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Results for “RNA Stability”

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At least 577 records · Page 32Linked to original sources

PubMed1997

Mechanisms of developmental regulation in Trypanosoma brucei: a polypyrimidine tract in the 3'-untranslated region of a surface protein mRNA affects RNA abundance and translation.

Salivarian trypanosomes are extracellular parasites of mammals that are transmitted by tsetse flies. The procyclic acidic repetitive proteins (PARPs) are the major surface glycoproteins of the form of Trypanosoma brucei that replicates in the fly. The abundance of PARP mRNA and protein is very strongly regulated, mostly at the post-transcriptional level. The 3'-untranslated regions of two PARP genes are of similar lengths, but are dissimilar in sequence apart from a 16mer stem-loop that stimulates translation and a 26mer polypyrimidine tract. Addition of either of these PARP 3'-untranslated regions immediately downstream of a reporter gene resulted in developmental regulation mimicking that of PARP. We show that the PARP 3'-UTR reduces RNA stability and translation in bloodstream forms and that the 26mer polypyrimidine tract is necessary for both effects.

Animals↗

PubMed1991

Regulation of asparagine synthetase gene expression by amino acid starvation.

We have studied the regulation of expression of the asparagine synthetase (AS) gene in ts11 cells, a mutant of BHK hamster cells which encodes a temperature-sensitive AS and therefore does not produce endogenous asparagine at 39.5 degrees C. Incubation of ts11 cells at the nonpermissive temperature drastically increases the level of AS mRNA, and the stimulation of AS mRNA expression is effectively suppressed by the addition of asparagine to the medium. We show here that regulation of AS gene expression involves cis-acting elements which are contained in the mRNA as well as in the 5' genomic region. When a plasmid containing the human AS cDNA under the control of the human AS promoter region was stably transfected into ts11 cells, the expression of human AS RNAs was regulated as that of the endogenous hamster transcripts, indicating that this construct contained all cis elements necessary for regulation. Expression of the AS cDNA in ts11 cells under the control of a constitutive foreign promoter was also regulated by the concentration of asparagine, and this regulation required translation. When we introduced by mutagenesis a number of stop codons in the AS cDNA, the mutant mRNAs with short open reading frames were expressed at low levels that were not increased by asparagine deprivation. Inhibition of protein and RNA synthesis also prevented down-regulation of AS mRNA levels by high concentrations of asparagine. In a parallel series of experiments, we showed that an AS DNA fragment including the promoter and first exon can also regulate RNA expression in response to asparagine concentration. Furthermore, similar increases in the levels of AS RNAs are produced not only by asparagine deprivation in ts11 cells but also by deprivation of human and wild-type BHK cells of leucine, isoleucine, or glutamine. Thus, regulation of AS gene expression is a response to amino acid starvation through mechanisms which appear to involve both changes in RNA stability and change in the rates of transcription initiation or elongation.

Amino Acids↗

PubMed2004

RNA-binding proteins heterogeneous nuclear ribonucleoprotein A1, E1, and K are involved in post-transcriptional control of collagen I and III synthesis.

Collagen types I and III, coded by COL1A1/COL1A2 and COL3A1 genes, are the major fibrillar collagens produced by fibroblasts, including cardiac fibroblasts of the adult heart. Characteristic for different cardiomyopathies is a remodeling process associated with an upregulation of collagen synthesis, which leads to fibrosis. We report identification of three mRNA-binding proteins, heterogeneous nuclear ribonucleoprote (hnRNP) A1, E1, and K, as positive effectors of collagen synthesis acting at the post-transcriptional level by interaction with the 3'-untranslated regions (3'-UTRs) of COL1A1, 1A2, and 3A1 mRNAs. In vitro, binding experiments (electromobility shift assay and UV cross-linking) reveal significant differences in binding to CU- and AU-rich binding motifs. Reporter gene cell transfection experiments and RNA stability assays show that hnRNPs A1, E1, and K stimulate collagen expression by stabilizing mRNAs. Collagen synthesis is activated via the angiotensin II type 1 (AT1) receptor. We demonstrate that transforming growth factor-beta1, a major product of stimulated AT1 receptor, does not activate solely collagen synthesis but synergistically the synthesis of hnRNP A1, E1, and K as well. Thus, post-transcriptional control of collagen synthesis at the mRNA level may substantially be caused by alteration of the expression of RNA-binding proteins. The pathophysiological impact of this finding was demonstrated by screening the expression of hnRNP E1 and K in cardiovascular diseases. In the heart muscle of patients experiencing aortic stenosis, ischemic cardiomyopathy, or dilatative cardiomyopathy, a significant increase in the expression of hnRNP E1, A1, and K was found between 1.5- and 4.5-fold relative to controls.

3' Untranslated Regions↗

PubMed1991

Analysis of unstable RNA transcripts of insecticidal crystal protein genes of Bacillus thuringiensis in transgenic plants and electroporated protoplasts.

We have examined expression of several insecticidal crystal protein (ICP) genes of Bacillus thuringiensis in transgenic tobacco plants and electroporated carrot protoplasts. We determined that low levels of lepidopteran toxin cryIA(b) ICP gene expression in plants and electroporated carrot cells is due to RNA instability. We used a series of 3' deleted by cryIA(b) constructs directed by the cauliflower mosaic virus 35S promoter to demonstrate that this instability is minimally contained in the first 579 bases of the gene in both systems. This instability may result from 5'----3' as well as 3'----5' RNA metabolism. The coleopteran toxic cryIIIA gene was also examined in electroporated carrot cells, and found to be poorly expressed. A model for improvement of ICP RNA stability in plants is presented.

Bacillus thuringiensis↗

PubMed1993

Functional in vivo analyses of the 3' flanking sequences of the Chlamydomonas chloroplast rbcL and psaB genes.

Possible roles of untranslated sequences at the 3' ends of chloroplast genes, which include inverted repeat elements, were investigated in Chlamydomonas reinhardtii in vivo. Chlamydomonas chloroplast rbcL or psaB 3' flanking regions were coupled in various arrangements 3' to a chimeric gene consisting of a Chlamydomonas chloroplast atpB promoter sequence fused 5' to the Escherichia coli uidA (GUS) structural gene. These genes were introduced into the Chlamydomonas chloroplast genome at the same location by homologous recombination following microprojectile bombardment. Transformants harboring chimeric GUS genes fused to rbcL or psaB gene 3' inverted repeat sequences in their normal forward orientations accumulated GUS transcripts of a single size, whereas GUS transcripts of heterogenous sizes accumulated in transformants harboring the same gene lacking an inverted repeat sequence at its 3' end. Thus, the 3' flanking regions of the rbcL and psaB genes can define the location of the 3' terminus of a transcript in vivo. In chloroplast transformants harboring chimeric GUS genes fused to multiple inverted repeat sequences in their normal forward orientations, only GUS transcripts accumulated that were terminated by the first inverted repeat sequence. The latter data suggest that the 3' ends of these RNAs are the products of either transcription termination or endonucleolytic cleavage. Analyses of GUS transcripts in transformants harboring GUS genes terminated by rbcL or psaB gene 3' flanking regions in reversed orientations indicate that transcript 3' end formation in vivo requires nucleotide sequences located outside the inverted repeat elements. Inasmuch as decay rates of GUS transcripts were found to be independent of the presence of a 3' inverted repeat sequence, RNA stabilization does not appear to be a major in vivo function of these elements in the Chlamydomonas chloroplast transcripts studied.

Animals↗

PubMed1996

The Plasmodium falciparum 6 kb element is polycistronically transcribed.

The Plasmodium falciparum 6 kb element encodes three protein coding genes and highly fragmented large and small subunit rRNAs; its gene content makes it the probable mitochondrial genome. Many of the genes are encoded so close to each other that there is insufficient room for specific promoters upstream of each gene. RNase protection analysis of two rRNA fragments whose genes are adjacent provided evidence for a polycistronic transcript containing sequences from both, as well as separate small RNAs. To evaluate the possibility of further polycistronic transcription, several sets of oligonucleotide primers located in different regions of the 6 kb element were employed to amplify cDNAs. These analyses have revealed the existence of 6 kb element transcripts as long as 5.9 kb. Both mRNA and rRNA sequences are included on these putative precursor transcripts. Since these types of RNA are known to have different patterns of abundance changes during the erythrocytic portion of the parasite life cycle, RNA stability is presumably an important feature in regulating mitochondrial transcript abundance.

Animals↗

PubMed1997

Evidence for transcriptional regulation of plastid photosynthesis genes in Arabidopsis thaliana roots.

Mechanisms underlying suppressed levels of transcripts for plastid photosynthesis genes in nongreen tissues such as roots and calli were analyzed in Arabidopsis thaliana, a plant suitable for further genetic dissection. A region encoding promoters of rbcL, the gene encoding the large subunit of ribulose-1,5-biphosphate carboxylase/oxygenase, and the atpB/E operon for the beta and epsilon subunits of coupling factor one were cloned and sequenced. Transcripts for rbcL, atpB/E, and psbA, the gene for the D1 protein in the photosystem II reaction center, were barely detectable in roots of A. thaliana, whereas 16S rRNA was detected at a low level. The run-on transcription experiment revealed that expression of rbcL, atpB/E, and psbA was regulated at transcription. The copy number of plastid DNA in roots was one-fifth that in green leaves on the basis of total cellular DNA, suggesting that in the latter the DNA copy-number regulation also exists in plastid gene expression. Digestion of DNA with methyl-sensitive and -insensitive isoschizomeric endonucleases and subsequent polymerase chain reaction, as well as in vitro transcription of plastid DNAs with Escherichia coli RNA polymerase, resulted in no evidence of regulation by DNA modification. In spite of predominant suppression of expression of rbcL, atpB/E, and psbA at transcription in roots and calli, 16S rRNA levels were decreased because of low RNA stability.

Arabidopsis↗

PubMed1992

Amyloid precursor protein mRNA encoding the Kunitz protease inhibitor domain is increased by kainic acid-induced seizures in rat hippocampus.

A 168-nucleotide exon, found in alternatively spliced amyloid precursor protein (APP) mRNAs, encodes a Kunitz protease inhibitor (KPI) domain. Kainic acid (ip) caused a selective increase of KPI mRNA in rat hippocampus. By in situ hybridization, KPI mRNA was induced in the neuronal layers of the hippocampus 11-12 h after the onset of kainate-induced seizures. The kainate-induced elevation of the KPI-containing APP-770 mRNA was blocked by pretreatment with the anticonvulsant pentobarbital. These data suggest that kainate-induced seizures cause alterations in APP RNA stability and/or processing in rat hippocampal neurons.

Amino Acid Sequence↗

PubMed1994

The expression and function of G-proteins in experimental intimal hyperplasia.

G-proteins are membrane-bound signal transduction proteins which couple extracellular receptor signals to various effectors. This study examines the expression and the function of G-proteins (alpha i, alpha s, alpha q, and alpha o) in experimental intimal hyperplasia. Vein bypass grafts were placed in 30 New Zealand White rabbits and were harvested after 28 d. The contralateral jugular veins served as controls. Isometric tension studies were performed on rings from veins and vein grafts (n = 10), and Western blot and mRNA analyses were performed in another 20 vessels. There was a fivefold increase in alpha q, a 2.7-fold increase in the alpha i2, and a 3.3-fold increase in alpha s expressions in vein grafts compared with veins. Detectable expression of alpha i3 was observed in vein grafts but not in jugular veins. In addition, there was a 3.8-fold increase in beta subunits in the vein grafts compared with the veins. mRNA for alpha s, alpha i3, and alpha i2 were all elevated in the vein grafts. No detectable levels of the alpha i1 protein or its mRNA were present in either veins or vein grafts. Contractile responses in the veins were not inhibited by pertussis toxin. The contractile responses to norepinephrine were enhanced by twofold, and the responses to serotonin developed de novo in vein grafts compared with veins. The contractile responses to both norepinephrine and serotonin were only partially inhibited by pertussis toxin in the vein grafts even though there was 100% ADP ribosylation with pertussis toxin in both veins and vein grafts. These data suggest that intimal hyperplasia is associated with increased or novel expression of G-proteins in vivo which occur simultaneously with the development of pertussis toxin-sensitive contractile responses. Changes in G-proteins at a transcriptional level or at the level of RNA stability may be involved in the response of smooth muscle cells to injury and to intimal hyperplasia formation.

Aluminum↗

PubMed2006

Coordinate enhancement of transgene transcription and translation in a lentiviral vector.

BACKGROUND: Coordinate enhancement of transgene transcription and translation would be a potent approach to significantly improve protein output in a broad array of viral vectors and nonviral expression systems. Many vector transgenes are complementary DNA (cDNA). The lack of splicing can significantly reduce the efficiency of their translation. Some retroviruses contain a 5' terminal post-transcriptional control element (PCE) that facilitates translation of unspliced mRNA. Here we evaluated the potential for spleen necrosis virus PCE to stimulate protein production from HIV-1 based lentiviral vector by: 1) improving translation of the internal transgene transcript; and 2) functionally synergizing with a transcriptional enhancer to achieve coordinate increases in RNA synthesis and translation. RESULTS: Derivatives of HIV-1 SIN self-inactivating lentiviral vector were created that contain PCE and cytomegalovirus immediate early enhancer (CMV IE). Results from transfected cells and four different transduced cell types indicate that: 1) PCE enhanced transgene protein synthesis; 2) transcription from the internal promoter is enhanced by CMV IE; 3) PCE and CMV IE functioned synergistically to significantly increase transgene protein yield; 4) the magnitude of translation enhancement by PCE was similar in transfected and transduced cells; 5) differences were observed in steady state level of PCE vector RNA in transfected and transduced cells; 6) the lower steady state was not attributable to reduced RNA stability, but to lower cytoplasmic accumulation in transduced cells. CONCLUSION: PCE is a useful tool to improve post-transcriptional expression of lentiviral vector transgene. Coordinate enhancement of transcription and translation is conferred by the combination of PCE with CMV IE transcriptional enhancer and increased protein yield up to 11 to 17-fold in transfected cells. The incorporation of the vector provirus into chromatin correlated with reduced cytoplasmic accumulation of PCE transgene RNA. We speculate that epigenetic modulation of promoter activity altered cotranscriptional recruitment of RNA processing factors and reduced the availability of fully processed transcript or the efficiency of export from the nucleus. Our results provide an example of the dynamic interplay between the transcription and post-transcription steps of gene expression and document that introduction of heterologous gene expression signals can yield disparate effects in transfected versus transduced cells.

Base Sequence↗

PubMed1998

Expressional control of the 'constitutive' isoforms of nitric oxide synthase (NOS I and NOS III).

Nitric oxide synthase (NOS) exists in three established isoforms. NOS I (NOS1, ncNOS) was originally discovered in neurons. This enzyme and splice variants thereof have since been found in many other cells and tissues. NOS II (NOS2, iNOS) was first identified in murine macrophages, but can also be induced in many other cell types. NOS III (NOS3, ecNOS) is expressed mainly in endothelial cells. Whereas NOS II is a transcriptionally regulated enzyme, NOS I and NOS III are considered constitutively expressed proteins. However, evidence generated in recent years indicates that these two isoforms are also subject to expressional regulation. In view of the important biological functions of these isoforms, changes in their expression may have physiological and pathophysiological consequences. This review recapitulates compounds and conditions that modulate the expression of NOS I and NOS III, summarizes transcriptional and posttranscriptional effects that underlie these changes, and-where known-describes the molecular mechanisms leading to changes in transcription, RNA stability, or translation of these enzymes.

Animals↗

PubMed2026

Functional analysis of stem-loop structures within the SARS-CoV-2 5' untranslated region using a plasmid-based reporter system.

The 5' untranslated region (5'UTR) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains highly conserved stem-loop structures that regulate viral gene expression. This study investigated the functional contributions of selected 5'UTR stem-loop elements to reporter gene expression using a plasmid-based mammalian expression system. Five constructs were tested using a non-integrating plasmid: the wild-type (WT) 5'UTR fused to GFP under the CMV promoter, and four deletion variants (ΔB, ΔC, ΔD, and ΔE) corresponding to deletions of stem-loop 4 (SL4), SL4.5, SL5, and SL5a, respectively. Following transfection into HEK293 cells, GFP fluorescence was quantified using a fluorescence microplate reader, and relative GFP transcript abundance was assessed by RT-qPCR. Deletion of SL4 (ΔB) resulted in marked reduction in both fluorescence and relative transcript abundance compared to WT construct, indicating substantially reduced reporter gene expression. In contrast, deletion of SL4.5, SL5, or SL5a did not produce the pronounced reduction observed for ΔB, although descriptive RT-qPCR analysis indicated differences in relative transcript abundance among these variants. Statistical analysis of fluorescence data demonstrated significant differences among constructs (one-way ANOVA, p < 0.05). Because the reporter assay was based on plasmid expression, the observed differences likely reflect combined contributions from transcription, transcript abundance, RNA stability, and translation rather than translation alone. These findings demonstrate that the SL4 region contributes substantially to reporter gene expression in this experimental system, whereas the remaining stem-loop regions examined exert comparatively modest effects. This study provides additional insight into the functional organization of the SARS-CoV-2 5'UTR and establishes a framework for future investigations aimed at distinguished the transcriptional, post-transcriptional, and translational contributions of individual RNA structural elements.

5' Untranslated Regions↗

PubMed2000

Intron-mediated enhancement of gene expression independent of unique intron sequences and splicing.

Either of the first two introns of the Arabidopsis tryptophan pathway gene PAT1 elevates mRNA accumulation from a PAT1:beta-glucuronidase (GUS) fusion roughly 5-fold without affecting the rate of PAT1:GUS transcription. To further explore the mechanism of this intron-mediated enhancement of gene expression, we wanted to determine whether splicing or specific intron sequences were necessary. In-frame derivatives of PAT1 intron 1, whose splicing was prevented by a point mutation or large deletions, were able to increase mRNA accumulation from a PAT1:GUS fusion, demonstrating that splicing per se is not required. Furthermore, each of a series of introns containing overlapping deletions that together span PAT1 intron 1 increased PAT1:GUS mRNA accumulation as much as the full-length intron did, indicating that all intron sequences are individually dispensable for this phenomenon. These results eliminate the simple idea that this intron stimulates mRNA accumulation via a unique RNA-stabilizing sequence or through the completed act of splicing. However, they are consistent with a possible role for redundant intron sequence elements or an association of the pre-mRNA with the spliceosome.

Base Sequence↗

PubMed1990

Synthesis and processing of small B2 transcripts in mouse embryonal carcinoma cells.

B2 genes are short repeated sequences which are transcribed by RNA polymerase III. Abundant transcripts accumulate in embryonic and transformed cells, but transcripts are rare or absent from normal differentiated cell types. During retinoic acid-induced differentiation of P19 embryonal carcinoma cells, an early transient increase in B2 RNA levels is followed by a rapid drop in expression. The marked changes in B2 RNA levels are most likely due to transcriptional modulation since B2 RNA stabilities are unaffected by differentiation. At least four short-lived B2 RNAs with apparent lengths of 150, 180, 240, and 500 nucleotides were characterized. The two larger RNAs are polyadenylated and are more stable in cells. A cDNA of a B2 gene was isolated which was over 99% identical to the consensus sequence. This B2 cDNA can be transcribed in human cells and yields at least two distinct transcripts. We propose a model for B2 RNA metabolism which describes transcription, posttranscriptional modification and processing, and nucleocytoplasmic transport.

Animals↗

PubMed2000

Synergism of mutations in bacteriophage Qbeta RNA affecting host factor dependence of Qbeta replicase.

We have recently shown that Escherichia coli cells deficient in Hfq protein (i.e. the Qbeta "host factor") support bacteriophage Qbeta replication inefficiently, but that the phage evolves rapidly in the mutant host to become essentially host factor independent. An identical set of four point mutations was identified as being responsible for the adapted phenotype in each of three independent adaptation experiments. Here we report the effects of the single mutations and of some of their combinations on host factor dependence of phage multiplication in vivo and of phage RNA replication by Qbeta replicase in vitro. We find that each single substitution produces only small effects, but that in combination the four mutations synergistically account for most of the observed adaptation of the evolved phages. Surprisingly, a reanalysis of the 3'-terminal sequence of the adapted phages resulted in the discovery of a fifth mutation in all three independently evolved phage populations, namely, a C to U residue transition at nucleotide 4214. This mutation had been missed previously because of its location only three nucleotides from the 3'-end. It appears to contribute little to the Hfq independence but may enhance RNA stability by re-establishing the possibility of forming a long-range base-pairing interaction involving the immediate 3'-terminal sequence.

Allolevivirus↗

PubMed1992

Post-transcriptional control of H3 histone variants synthesis.

In cultured HeLa cells the rates of H3.1 and H3.2 synthesis measured by pulse labeling experiments reflect the steady state content of the two histone variants. This pattern, however, is largely modified when histone translation is carried out in vitro on RNA isolated from the same cell line. In vivo, H3.1 and H3.2 are synthesized approximately at the same rates while the product of H3 mRNA translation in vitro is mostly represented by H3.1 histones. Factors which have so far been invoked for the control of histone messenger RNA stability and translation efficiency are not sufficient to explain our data which in addition indicate that histone H3.1 and H3.2 have different roles in the organization of the genetic material.

Autoradiography↗

PubMed1998

Synergism between interferon gamma and tumour necrosis factor alpha in the regulation of lipoprotein lipase in the macrophage J774.2 cell line.

The regulation of macrophage lipoprotein lipase (LPL) by cytokines is of potentially crucial importance in the pathogenesis of atherosclerosis. The effect of combinations of interleukin 1 (IL-1), 6 (IL-6), and 11 (IL-11), interferon gamma (INF-gamma), leukaemia inhibitory factor (LIF) and tumour necrosis factor alpha (TNF-alpha) on the expression of LPL in macrophages was studied using the murine J774.2 cell line. The suppression of heparin-releasable LPL activity produced by combinations of IL-1 and IL-11, IL-1 and TNF-alpha, IL-11 and TNF-alpha, and, IL-11 and INF-gamma was substantially lower than that expected from the additive action of the corresponding two cytokines. By contrast, co-exposure of cells to LIF and IFN-gamma, IL-6 and LIF, and INF-gamma and TNF-alpha resulted in a more than additive, synergistic, suppression of LPL activity with the maximum reduction and maximum degree of synergism produced by combinations of IFN-gamma and TNF-alpha. The synergism between IFN-gamma and TNF-alpha was observed over a range of complementary dose combinations and also occurred when the cells were exposed first to INF-gamma (priming), washed, and then stimulated subsequently with TNF-alpha. The reduction in LPL activity by combinations of IFN-gamma and TNF-alpha and the priming action of IFN-gamma were accompanied by a comparable decrease in LPL mRNA concentrations, thereby indicating that the major control responsible for the changes in LPL activity was being exerted at the level of mRNA metabolism (decreased transcription or RNA stability). These results suggest that the modulation of macrophage LPL function in atherosclerosis by cytokine combinations may be more important than the presence or absence of any given cytokine.

Cell Line↗

PubMed1989

Different gamma delta T-cell receptors are expressed on thymocytes at different stages of development.

We have analyzed the structural diversity of the murine gamma delta T-cell receptor (TCR) heterodimer expressed on CD4- CD8- thymocyte populations and on TCR gamma delta-expressing hybridomas derived from thymocytes of fetal, newborn, and adult mice. We found that CD4- CD8- thymocytes derived from mice of different pre- and postnatal age preferentially express a gamma delta TCR encoded by different subsets of gamma and delta gene segments. This age-dependent differential expression of gamma delta TCR on thymocytes seems to be accomplished in part by a specific control of rearranged gamma genes operating at the level of transcription and/or RNA stability. We discuss the implications of these findings with respect to the recognition roles of the gamma delta TCR.

Animals↗