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PubMed2003

An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material.

We have developed an improved method for constructing a full-length cDNA library using small quantity of material by modifying the original oligo-capping method. In our devised method, total RNAs are used in sequential oligo-capping steps directly without preliminary mRNA purification. Using this method, we constructed full- length cDNA libraries from 100 mg of total RNA. These libraries contained 8x10(5) to 8x10(6) independent clones with average insert sizes of 2.0 kb. Moreover, the number of full-length cDNAs containing the translation initiation codon ATG in the constructed libraries was estimated to 60-70%. In addition, 54% of the known cDNAs had a longer 5' end than the corresponding genes in the public database. Our results show that the method can be effectively used to construct full-length enriched cDNA libraries, especially, if starting material is limited.

Base Sequence↗

PubMed1982

RNA synthesis in immature mouse oocyte development.

Oocyte development in several nonmammalian species is characterized by the synthesis of large quantities of ribonucleic acids during lampbrush stages of meiosis. These are stored in the oocyte and used during later oocyte maturation and early embryogenesis. This autoradiographic study examined the incorporation and persistence of ribonucleic acid in mouse oocytes during comparable stages of development. At each age examined, fetal through juvenile, the radiolabeled RNA precursors were incorporated into mouse oocytes during the growth stages. The RNAase-digestible label appeared first over nucleoli and meiotic chromosomes, becoming cytoplasmic after 24 hours, and remaining cytoplasmic through all remaining stages. Once incorporated the label persisted during subsequent oocyte growth and maturation through preimplantation embryo stages with apparently undiminished levels. It is suggested that this persistently labeled RNA represents maternal RNA stored for use during early embryonic development.

Animals↗

PubMed1977

Large scale preparation of calf liver nuclei by continuous flow centrifugation.

Large scale purification and preparation of calf liver nuclei was accomplished by high speed centrifugation of a fraction enriched in nuclei ('nuclear homogenate') through 1.8 M sucrose by means of a Beckman CF-32 Ti continuous flow rotor. In comparison with methods involving the use of conventional high capacity rotors, larger volumes of homogenate could be processed. This method was used to prepare nuclei from calf liver for the preparation of DNA-dependent RNA polymerases. The use of continuous flow ultracentrifugation avoids time-consuming manipulations, thus allowing handling of large quantities of tissue.

Animals↗

PubMed1997

Infectious RNA transcripts from full-length dengue virus type 2 cDNA clones made in yeast.

The dengue virus type 2 genomic RNA was amplified by reverse transcription-PCR and cloned as four cDNA fragments. We could not assemble these four fragments into full-length cDNA in Escherichia coli. The full-length dengue virus cDNA was constructed by homologous recombination in yeast, either as part of a yeast artificial chromosome or in a yeast-E. coli shuttle vector. Full-length cDNA clones were propagated once in E. coli to prepare useful quantities of DNA. In vitro transcription of these clones produced full-length RNA transcripts. Introduction of these transcripts into LLC-MK2 cells produced typical dengue infection, as judged by cytopathic effects and indirect immunofluorescence. Infectivity was sensitive to RNase digestion and was dependent on the presence of cap analog in the transcription reaction mixture. Virus in the medium was passaged on C6-36 cells to produce stocks, and these stocks had titers and plaque morphologies similar to those of the parental dengue virus type 2. Intracellular dengue virus RNA from cells infected with transcript-derived virus contained an introduced BstEII site, proving that infectivity was derived from RNA transcripts and not from contamination with parental dengue virus. Transcript-derived virus was comparable to dengue virus type 2 for growth and protein expression in tissue culture cells. Sequence analysis of the dengue virus cDNA in one full-length clone revealed only one unexpected silent mutation. By using yeast technology, it will be easy to introduce specific mutations into the dengue virus cDNA, allowing analysis of the virus phenotype in cells transfected with mutant transcripts.

Aedes↗

PubMed2000

Hepatitis C-induced hepatic allograft injury is associated with a pretransplantation elevated viral replication rate.

Hepatitis C virus (HCV) allograft infection after liver transplantation follows a variable but accelerated course compared with the nontransplantation population. Predictors of outcome and mechanisms of reinfection remain elusive. The accelerated HCV-induced allograft injury associated with a 10- to 20-fold increase in serum viral quantity posttransplantation was hypothesized to be the result of elevated intrahepatic viral replication rates. Patients (N = 23) with HCV-induced end-stage liver disease who underwent liver transplantation between October 1995 and December 1998 were prospectively studied. HCV-induced allograft injury was defined by posttransplantation persistent biochemical hepatitis or allograft fibrosis not explained by other diagnoses. Liver biopsies (N = 92) were obtained by protocol and when clinically indicated. Negative-strand HCV RNA (putative intermediate for replication) was detected by a strand-specific reverse-transcription polymerase chain reaction (RT-PCR) assay and semiquantatively compared with constitutively expressed 18S rRNA. Recipients with increased pretransplantation replication were at increased risk for the development of posttransplantation biochemical hepatitis (P =.03), an increased rate of allograft fibrosis (P =.006), and increased mortality rate (40.0% vs. 0.0%; P =.02). There was no correlation with quantities of genomic HCV RNA in the serum with relative intrahepatic viral replication either before or after liver transplantation. The relative rate of HCV replication within the allograft was not elevated in the posttransplantation period compared with that seen within the explanted liver. Accelerated allograft injury caused by HCV may be predicted by viral replication rates within the explanted liver. The stable intrahepatic replication rate after transplantation suggests that elevated serum viral loads are the result of decreased viral clearance, possibly secondary to immunosuppressive therapy.

Adolescent↗

PubMed1984

Cloning and expression of a yeast copper metallothionein gene.

The induction of a copper-binding metallothionein (Cu-MT) was studied in yeast, Saccharomyces cerevisiae, and a relationship between copper resistance and intracellular levels of Cu-MT in these eukaryotes was established. Poly(A)-containing RNA from a copper-resistant (Cur) yeast strain, which synthesized abundant quantities of Cu-MT and in which Cu-MT gene transcription was enhanced 50-fold upon exposure to CuSO4, was used to screen yeast genomic DNA clones. Restriction analysis revealed common XbaI and KpnI sites in five genomic clones isolated. The transcription of these clones was regulated by copper. Transformation of a copper-sensitive (Cus) yeast strain by one of these clones confers copper resistance in yeast. The results suggest that the expression of the Cu-MT gene is, in part, responsible for mediating copper resistance in yeast.

Cloning, Molecular↗

PubMed1975

Use of nucleic acid hybridization for specific detection of submicrogram quantities of DNA, and its application to human plasma.

A technique is described for using radiolabeled RNA complementary to human DNA as a probe for the specific identification of submicrogram concentrations of human DNA by formation of RNA-DNA hybrids. An example is given of its application to the semiquantitation of human DNA in human plasma, a substance that is ordinarily difficult to examine because materials are present that interfere with the usual colorimetric or fluorometric assays. An example is also given of the use of an analogous approach to analyzing rabbit serum for circulating bacterial DNA. Unique to the hybridization technique is a degree of specificity sufficient to identify specific base sequences and hence the origin of the DNA being detected, a point that may be important in the examination of circulating DNA reported to occur in patients with systemic lupus erythematosis. This technique may also be of value in clarifying the presently conflicting data regarding the occurrence of free DNA in the normal human circulation.

Animals↗

PubMed1972

Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose.

A convenient technique for the partial purification of large quantities of functional, poly(adenylic acid)-rich mRNA is described. The method depends upon annealing poly(adenylic acid)-rich mRNA to oligothymidylic acid-cellulose columns and its elution with buffers of low ionic strength. Biologically active rabbit globin mRNA has been purified by this procedure and assayed for its ability to direct the synthesis of rabbit globin in a cell-free extract of ascites tumor. Inasmuch as various mammalian mRNAs appear to be rich in poly(adenylic acid) and can likely be translated in the ascites cell-free extract, this approach should prove generally useful as an initial step in the isolation of specific mRNAs.

Acrylamides↗

PubMed1975

Different binding of poly(A)-containing and poly(A)-free fractions of nuclear ribonucleic acid to ribosomes from rat liver.

Total nuclear RNA extracted from nuclei of rat liver cells by phenol/chloroform in the presence of sodium dodecyl sulphate was separated by combined gel filtration on Sepharose 4 B and affinity chromatography on poly(U) Sepharose into fractions differing in their molecular weights and contents of poly(A) sequences. The poly(A)-containing 45-S RNA became labelled most rapidly if rats were administered [3H] orotic acid. This fraction showed a high template activity when added to postmitochondrial supernatants of the Krebs ascites tumour. Fractions of nRNA, free of poly(A) sequences, had no stimulating effect on protein synthesis in this system. The 45-S RNA-containing poly(A) was readily bound to crude polyribosomes from rat liver at 0 degrees C and both ATP and GTP were necessary for this reaction. Sucrose gradient analyses provided evidence that this RNA species is bound predominantly to 80-S ribosomes. No binding was obtained with polyribosomes washed with 0.5 M KCl. The binding ability of washed polyribosomes was restored by the addition of the ribosomal wash fraction or rat liver cytosol. Crude polyribosomes bound significantly lower quantities of nRNA species free of poly(A) when compared with poly(A)-45-S RNA. The label was scattered through the whole ribosomal sedimentation pattern with no predominant peaks and the binding reaction required neither soluble factors nor nucleotide cofactors. The labelling kinetics and high template activity of poly(A)-45-S nRNA indicate that this fraction contains precursors of cytoplasmic mRNA. Requirements for soluble factors and nucleotide cofactors in the binding of this RNA species to 80-S ribosomes suggest that this binding, unlike that of other nRNA species, has a specific mechanism resembling that of mRNA binding during peptide initiation.

Animals↗

PubMed1997

Measurement of the linking number change in transcribing chromatin.

The in vivo-initiated, transcribing simian virus 40 (SV40) minichromosome was analyzed to determine its DNA linking number change, i.e. the difference between the linking number of the minichromosomal DNA and that of relaxed bare DNA. As part of this measurement, the linking number change due to the in vivo-initiated RNA polymerase II was determined, the first time a value for this quantity has been reported. The topological contribution of the polymerase was combined with values determined for constrained and non-constrained linking number contributions from the native transcription complex chromatin to yield the linking number change for the complex. The linking number change of the native non-transcribed SV40 minichromosome was independently determined and was found to be virtually the same as that for the chromatin of the transcription complex. This indicates that there is little difference between the two structures. The plausibility of several current models for the contribution of chromatin structure to transcription regulation is discussed in light of this finding.

Cell Extracts↗

PubMed2006

Amount changes of tRNA modification enzymes in Thermus thermophilus HB8 cells according to culture temperatures.

Thermus thermophilus HB8 is an extreme thermophilic eubacrium, which grows at 50-80 degrees C. Transfer RNA molecules in T. thermophilus HB8 contains modified nucleosides such as Gm18, m(7)G46, m(5)s(2)U54, Psi55, and m(1)A58. Recently, all responsible genes for these modifications have been identified. To clarify the relationship of the amounts of the RNA modification enzymes (proteins) and culture conditions, we investigated the activities and quantities of the proteins. In this meeting, we report the amount changes of tRNA (Gm18) methyltransferase [TrmH] in T. thermophilus HB8 cells cultured at 52, 67, 75, and 79 degrees C. 60 mug of total proteins in the crude extract from cells cultured at 67 degrees C contained about 10-30 ng of the TrmH protein. Thus, the content of the TrmH protein was estimated to be around 1/5000 of the total proteins. Through the log phase, the content of the TrmH protein was not changed obviously. However, in the stationary phase, the content of the TrmH protein was slowly reduced. The TrmH contents in the cells cultured at 75 or 79 degrees C were similar to that at 67 degrees C. However, the content of the TrmH protein in the extract from 52 degrees C cultured cells slightly decreased as compared with that in the 67 degrees C cultured cells.

Bacterial Proteins↗

PubMed1996

Synthesis of leader RNA and editing of P mRNA during transcription by rinderpest virus.

Purified rinderpest virus was earlier shown to transcribe in vitro, all virus-specific mRNAs with the promoter-proximal N mRNA being the most abundant. Presently, this transcription system has been shown to synthesize full length monocistronic mRNAs comparable to those made in infected cells. Small quantities of bi- and tricistronic mRNAs are also synthesized. Rinderpest virus synthesizes in vitro, a leader RNA of approximately 55 nucleotides in length. Purified rinderpest virus also exhibits RNA editing activity during the synthesis of P mRNA as shown by primer extension analysis of the mRNA products.

Animals↗

PubMed1983

Physical studies on a nucleoprotein from the ribosome of E. coli.

Bacterial 5S RNA and its cognate proteins constitute an attractive system to study nucleoprotein interactions. The molecular weights of the components involved are modest and they can be prepared in the quantities necessary to permit the application of material-intensive techniques like NMR and X-ray crystallography. 5S RNA is being examined by proton NMR at 500 MHz with special attention paid to the downfield NH proton region. A substantial number of assignments can be suggested in this region based on nuclear Overhauser results. The binding of protein L25 (E. coli) to the RNA gives rise to a highly characteristic set of perturbations in the spectrum of the RNA. The data suggest a localized and assignable alteration in RNA structure upon formation of the complex. In addition we have grown large crystals of RNAs related to 5S RNA and their complexes with a cognate protein. The properties of these crystals and the progress made in analyzing their structure are discussed.

Base Sequence↗

PubMed1970

Regulation of initiation of DNA synthesis in Chinese hamster cells. I. Production of stable, reversible G1-arrested populations in suspension culture.

Suspension cultures of Chinese hamster cells (line CHO) were grown to stationary phase (approximately 8-9 x 10(5) cells/ml) in F-10 medium. Cells remained viable (95%) for at least 80 hr in stationary phase, and essentially all of the cells were in G(1) Upon resuspension or dilution with fresh medium, the cells were induced to resume traverse of the life cycle in in synchrony, and the patterns of DNA synthesis and division were similar to those observed in cultures prepared by mitotic selection. Immediately after dilution, the rates of synthesis of RNA and protein increased threefold. This system provides a simple technique for production of large quantities of highly synchronized cells and may ultimately provide information on the biochemical mechanisms regulating cell-cycle traverse.

Animals↗

PubMed1986

A cloned cDNA encoding MAP1 detects a single copy gene in mouse and a brain-abundant RNA whose level decreases during development.

Screening of a bacteriophage lambda gt11 cDNA expression library with a polyclonal anti-microtubule associated protein (MAP) antiserum resulted in the isolation of two non-cross-hybridizing sets of cDNA clones. One set was shown to encode MAP2 (Lewis, S. A., A. Villasante, P. Sherline, and N. J. Cowan, 1986, J. Cell Biol., 102:2098-2105). To determine the specificity of the second set, three non-overlapping fragments cloned from the same mRNA molecule via a series of "walking" experiments were separately subcloned into inducible plasmid expression vectors in the appropriate orientation and reading frame. Upon induction and analysis by immunoblotting, two of the fusion proteins synthesized were shown to be immunoreactive with an anti-MAP1-specific antibody, but not with an anti-MAP2-specific antibody. Since these MAP1-specific epitopes are encoded in non-overlapping cDNAs cloned from a single contiguous mRNA, these clones cannot encode polypeptides that contain adventitiously cross-reactive epitopes. Furthermore, these cDNA clones detected an abundant mRNA species of greater than 10 kb in mouse brain, consistent with the coding requirement of a 350,000-D polypeptide and the known abundance of MAP1 in that tissue. The MAP1-specific cDNA probes were used in blot transfer experiments with RNA prepared from brain, liver, kidney, stomach, spleen, and thymus. While detectable quantities of MAP1-specific mRNA were observed in these tissues, the level of MAP1 expression was approximately 500-fold lower than in brain. The levels of both MAP1-specific and MAP2-specific mRNAs decline in the postnatal developing brain; the level of MAP1-specific mRNA also increases slightly in rat PC12 cells upon exposure to nerve growth factor. These surprising results contrast sharply with reported dramatic developmental increases in the amount of MAP1 in brain and in nerve growth factor-induced PC12 cells. The cDNA clones encoding MAP1 detect a single copy sequence in mouse DNA, even under conditions of low stringency that would allow the detection of related but mismatched sequences. The cDNAs cross-hybridize with genomic sequences in rat, human, and chicken DNA, but not with DNA from frog, Drosophila, or sea urchin. These data are discussed in terms of the evolution and possible biological role of MAP1.

Animals↗

PubMed1991

Identification of Gz alpha as a pertussis toxin-insensitive G protein in human platelets and megakaryocytes.

G proteins mediate the interaction between cell surface receptors and intracellular effectors. Recent studies have shown that human retina and rat brain contain mRNA encoding a novel 40-Kd G protein alpha subunit referred to as Gz alpha. Studies with an antiserum selective for the predicted sequence of this protein have suggested that a similar protein is present in human platelets and is phosphorylated during platelet activation. To better understand the structure and function of this protein, the present studies examine its sequence in platelets and compare its abundance in human platelets, megakaryocytes, and two megakaryoblastic cell lines, HEL cells and Dami cells. Three different Gz alpha-selective antisera reacted with a 40-Kd protein in platelet membranes. None of these detected a corresponding protein in HEL or Dami cells, despite the presence in both cell lines of proteins recognized by antisera selective for three members of the Gi alpha family. Northern blotting with a Gz alpha-specific probe prepared from retinal Gz alpha showed two hybridizing species in platelet RNA: a major band at 3.5 kb and a minor band at 2.2 kb. Both were detectable in HEL and Dami cells, but at greatly reduced levels compared with platelets. RNA encoding Gz alpha was also detected in individual human megakaryocytes by in situ hybridization. The amount present approached that of Gi alpha 2' the most abundant of the Gi alpha species present in platelets. The complete sequence of the platelet homolog to Gz alpha was determined from platelet RNA amplified by the polymerase chain reaction. The encoded protein was the same as those obtained in brain and retina. Thus, based on immunoreactivity and nucleotide sequencing, platelets and megakaryocytes contain substantial quantities of a protein identical to brain and retinal Gz alpha. The paucity of Gz alpha protein and RNA in the megakaryoblastic cell lines suggests that either there has been a selective loss of the ability to synthesize Gz alpha from these cells or that Gz alpha appears at a later stage in megakaryocyte development than does Gi alpha.

Base Sequence↗

PubMed1988

Expression of apolipoprotein E by cultured vascular smooth muscle cells is controlled by growth state.

Rat vascular smooth muscle cells (SMC) in culture synthesize and secrete a approximately 38,000-Mr protein doublet or triplet that, as previously described (Majack and Bornstein. 1984. J. Cell Biol. 99:1688-1695), rapidly and reversibly accumulates in the SMC culture medium upon addition of heparin. In the present study, we show that this approximately 38,000-Mr heparin-regulated protein is electrophoretically and immunologically identical to apolipoprotein E (apo-E), a major plasma apolipoprotein involved in cholesterol transport. In addition, we show that expression of apo-E by cultured SMC varies according to growth state: while proliferating SMC produced little apo-E and expressed low levels of apo-E mRNA, quiescent SMC produced significantly more apo-E (relative to other proteins) and expressed markedly increased levels of apo-E mRNA. Northern analysis of RNA extracted from aortic tissue revealed that fully differentiated, quiescent SMC contain significant quantities of apo-E mRNA. These data establish aortic SMC as a vascular source for apo-E and suggest new functional roles for this apolipoprotein, possibly unrelated to traditional concepts of lipid metabolism.

Animals↗

PubMed1997

Novel method for detection of small amounts of RNA based on the semi-nested polymerase chain reaction.

A technique for the amplification of very small quantities of cDNA based on a semi-nested polymerase chain reaction system has been developed. The technique uses an additional blocking oligonucleotide "primer" in the second round nest which is complementary to one of the first round primers. This prevents amplification of first round product or of any other unwanted products dependent on that primer, but allows amplification of second round product, using first round product as the template. The second round primers are added through the oil layer, eliminating the possibility of introducing first round product aerosol into the atmosphere, as would be the case in a fully nested system. Contamination is therefore minimised, while amplification of the desired product is maximised.

Animals↗