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PubMed1999

Reverse transcription-competitive multiplex PCR improves quantification of mRNA in clinical samples--application to the low abundance CFTR mRNA.

BACKGROUND: To monitor gene therapy, we wished to quantify cystic fibrosis transmembrane conductance regulator (CFTR) mRNA. We developed a PCR-based method to measure CFTR mRNA in clinical samples. METHODS: Expression was determined by reverse transcription-competitive multiplex PCR (RCMP) for CFTR and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) transcripts, and for serial dilutions of two internal cDNA standards consisting of CFTR and GAPDH mutants containing short deletions. The RCMP used simultaneous amplification of the gene of interest with a reporter gene in one reaction tube. The expression of CFTR was calculated with reference to the amount of GAPDH to correct for variations in initial RNA loading. RESULTS: Amplification of cDNAs derived from different amounts of RNA (1-4 microgram) gave similar GAPDH/CFTR ratios, with a coefficient of variation (CV) below 7.5%. RCMP was applied on nasal and bronchial brushings and shows a high variability of CFTR expression in non-cystic fibrosis donors. CONCLUSION: This method is precise and reproducible and advantageous for use with limited amounts of tissue, such as from biopsies or from nasal or bronchial brushings.

Bronchi↗

PubMed1975

Structure of nuclear pre-mRNA. VI. "Reversed repeats" in animal DNA and their hybridization with double-stranded regions of pre-mRNA.

About 2% of mouse DNA reassociates at extremely low Cot values (10-7-10-6 mole-liter-1-sec). This DNA fraction was isolated with the aid of nuclease S1 and purified by chromatography on hydroxyapatite. The study of this fraction suggests that it has a structure of hairpin type. The DNA of the hairpins can hybridize with sequences forming the double-stranded regions in pre-mRNA. Probably at least some of the DNA of the hairpins, described as "reversed repeating sequences" of DNA, is transcribed with the formation of structures of hairpin type in pre-mRNA.

Animals↗

PubMed1985

[Hybridization of low molecular weight nuclear RNA with pre-mRNA from erythroid bone marrow cells and rabbit mRNA].

Hybridization of labeled low molecular weight (LMW) nuclear RNA's to pre-mRNA from rabbit non-matured erythroid bone marrow cells or globin mRNA from reticulocytes revealed three RNA species having approximately 90, 100 and 160 nucleotides which are were specifically hybridized with purified cytoplasmic globin messenger RNA, while one (100 nucleotides) was also hybridized with rabbit 18S rRNA. The identity of these rabbit RNAs to LMW RNAs described for other animal species, as well as their possible hybridization sites and function are discussed.

Animals↗

PubMed1989

Isolation and characterization of human blood platelet mRNA and construction of a cDNA library in lambda gt11. Confirmation of the platelet derivation by identification of GPIb coding mRNA and cloning of a GPIb coding cDNA insert.

We have developed a purification method for the isolation of platelet-specific poly (A+) RNA and demonstrated that human blood platelets, despite the absence of a nucleus, contain stable mRNA. The poly (A+) RNA was used to construct a platelet-specific cDNA expression library in lambda gt11. The platelet derivation of the purified mRNA was confirmed by identification of membrane glycoprotein Ib (GPIb) message by immunoprecipitation of rabbit reticulocyte lysate translation products with poly- and monoclonal antibodies against GPIb alpha and by sequencing of a GPIb alpha cDNA clone.

Amino Acid Sequence↗

PubMed1988

A functionally redundant downstream sequence in SV40 late pre-mRNA is required for mRNA 3'-end formation and for assembly of a precleavage complex in vitro.

In eukaryotes, mRNA 3' termini are formed by endonucleolytic cleavage of a long primary transcript and polyadenylation of the new end. Here we show that sequences downstream of the poly(A) site are required for cleavage of simian virus 40 (SV40) late pre-mRNAs in vitro in a crude nuclear extract from HeLa cells. The critical sequences are functionally redundant: extensive deletions or substitutions of downstream sequences prevent cleavage, but small substitutions do not. This functional redundancy is not due to a repetition of the same sequence. Either two or more different sequences can promote cleavage, or a single element exists which is long and diffuse. Although pre-mRNAs transcribed from certain genes require a U- or UG-rich sequence downstream of the poly(A) site for efficient cleavage, SV40 does not. Removal of these sequences from SV40 late pre-mRNAs does not significantly reduce cleavage efficiency. Downstream sequences also are required for formation of a specific precleavage complex between SV40 pre-mRNA and components present in the extract. Mutant RNAs that are cleaved efficiently form such complexes, while those that are cleaved inefficiently do not. Based on these and previous results (Zarkower, D., and Wickens, M. (1987b) EMBO J. 6, 4185-4192), we propose that a critical role of the region downstream of the poly(A) site is to facilitate formation of a specific precleavage complex in which cleavage subsequently occurs.

Animals↗

PubMed1978

Sinefungin, a potent inhibitor of virion mRNA(guanine-7-)-methyltransferase, mRNA(nucleoside-2'-)-methyltransferase, and viral multiplication.

Sinefungin (A9145) and a related metabolite, A9145C, were found to be potent inhibitors of Newcastle disease virion and vaccinia virion mRNA(guanine-7-)-methyltransferase and vaccinia virion mRNA(nucleoside-2'-)-methyltransferase. Both Sinefungin and A9145C were competitive inhibitors of these S-adenosyl-L-methionine-dependent enzymes having inhibition constants substantially less than S-adenosyl-L-homocysteine. These compounds also inhibited plaque formation by vaccinia virus in mouse L-cells.

Adenosine↗

PubMedDate not supplied

Increase in tumor necrosis factor-alpha mRNA but not perforin mRNA expression in response to two newly characterized anti-LFA-1 monoclonal antibodies.

We have generated two monoclonal antibodies (mAb), designated anti-1B11 and anti-4F9, directed to the human lymphocyte-function-associated antigen-1 (LFA-1). Indirect immunofluorescence with both mAb showed a bimodal distribution of antigen on the surface of T, natural killer (NK), and lymphokine-activated killer (LAK) cells. Neither mAb reacted with the epitopes recognized by TA1 and Mo-1 mAb on the alpha-chain of the heterodimer. Anti-1B11 and anti-4F9 immunoprecipitated polypeptide chains with molecular weights of 177 and 95 kD. Both mAb inhibited cytolytic T lymphocytes (CTL), NK, and LAK cell-mediated cytotoxicity without affecting antibody-dependent cellular cytotoxicity (ADCC). The proliferative responses of T cells to allogeneic cells were inhibited by anti-1B11 and anti-4F9, whereas the responses to phytohemagglutinin P and concanavalin A were not affected. Anti-1B11 and anti-4F9 blocked effector cell (EC)-target cell (TC) conjugate formation by 50%. Only anti-4F9 cross-reacted with LFA-1 on porcine peripheral blood lymphocytes and inhibited porcine NK, LAK, and ADCC activities. Because LFA-1 also functions at the level of signal transduction during T cell activation and we previously showed that CTL rapidly degraded perforin and tumor necrosis factor-alpha (TNF alpha) mRNA after interaction with sensitive TC, we examined the effects of the mAb on the messages for perforin and TNF alpha. Treatment of CTL with anti-1B11 and anti-4F9 induced TNF alpha message and protein levels of TNF alpha, but did not alter perforin mRNA levels.

Animals↗

PubMedDate not supplied

Stromelysin-3 mRNA expression and malignancy: comparison with clinicopathological features and type IV collagenase mRNA expression in breast tumors.

mRNA expression of stromelysin-3 (ST3) and 72K type IV collagenase (cIVase) in 4 human breast cancer cell lines and 55 resected breast tumors were examined using Northern blot analysis. In 4 cell lines ST3 was not expressed at all, while cIVase gene expression was detected in 3 of them. The ST3 expression was found more specifically in malignant tumors (39/40, 97.5%) than in benign ones (4/15, 26.7%), although cIVase was expressed in all tumor specimens. The quantitative analysis showed that ST3 expression in malignancies was significantly greater than that in benign tumors (P = 0.0007), while cIVase expression was not (P = 0.1381). ST3 gene expression was also closely related to the presence of lymph node metastasis (P = 0.047), while cIVase was not (P = 0.1091). These results suggest, therefore, that ST3 is expressed more specifically by stromal cells surrounding cancer cells than cIVase. Since ST3 mRNA expression was independent of the EGFR, ER and erbB2 protein expression, ST3 may be a new potent prognostic guide for breast carcinomas, which can detect highly malignant subpopulations.

Breast Neoplasms↗

PubMed1995

The 5' coding sequence of IL-2 receptor alpha chain mRNA mediates mRNA stabilization by HTLV-1 Rex.

The interleukin-2 receptor alpha chain (IL-2R alpha) is a T-cell growth factor receptor and is known to be induced in helper T cells by infection with human T-cell leukaemia virus type-1 (HTLV-1). The Rex protein of HTLV-1 has been shown to stabilize IL-2R alpha mRNA. Although the 3' untranslated region of many RNA has been regarded as a key element for stabilization, we found that the first 300 bases of the IL-2R alpha protein coding sequence were necessary for stabilization of the mRNA. As the first 201 bases were not sufficient for this effect, we conclude that the bases at position 201-300 downstream of the AUG start are important for stabilization.

Cell Culture Techniques↗

PubMed1998

Androgen-independent basal cell re-epithelialization, c-erbB-2 mRNA expression and androgen-dependent EGFr mRNA expression in benign prostatic hyperplasia explant cultures treated with finasteride.

We have analyzed the effects of the 5alpha-reductase inhibitor, finasteride (MK906), on the mRNA expression of the epidermal growth factor receptor and c-erbB-2 genes, in benign prostatic hyperplasia explant cultures treated with testosterone and with testosterone plus finasteride. A decrease of the epithelial cell content and an androgen-independent basal cell re-epithelialization was observed during the first 10 days of culture, suggesting a role of basal cells as stem cells involved in androgen-independent epithelial regeneration. Using a semi-quantitative reverse transcription polymerase chain reaction technique, we observed a significant decrease in expression of the epidermal growth factor receptor in the cultures treated with finasteride whereas no effect of finasteride on c-erbB-2 transcription was detected, although the expression of both genes was increased by dihydrotestosterone.

Cholestenone 5 alpha-Reductase↗

PubMed1991

The path of mRNA through the Escherichia coli ribosome; site-directed cross-linking of mRNA analogues carrying a photo-reactive label at various points 3' to the decoding site.

mRNA analogues approximately 40 bases long were prepared by T7 transcription from synthetic DNA templates. Each message contained the sequence ACC-GCG (coding for threonine and alanine, respectively), together with a single thio-U residue located at a variable position on the 3'-side of these coding triplets. The thio-U residue was either substituted with 4-azidophenacyl bromide to introduce a photo-reactive group, or was left unsubstituted for direct UV cross-linking. After binding to Escherichia coli 70S ribosomes in the presence of tRNA-Thr or tRNA-Ala, the thio-U residue or azidophenyl group was photo-activated and the products of cross-linking (which was exclusively to the 30S subunit) were analysed. Immunological analysis of the cross-linked proteins showed that S5 and S3, together with S1, were the targets of cross-linking at positions close to the decoding site, with the cross-linking to S3 and S1 persisting at positions further away. Analysis of the 16S RNA showed cross-links to the region of bases 1390-1400 in all cases, but in one instance (with the reactive nucleotide 11 bases from the decoding site) simultaneous cross-linking was observed to the latter region and to position 532; these two RNA regions are far apart in current three-dimensional models of the 30S subunit.

Amino Acid Sequence↗

PubMed2001

Cytokine mRNA expression in mouse colon: IL-15 mRNA is overexpressed and is highly sensitive to a fibre-like dietary component (short-chain fructo-oligosaccharides) in an Apc gene manner.

On the basis of studies using the Min mouse model of colon carcinogenesis, we have recently proposed that a fibre-like food (short-chain fructo-oligosaccharides, sc-FOS) fermented in the colon may stimulate a mechanism of cancer immunosurveillance. In the present paper, we have investigated the expression of cytokines as potential effector molecules. Interleukin (IL-)4, IL-5, IL-13, IL-15 and interferon (INF)-gamma mRNAs were detected by a multi-probe ribonuclease protection assay in C57BL/6J and Min mouse colons. IL-15 mRNA expression was significantly amplified (P=0.01) by the sc-FOS-enriched diet in the colon of Min mice.

Animals↗

PubMed2001

High abundance of GluR1 mRNA and reduced Q/R editing of GluR2 mRNA in individual NADPH-diaphorase neurons.

Striatal and cortical neurons containing NADPH-diaphorase [NADPH-d(+)] are highly vulnerable to excitotoxicity that is induced by activation of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)- or kainate-sensitive glutamate receptors. This has been attributed to Ca2+ entry through AMPA/kainate receptors in NADPH-d(+) neurons. In this study, we applied single cell RT-PCR technique to test the hypothesis that differences in levels and processing of the GluR2 subunit would contribute to the selective vulnerability of NADPH-d(+) neurons to AMPA. The nested PCR specific for GluR1-GluR4 showed that rat striatal NADPH-d(+) neurons expressed twice as much GluR1 mRNA as NADPH-d(-) neurons did. The percentage of RNA editing at the Q/R site of GluR2 was 46% in NADPH-d(+) neurons and 92% in NADPH-d(-) neurons. These results suggest that the unedited expression of GluR2 and the reduced ratio of GluR2/GluR1 render NADPH-d(+) neurons highly sensitive to Ca2+-mediated AMPA neurotoxicity. In support of this, most NADPH-d(+) neurons exposed to 100 microM AMPA showed Co2+ uptake and survived AMPA challenge only in the absence of extracellular Ca2+.

Animals↗

PubMed1990

Isolation of a GC-rich cDNA identifying mRNA present in human epidermis and modulated by calcium and retinoic acid in cultured keratinocytes. Homology with murine loricrin mRNA.

Differential screening of a human epidermal cDNA library led to the isolation of cDNA clones homologous to mRNAs specifically expressed in epidermis but weakly or not expressed in the undifferentiated squamous carcinoma cell line TR146. One of these 'differentiation-specific' cDNA clones, A8, hybridized with a 1.7 kb transcript among RNAs isolated from normal human epidermis, but with several transcripts ranging from 1.4 to 2.1 kb when mRNAs were isolated from cultured keratinocytes. We examined the effects of modulators of epidermal differentiation such as calcium and retinoic acid on the production of these transcripts. Their amount was found to increase in the presence of high calcium concentration, but to decrease in the presence of retinoic acid. These results strongly suggest that A8 messages are up-regulated during epidermal differentiation. The sequence of the 1371 bp of A8 cDNA shows a very high GC content. Because of its homology with the murine loricrin mRNA, A8 is likely to correspond either to the human loricrin or to a related protein.

Animals↗

PubMed1992

Thymocytes express a mRNA that is identical to hypothalamic luteinizing hormone-releasing hormone mRNA.

1. A luteinizing hormone-releasing hormone (LHRH)-like molecule produced by thymocytes is similar to hypothalamic LHRH in both bioactivity and antigenicity. 2. We determined whether this thymic LHRH is identical to or only homologous with hypothalamic LHRH by synthesizing and sequencing the cDNA of rat thymus LHRH. 3. The thymocyte and hypothalamic LHRH cDNAs are identical, indicating, that the amino acid sequences of LHRH produced in the hypothalamus and the immune system are also identical. 4. This is the first report showing conclusively that cell of the immune system transcribe the authentic mRNA for a hypothalamic releasing factor, LHRH.

Amino Acid Sequence↗

PubMedDate not supplied

[Alternative splicing of pre-mRNA encoding the Musca domestica latrophilin-like protein(LLP): primary structures of four spliced forms of mRNA and their protein products].

An internal DNA fragment (approximately 2000 bp) homologous to the conserved regions of genes encoding latrophilin-like proteins (LLPs) was obtained by the PCR technique using degenerate primers to these gene regions. The gene-specific primers were synthesized based on the results of sequencing of the isolated fragment, and all overlapping cDNA fragments of the llp gene encoding the Musca domestica LLP were obtained by the rapid amplification of cDNA 5'- and 3'-ends (5'- and 3'-RACE). Four alternatively spliced mRNAs were found while sequencing the obtained cDNA fragments. Two long mRNAs (approximately 6000 nt) differ in the structures of both the sites encoding signal peptides and 5'-terminal untranslated regions. They encode large proteins (approximately 1800 aa), whose domain organization is similar to that of mammalian latrophilins. Each deduced protein contains a domain with seven transmembrane regions followed by an extended cytoplasmic C-terminal domain. Two other mRNA forms are derived from these long mRNAs; they encode proteins severly truncated at their C-termini (approximately 900 aa). They are composed of only three transmembrane regions and a short unique cytoplasmic C-terminal domain (23 aa). The limitations and drawbacks of the existing 3'-RACE techniques found during study of the long alternatively spliced cDNAs are analyzed, and ways for overcoming these difficulties are proposed.

Alternative Splicing↗

PubMed1991

Structural and expression analyses of normal and mutant mRNA encoding glycine decarboxylase: three-base deletion in mRNA causes nonketotic hyperglycinemia.

Full-length cDNA clone encoding human glycine decarboxylase (P-protein) was isolated from the human placental lambda gt11 expression library using specific antibodies. This clone was 3,705 bp in length and encoded 1,020 amino acids. We studied the structure of the mutant P-protein mRNA expressed in the liver of a patient with nonketotic hyperglycinemia (NKH) deficient of P-protein. A three-base deletion, which resulted in deletion of Phe756, was found. Cos7 cells in which normal P-protein cDNA was expressed presented an activity of 6.9 +/- 0.41 nmole/milligram of protein/hour, which was almost equivalent to that of human liver. In contrast, Cos7 cells in which the mutant cDNA was expressed showed no activity, indicating that the three-base deletion could cause NKH.

Amino Acid Metabolism, Inborn Errors↗

PubMed1996

Enhancement of nucleocytoplasmic export of HTLV-1 Rex mRNA through cis and trans interactions of the mRNA with the complex of Rex protein and Rex-responsive element.

p27 rex of HTLV-1 promotes nucleocytoplasmic export of viral mRNAs through binding of the Rex-response element (RexRE) present at the 3' end of the viral transcripts in cis with respect to the ORFs of the viral mRNAs. We have found that expression of the RexRE in trans, as a separate RNA, still allows Rex protein to promote export of viral mRNAs lacking the RexRE. The data suggest the formation of a ternary complex between Rex protein, RexRE and upstream elements of viral mRNA and hence the existence of secondary sites of interaction between Rex protein and viral RNAs.

Animals↗