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PubMed2003

The reduction of Raf-1 protein by phosphorothioate ODNs and siRNAs targeted to the same two mRNA sequences.

Two sets of 20-mer phosphorothioate-modified oligodeoxynucleotide DNAs (sODN) and 21-mer or 22-mer small interfering RNAs (siRNAs), targeted to the same coding sites in raf-1 mRNA, were compared for their abilities to reduce the amount of endogenously expressed Raf-1 protein in T24 cells. The amount of Raf-1 protein was monitored by careful quantitation of Western blots. We found that the siRNAs were somewhat less effective than the S-ODNs in reducing the Raf-1 protein level 20 hours after a 4-hour transfection. The siRNA duplexes were characterized by circular dichroism (CD) spectra, and melting temperatures (Tm) were obtained for the siRNA duplexes and DNA x RNA hybrids formed by the S-ODNs. The S-ODNs differed in their effectiveness, the S-ODN that formed the more stable hybrid being the more effective in reducing the Raf-1 protein level, but the two siRNAs were equally effective despite a difference in Tm of about 20 degrees C. Finally, the siRNAs and S-ODNs had a comparable nonspecific effect on a nontargeted (Bcl-2) protein. Our data add to others in the literature that show it can be difficult to select siRNAs that are more effective than antisense ODNs in downregulating endogenously expressed proteins.

Base Sequence↗
PubMed1993

Expression of two cloned mRNA sequences during development and germination of spores of the sensitive fern, Onoclea sensibilis L.

A library of complementary DNA (cDNA) clones has been prepared from poly(A)+RNA of spores of the sensitive fern, Onoclea sensibilis L. By differential hybridization with labeled probes made to poly(A)+RNA of spores, gametophytes and leaves, two spore-specific clones (pOSS68 and pOSS194) were selected and characterized. Northern blot analysis showed that RNA sequences homologous to the two cDNA clones first appear in the post-meiotic spore and increase in abundance during spore maturity. Both RNA sequences decay during photoinduced germination of the spores and do not reappear in the gametophytes. In spores imbibed in the dark under conditions which do not favor germination, no significant decrease in pOSS194-mRNA abundance is noted. In contrast, the decrease in pOSS68 mRNA in dark-imbibed spores parallels that observed in photoinduced spores. The predicted amino-acid sequence of pOSS194 has a striking similarity to the early light-inducible proteins expressed during the greening of etiolated pea and barley seedlings, whereas that of pOSS68 shows some homology to proteins encoded by late-embryogenesis-abundant mRNAs of angiosperm embryos.

Base Sequence↗
PubMed1995

Downregulation of c-myc expression after heat shock in human B-cell lines is independent of 5' mRNA sequences.

The effect of heat-shock on the expression of c-myc genes in different chromosomal contexts was investigated in a panel of human B-lymphoid cell lines. Burkitt's lymphoma cell lines with c-myc translocation breakpoints upstream of the first exon, within the exon itself, or in the first intron showed downregulation of c-myc levels as did a cell line without any translocation. The c-myc mRNA of cell lines with translocation breakpoints within the c-myc gene have previously been reported to have prolonged half-lives. After heat shock, the levels of these mRNA species were reduced with similar kinetics as the normal c-myc mRNA. An exception was an RNA species where the only c-myc sequences are derived from exon 1, showing that sequences from this part of the c-myc gene are not sufficient to mediate the rapid downregulation. Nuclear run-on analysis did not show reduced transcription of c-myc after heat shock and a comparison of cytoplasmic and total RNA did not indicate accumulation of longer, unspliced c-myc mRNA species. These observations suggest a posttranscriptional, cytoplasmic downregulation targeting exons 2 and/or 3. B-lymphoma lines transfected with a hsp70 promoter-linked c-myc gene were deficient in their ability to reinitiate proliferation after heat shock, providing a physiological rationale for the normal downregulation of c-myc after this type of physical stress.

B-Lymphocytes↗
PubMed1984

Isolation of hybridomas expressing a specific heavy chain variable region gene segment by using a screening technique that detects mRNA sequences in whole cell lysates.

A technique is described that allows single hybridoma cell colonies to be assayed for the productive rearrangement of a single immunoglobulin variable region (V) gene segment by utilizing expression of V mRNA for analysis. Hybridomas growing in microwell tissue culture plates are lysed in situ, cellular RNA is directly transferred to nitrocellulose by filtration, and specific immunoglobulin mRNA is detected by hybridization of the filter with a DNA probe. The method is simple and sensitive. A single species of mRNA can be detected in a lysate of 1000 cells; 5000 hybridoma colonies can be easily screened per day. The technique has been successfully used to isolate cell lines from nonimmune mice expressing a particular heavy chain variable region (VH) gene segment.

Animals↗
PubMed2002

A method for prediction of accessible sites on an mRNA sequence for target selection of hammerhead ribozymes.

Hammerhead ribozymes are short RNA molecules endowed with endoribonucleolytic activity. Their use as molecular tools for specific inhibition of gene translation is affected by many factors including the target accessibility. A method for the prediction of accessible target sites for hammerhead ribozymes within a given RNA sequence is described. This method maps all putative NUH cleavage sites (N = A, C, G, U and H = A, C, U) and picks out short flanking regions as the binding domain for the corresponding ribozyme. The probabilistic level of unfolding, accessibility score (AS), is then calculated for each target region on the basis of a comparison of all folding structures obtained for the target RNA and arranged according to the Boltzmann's distribution. At the end, a series of imposed limits gives the best target sequences endowed with highly probable accessibility and with a potentially active catalytic structure of the hammerhead sequence. A successive experimental approach to verify the effective accessibility of selected targets was used. For that, antisense oligonucleotides addressed to the coding region of bcl2 mRNA were synthesized and administered to the MCF7 human cell line. The inhibition of gene expression, as measured by western analysis of the BCL2 protein, demonstrated that all target sites selected on the basis of their putative accessibility were actually sensitive to antisense treatments while the inaccessible ones were not. The application of this target discovery method to ribozyme design is proposed in order to satisfy a crucial condition.

Algorithms↗
PubMed1980

Dietary alteration of translatable mRNA sequences coding for rat liver pyruvate kinase.

Poly(A+) RNA (RNA containing a polyadenylic acid sequence) was isolated from individual livers of rats fed standard lab chow, fasted, or fasted and refed a high carbohydrate diet. The level of functional mRNA coding for pyruvate kinase was assayed using a rabbit reticulocyte in vitro translation system. The total 35S incorporation into newly synthesized liver pyruvate kinase was measured and compared to 35S incorporation into albumin, total trichloroacetic acid-precipitated proteins, and released polypeptide chains. The relative level of mRNA coding for liver pyruvate kinase decreases almost 60% upon fasting and increases approximately 15-fold upon refeeding with a high carbohydrate diet for 24 h. These observed changes in the amount of mRNA coding for liver pyruvate kinase agree with the previously reported changes in the relative rates of liver pyruvate kinase synthesis measured in vivo during these dietary stresses. Thus, it is suggested that the alterations in the amount of pyruvate kinase in liver in response to these dietary stresses primarily result from alteration in the amount of functional mRNA coding for the enzyme.

Animals↗
PubMed1985

Regulation by calcium of prolactin and growth hormone mRNA sequences in primary cultures of rat pituitary cells.

Addition of Ca2+ to primary cultures of female pituitary cells incubated in serum-free medium lacking added Ca2+ yielded no effects on levels of prolactin or growth hormone mRNA, assayed by cytoplasmic dot hybridization. However, incubation of the cells in serum-free medium containing sufficient ethylene glycol bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid to reduce medium Ca2+ levels below the 10-40 microM present as a trace contaminant yielded a decrease in the levels of both mRNAs. The decrease was dose-dependent at extracellular Ca2+ concentrations below 1.0 microM, had an apparent half-maximum at about 0.3 microM, and did not appear to plateau with increasing incubation times. Following 2-3-day incubations of cells in low Ca2+, a reduction of prolactin mRNA (23-70-fold) consistently greater than the reduction of growth hormone mRNA (9-15-fold) was observed. Similar effects of reduced extracellular Ca2+ were obtained with primary cultures of male pituitary cells. The specificity of these effects of lowered extracellular Ca2+ was demonstrated by the following observations. The decreases in these mRNAs were substantially reversible by readdition of Ca2+ to the incubation medium. Reduction of extracellular Ca2+ led to no detectable changes in cellular ribosomal RNA levels or over-all RNA synthesis. In male pituitary cells, the level of another metal-regulated mRNA, that for metallothionein, was not decreased by a reduction of extracellular Ca2+ that caused a 40-fold decrease in levels of prolactin and growth hormone mRNA. Hence, Ca2+ exhibits specificity in its regulation of pituitary prolactin and growth hormone gene expression.

Animals↗
PubMed1999

cDNA sequence, mRNA expression, and chromosomal localization of human carbonic anhydrase-related protein, CA-RP XI.

A full-length cDNA clone of a human carbonic anhydrase-related protein, CA-RP XI encoded by CA11, was obtained and sequenced. The cDNA sequence was 1475 bp long and predicted to encode a 328-amino acid polypeptide with a molecular mass of 36200 Da. The deduced amino acid sequence of CA-RP XI showed an overall similarity of 42-53% to the active site residues of other active CA isozymes; however, it lacked three zinc-binding histidine residues, raising questions regarding its CA catalytic activity. Northern blot analysis demonstrated strong expression of an approx. 1.5 kb transcript in the human brain, particularly in the cerebellum, cerebral cortex, and putamen. A single copy of the CA11 gene was localized to the human chromosome 19q13.2-3. These results suggest that CA-RP XI plays a general role in the human central nervous system.

Amino Acid Sequence↗
PubMed1981

Molecular cloning of mRNA sequences encoding rat lens crystallins.

To provide access to crystallin-specific DNA sequences, we have constructed plasmid clones bearing duplex DNA sequences complementary to crystallin mRNAs isolated from rat lens. Optimization of the cDNA reaction conditions enabled us to fractionate three double-stranded (ds) cDNA groups. Molecular cloning of dC-tailed ds cDNAs into the Pst I site of dG-tailed pBR322 yielded crystallin-specific clones of each group. By means of positive hybridization selection and translation, recombinant plasmids containing cDNA sequences coding for rat lens polypeptides from alpha-, beta-, and gamma-crystallins could be identified. The established cDNA clones have been used for a blot-hybridization analysis to map the crystallin mRNAs from which they originated. Both procedures revealed a high degree of homology between the gamma-crystallin sequences. From the beta-crystallin class, the beta H-specific cDNA coding for the beta B1a polypeptide was obtained. The alpha A-chain clone did not show any cross-hybridization to the alpha B-chain mRNA despite the existence of 60% homology between the corresponding gene products. As this clone hybridized to both alpha A2 and alpha AIns mRNAs, sequence analysis was applied for further characterization. The results showed that the cloned cDNA corresponds to the alpha A2 sequence exclusively.

Animals↗
PubMed1983

Cloned mRNA sequences for two types of embryonic myosin heavy chains from chick skeletal muscle. II. Expression during development using S1 nuclease mapping.

We have examined the expression of two embryonic myosin HC mRNAs using two cDNA clones (110 and 251) which we have previously constructed from RNA isolated from 14-day-old embryonic chick skeletal muscle. Sequence divergence in the 3' nontranslated regions enabled us to analyze the differential expression of the mRNAs corresponding to the two clones using the S1 nuclease mapping procedure. Clone 251 mRNA is expressed primarily in embryonic fast muscle, where its transcripts appear to be the predominant species. This mRNA is minimally expressed in the posthatching period, but it is not detected in adult leg and breast muscle. Messenger RNA for clone 110 is also primarily expressed in embryonic fast muscle. However, in the posthatching and adult stages of development, it continues to be expressed at a low level in leg muscle but not in breast muscle. The differential expression of these mRNAs during development strongly indicates that they correspond to two different genes coding for embryonic myosin HCs. Other myosin HC mRNAs which were partially homologous to the clone 110 or 251 mRNAs were also identified by S1 nuclease mapping. Using the probes from these two clones, a minimum of four other developmentally expressed forms were detected. Two of these correspond to "neonatal" myosin HCs, while the other two code for different adult myosin HCs present in leg and in breast muscle, respectively. The results therefore suggest a much greater diversity of myosin HC mRNAs expressed during development than previously reported.

Animals↗
PubMed1995

Patients with congenital myasthenia associated with end-plate acetylcholinesterase deficiency show normal sequence, mRNA splicing, and assembly of catalytic subunits.

A congenital myasthenic condition has been described in several patients characterized by a deficiency in end-plate acetylcholinesterase (AChE). The characteristic form of AChE in the end-plate basal lamina has the catalytic subunits disulfide linked to a collagen-like tail unit. Southern analysis of the gene encoding the catalytic subunits revealed no differences between patient and control DNA. Genomic DNA clones covering exon 4 and the alternatively spliced exons 5 and 6 were analyzed by nuclease protection and sequencing. Although allelic differences were detected between controls, we found no differences in exonic and intronic areas that might yield distinctive splicing patterns in patients and controls. The ACHE gene was cloned from genomic libraries from a patient and a control. Transfection of the cloned genes revealed identical species of mRNA and expressed AChE. Cotransfection of the genes expressing the catalytic subunits with a cDNA from Torpedo encoding the tail unit yielded asymmetric species that require assembly of catalytic subunits and tail unit. thus the catalytic subunits of AChE expressed in the congenital myasthenic syndrome appear identical in sequence, arise from similar splicing patterns, and assemble normally with a tail unit to form a heteromeric species.

Acetylcholinesterase↗
PubMed1993

Maxicircle DNA and edited mRNA sequences of closely related trypanosome species: implications of kRNA editing for evolution of maxicircle genomes.

kRNA editing produces functional mRNAs by uridine insertion and deletion. We analyzed portions of the apocytochrome b and NADH dehydrogenase subunits 7 and 8 (ND7 and 8) genes and their edited mRNAs in Trypanosoma congolense and compared these to the corresponding sequences in T.brucei. We find that these genes are highly diverged between the two species, especially in the positions of thymidines and in nucleotide transitions. Editing eliminates differences in encoded uridines producing edited mRNAs that are identical except for the nucleotide substitutions. The resulting predicted proteins are identical since all nucleotide substitutions are silent. A T.congolense minicircle-encoded gRNA which can specify editing of ND8 mRNA was identified. This gRNA can basepair with both T.congolense and T.brucei ND8 mRNA despite nucleotide transitions due to the flexibility of G:U base-pairing. These results illustrate how editing affects the characteristics of maxicircle sequence divergence and allows protein sequence conservation despite a level of DNA sequence divergence which would be predicted to be intolerable in the absence of editing.

Amino Acid Sequence↗
PubMed1997

Dihydrofolate reductase protein inhibits its own translation by binding to dihydrofolate reductase mRNA sequences within the coding region.

Previous studies suggest that dihydrofolate reductase (DHFR) regulates its own translation. Moreover, intracellular levels of DHFR protein increase following exposure to the antifolate methotrexate (MTX), suggesting that MTX may release the translational inhibition mediated by DHFR [Chu et al. (1993) Biochemistry 32,4756-4760; Ercikan et al. (1993) Adv. Exp. Med. Biol. 338, 537-540]. To further investigate the role of DHFR in translational autoregulation, we have considered the possibility that DHFR directly contacts its cognate mRNA. Binding studies using a series of truncated DHFR mRNAs as probes localized the DHFR/RNA interaction to a 100-base-pair region containing two putative stem-loop structures; initial studies indicated that both of these loop structures are involved in protein binding. Moreover, the binding of MTX to DHFR prevents interaction of the protein with its cognate mRNA, thereby relieving translational autoregulation.

Base Sequence↗
PubMed2006

Transcript stabilization by mRNA sequences from hrpA of Pseudomonas syringae.

Production of heterologous proteins in bacteria is one of the main applications of biotechnology. Although several high-efficiency expression systems have been developed, different steps in protein production may become rate-limiting depending on the production system and the protein being produced. One bottle neck can be the instability of the mRNA. We have used fragments of the unusually long-living mRNA hrpA from the plant pathogenic bacteria Pseudomonas syringae pathovars tomato and phaseolicola to increase the half-lives of heterologous transcripts. The stabilizing effect was extended to Escherichia coli, as half-lives of several heterologous transcripts were increased from a few minutes to up to 19min. Production of heterologous proteins was also increased manifold by the addition of the stabilizing hrpA elements. We have mapped the regions of the hrpA transcript necessary and sufficient for the stabilization process.

Bacterial Proteins↗
PubMed1983

Identification of thyroglobulin mRNA sequences in the nucleus and the cytoplasm of cultured thyroid cells: a post-transcriptional effect of thyrotropin.

Cytoplasmic and nuclear RNA were isolated from porcine thyroid cells cultured with or without thyrotropin. After denaturation by glyoxal-DMSO treatment, the RNAs were analyzed on agarose gels, transferred onto nitrocellulose filters and hybridized with a [32P]-labelled thyroglobulin cDNA clone. In the cytoplasmic RNA a single mature thyroglobulin mRNA molecule (9 Kb) was present whereas in the nuclear RNA several molecular species (24 to 3.3 Kb) were identified. In the nucleus only the 9 Kb mRNA was polyadenylated. In cytoplasmic preparations the level of mature thyroglobulin mRNA was two-fold higher when cells were cultured with thyrotropin. In nuclear preparations only the level of the mature transcript was affected by the presence of thyrotropin, increasing relative to the concentration of the higher molecular weight species. These results suggest a hormonal effect at the post-transcriptional level that may serve to stabilize the mature mRNA molecule.

Animals↗
PubMed2005

A second look at cellular mRNA sequences said to function as internal ribosome entry sites.

This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putative internal ribosome entry sequences (IRESs) are examined more carefully, they often turn out to harbor cryptic promoters or splice sites. This undermines the dicistronic assay, wherein IRES activity is measured by the ability to support translation of the 3' cistron. Most putative IRESs still have not been checked carefully to determine whether the dicistronic vector produces only the intended dicistronic mRNA. The widespread use of the pRF vector is a major problem because this vector, which has Renilla luciferase as the 5' cistron and firefly luciferase as the 3' cistron, has been found to generate spliced transcripts. RNA transfection assays could theoretically circumvent these problems, but most candidate IRESs score very weakly in that test. The practice of calling even very weak results 'positive' is one of the problems discussed herein. The extremely low efficiency of putative IRESs is inconsistent with their postulated biological roles.'

Humans↗
PubMed1991

Characterization of rat ARPP-21 mRNA: sequence analysis, tissue distribution, and regulation.

ARPP-21 (cyclic AMP-regulated phosphoprotein; Mr = 21,000) is a cytosolic neuronal phosphoprotein that is highly enriched in the striatum and in other dopaminoceptive regions of the brain. The state of phosphorylation of ARPP-21 is also regulated by vasoactive intestinal peptide in intact cells. We previously reported the sequence analysis of bovine ARPP-21 cDNA and have now characterized rat ARPP-21 cDNA to study further the molecular biology of this protein. The sequence of the coding region is 82 and 85% identical at the nucleotide and amino acid levels, respectively, between the two species. There are two major classes of clones, differing only in the lengths of their 3' untranslated ends, suggesting that the different ARPP-21 mRNAs are derived from the use of alternate polyadenylation sites. Both major mRNA species, 2.6 and 0.7 kb, are present at the highest concentration in the striatum, followed by the cortex, consistent with previous immunocytochemical results. Southern blot analysis reveals a simple hybridization pattern, consistent with the presence of a single rat gene encoding ARPP-21. The steady-state levels of the ARPP-21 mRNAs are developmentally regulated but, in the neonatal and mature animal, are not altered following 6-hydroxydopamine lesions of the substantia nigra or by pharmacologic treatments that up-regulate the D1- or D2-dopamine receptors.

Animals↗
PubMed1996

mRNA sequences influencing translation and the selection of AUG initiator codons in the yeast Saccharomyces cerevisiae.

The secondary structure and sequences influencing the expression and selection of the AUG initiator codon in the yeast Saccharomyces cerevisiae were investigated with two fused genes, which were composed of either the CYC7 or CYC1 leader regions, respectively, linked to the lacZ coding region. In addition, the strains contained the upf1-delta disruption, which stabilized mRNAs that had premature termination codons, resulting in wild-type levels. The following major conclusions were reached by measuring beta-galactosidase activities in yeast strains having integrated single copies of the fused genes with various alterations in the 89 and 38 nucleotide-long untranslated CYC7 and CYC1 leader regions, respectively. The leader region adjacent to the AUG initiator codon was dispensable, but the nucleotide preceding the AUG initiator at position -3 modified the efficiency of translation by less than twofold, exhibiting an order of preference A > G > C > U. Upstream out-of-frame AUG triplets diminished initiation at the normal site, from essentially complete inhibition to approximately 50% inhibition, depending on the position of the upstream AUG triplet and on the context (-3 position nucleotides) of the two AUG triplets. In this regard, complete inhibition occurred when the upstream and downstream AUG triplets were closer together, and when the upstream and downstream AUG triplets had, respectively, optimal and suboptimal contexts. Thus, leaky scanning occurs in yeast, similar to its occurrence in higher eukaryotes. In contrast, termination codons between two AUG triplets causes reinitiation at the downstream AUG in higher eukaryotes, but not generally in yeast. Our results and the results of others with GCN4 mRNA and its derivatives indicate that reinitiation is not a general phenomenon in yeast, and that special sequences are required.

Base Sequence↗