and 2 componnents - between 7-10(5) and 1.7-10(6) dalton. Incorporation of 3H-uridine into the rRNA was the maximal 24 hours after the administration of the antigen, whereas the RNA with the mol wt between 0.4-10(5) dalton remaining practically unchanged for a period of three days after the immunization. 3H-uridine incorporation into these RNA was resistant to the action of low antibiotic (actinomycin D) doses. Immunization was not accompanied by the appearance of new, by molecular weight, RNA components.     

RNA扩增的研究进展

RNA扩增是伴随着基因芯片技术的应用而发展起来的一项技术,但不仅仅应用于芯片杂交。本文对RNA扩增的技术方法进行了综述,重点介绍了mRNA的线性扩增、指数扩增以及两者相结合的扩增方法以及优缺点,对microRNA的扩增方法也作了介绍,并对将来的发展作了展望。     

Use of bromovirus RNA3 hybrids to study template specificity in viral RNA amplification.

Brome mosaic virus (BMV) and cowpea chlorotic mottle virus (CCMV) are related positive-strand RNA viruses with genomes divided among RNAs 1, 2, and 3. RNAs 1 and 2 encode the viral RNA replication factors, which share extensive conservation with proteins encoded by the animal alphaviruses and diverse plant viruses. In barley protoplasts, CCMV RNAs 1 and 2 support high but distinguishable amplification of either BMV RNA3 (B3) or CCMV RNA3 (C3), while BMV RNAs 1 and 2 show even greater discrimination, amplifying C3 poorly relative to B3. To identify the cis-acting determinants of these template-specific and virus-specific differences in RNA3 accumulation, we constructed and tested a series of B3/C3 hybrids that exchange in turn the 5',3', and intercistronic noncoding regions, which contain all sequences required in cis for efficient B3 and C3 amplification. Despite suggestive prior in vitro results, the 3' noncoding regions were not the major determinant of the differences in amplification of B3 and C3 in vivo. Rather, 3' exchanges had relatively modest effects and did not transfer the distinctive asymmetry of amplification between B3 and C3. Intercistronic exchanges produced larger effects on RNA3 accumulation and transferred some of the polarized characteristics of the wild-type B3 and C3 behaviors. 5' exchanges revealed context-specific effects showing that the contribution of the B3 5' region to RNA3 amplification is dependent on some other B3 segment or segments. Together with previous results implicating the BMV and CCMV 1a genes in trans-acting discrimination between B3 and C3 (P. Traynor and P. Ahlquist, J. Virol. 64:69-77, 1990), these observations should help to guide studies of protein-RNA interactions governing template specificity in bromovirus RNA replication.     

Further studies on amplification of cell-associated immunological memory by secondary antigenic stimulus.

Using the hapten-carrier system in which the dinitrophenyl group (DNP) served as a B cell reactive hapten and bovine serum albumin (BSA) or human gammaglobulin (HGG) as a T cell reactive carrier, changes in the hapten-specific memory (B cell-associated memory) and the carrier-specific memory (T cell-associated memory) after a secondary antigenic stimulus were analyzed in mice. Since an immunological adjuvant was indispensable in the induction of the primary increase in memory, antigen used for the primary antigenic stimulus was injected together with the capsular polysaccharide of Klebsiella pneumoniae (CPS-K) which has already been shown to exhibit a potent adjuvant effect. With the cell-transfer technique, it was found that the cell-associated hapten-specific memory for anti-DNP antibody response to DNP-BSA was truly amplified by the secondary injection of DNP-HGG into mice primed with DNP-HGG, and that the cell-associated carrier-specific memory as judged by the helper effect on anti-DNP response to DNP-BSA was also truly amplified by the secondary injection of BSA into mice primed with BSA. However, when memory was assessed in actively immunized mice, the secondary injection of BSA into mice primed with DNP-BSA and HGG decreased anti-DNP responsiveness to the tertiary injection of DNP-BSA, whereas the secondary injection of DNP-HGG secondarily increased anti-DNP responsiveness. In mice primed with DNP-BSA the titers of serum antibodies to BSA increased after the secondary injection of DNP-BSA or BSA. From these results it has been concluded that, like B cell-associated memory, T cell-associated memory is also amplified by a secondary antigenic stimulus, although its expression is inhibited in actively immunized mice through negative control by their antibodies.     

Regulation of the SOS response analyzed by RecA protein amplification.

A split UV light dose procedure was used in Escherichia coli to induce an SOS function, RecA protein amplification, which was measured by an immunoradiometric assay. The SOS system was partially induced after the first UV irradiation, and the inducing effects of subsequent identical UV doses were quantified. Variations in the inducing effects of successive UV doses were related to modulations of the SOS signal level during SOS induction. A reduction in the level of SOS signal was found after 20 min in the wild-type strain, hypothesized to result from negative control of repair functions. A few DNA repair mutants were tested by the same procedure; the uvrA, recF, and umuC genes were involved in SOS induction control, but we found differences in their respective kinetics of expression. On the contrary, in a recB mutant, only a slight effect was obtained on this control.     

Boosting riboswitch efficiency by RNA amplification

Riboswitches are RNA sensors that regulate gene expression in response to binding of small molecules. Although they conceptually represent simple on/off switches and, therefore, hold great promise for biotechnology and future synthetic biology applications, the induction of gene expression by natural riboswitches after ligand addition or removal is often only moderate and, consequently, the achievable expression levels are not very high. Here, we have designed an RNA amplification-based system that strongly improves the efficiency of riboswitches. We have successfully implemented the method in a biological system for which currently no efficient endogenous tools for inducible (trans)gene expression are available: the chloroplasts of higher plants. We further show that an HIV antigen whose constitutive expression from the chloroplast genome is deleterious to the plant can be inducibly expressed under the control of the RNA amplification-enhanced riboswitch (RAmpER) without causing a mutant phenotype, demonstrating the potential of the method for the production of proteins and metabolites that are toxic to the host cell.     

Reliable amplification method for bacterial RNA

DNA microarray technology has been increasingly applied for studies of clinical samples. Frequently, RNA probes from clinical samples are available in limited amounts. We describe a reliable amplification method for bacterial RNA. We verified this method on mycobacterial RNA applying mycobacterial genome-directed primers (mtGDPs). Glass slide-based oligoarrays were employed to assess the quality of the amplification method. We observed a relatively small bias in amplified RNA pool when compared to the unamplified one. Up to 1000-fold linear RNA amplification in a single amplification round was obtained. To our knowledge, this study describes the first amplification method for mycobacterial RNA.     

Size heterogeneity of the largest subunit of nuclear RNA polymerase II. An immunological analysis

Antibodies raised against the 180-kDa subunit of cauliflower RNA polymerase II bind selectively to the largest subunit of RNA polymerase II purified from a variety of plant species. The selective binding of this antibody to the largest RNA polymerase II subunit has allowed us to probe for the size of this subunit in crude cell extracts, in fractions containing partially purified RNA polymerase II, and in isolated nuclei. Fractions containing RNA polymerase II were subjected to electrophoresis in the presence of sodium dodecyl sulfate, blotted onto nitrocellulose, and blots were probed with antibody. Immunoglobulin complexes were revealed with 125I-Protein A. Published purification procedures result in rapid conversion of a 220-kDa subunit to a 180-kDa polypeptide, but purification at high pH (pH 9.0) retards this proteolysis. RNA polymerase II associated with isolated nuclei is largely protected from proteolytic degradation, and a 240-kDa polypeptide as well as a 220-kDa polypeptide can be detected. These results suggest that the 180-kDa subunit of RNA polymerase II arises artificially during cell lysis and enzyme purification, and that even the 220-kDa polypeptide may be a degradation product of a 240-kDa polypeptide in plants.     

Humoral components of immunological response in nephrotic syndrome

Serum and urine were collected from 58 patients with nephrotic syndrome. Immunoglobulins (IgA, IgG and IgM), complement (C3) and transferrin levels were measured by single radial immunodiffusion. The extent of glomerular injury was estimated by determining the selectivity of proteinuria. The relationship between the severity of glomerular damage and serum concentrations of immunoglobulins and complement was assessed. Higher IgM and lower IgG serum concentrations were found in nephrotic patients than in normal controls (157 +/- 108 mg+ vs 127 +/- 38 mg% for IgM, 929 +/- 537 mg% for IgG). The difference was statistically significant (p less than 0.05 for IgM, p less than 0.001 for IgG). No correlation was present between the selectivity of proteinuria and serum levels of IgA, IgM, IgG or C3. The results indicate that abnormalities in humoral components of the immune system are present in nephrotic patients and are probably related to a basic immunological defect in the patients rather than to the severity of glomerular damage.     

Ribosomal RNA gene amplification by rolling circles

Previous work has raised the possibility that gene amplification in Xenopus laevis oocytes involves a rolling circle intermediate (Hourcade et al., 1973a,b). We have combined electron microscopy with autoradiography in order to examine the structure of replicating ribosomal DNA molecules. The frequency of lariats (the presumptive rolling circles) in unlabelled ribosomal DNA is about 1%. If only labelled molecules are scored after a six-hour pulse with radioactively labelled DNA precursors, the proportion of lariats increases to about 8.5%. After pulses of two hours or less, the frequency rises still further to about 18%. In pulse and pulse-chase experiments, the lariats display a labelling pattern that is consistent with a rolling circle model: (1) as the pulse length is increased the labelled region in the tail grows from the replication fork towards the free end of the tail; (2) after a pulse-chase the labelled region is displaced towards the free end of the tail and no label remains associated with the lariat circle. The frequency of labelled free circles is lower by 80% in pulse-chased DNA than in DNA that has not been chased. This suggests that most of the radioactive circles are derived from broken rolling circles. Cyclization of lariat tails could account for the remaining labelled circles.     

Many-trillionfold amplification of single RNA virus particles fails to overcome the Muller's ratchet effect.

We showed earlier that transfers of large populations of RNA viruses lead to fitness gains and that repeated genetic bottleneck transfers result in fitness losses due to Muller's ratchet. In the present study, we examined the effects of genetic bottleneck passages intervening between population passages, a process akin to some natural viral transmissions, using vesicular stomatitis virus as a model. Our findings show that the pronounced fitness increases that occur during two successive population passages cannot overcome the fitness decreases caused by a single intervening genetic bottleneck passage. The implications for natural transmissions of RNA viruses are discussed.