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Results for “RNA Stability”

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At least 523 records · Page 29Linked to original sources

PubMed1996

Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization.

The hallmark features of rho-independent transcription terminators are a G(+)C-rich dyad symmetry sequence followed by a run of T residues on a sense strand. Both of these structural elements are required for efficient transcription termination. Besides its primary function, rho-independent terminators are also known to enhance expression of an upstream gene by stabilizing RNA in a few cases. The Escherichia coli crp gene encoding cAMP receptor protein (CRP) contains a typical rho-independent terminator. To gain further insight into the roles of the G(+)C-rich dyad symmetry sequence and the poly(T) tract both in transcription termination and mRNA stabilization, we constructed a series of variant crp terminators and analyzed their abilities regarding these two functions. Disruption of the G(+)C-rich dyad symmetry sequence almost completely eliminated terminator activity while disruption of the poly(T) tract reduced terminator activity significantly but not completely. Thus, the contribution of the G(+)C-rich dyad symmetry sequence to transcription termination is larger than that of the poly(T) tract. Disruption of the G(+)C-rich dyad symmetry region reduced expression of the upstream crp gene by accelerating the rate of mRNA degradation. However, disruption of the poly(T) sequence had no effect on the stability of the crp mRNA, indicating that the poly(T) tract plays no role in mRNA stabilization. When the crp terminator was replaced by terminators derived from other genes, the fusion genes expressed the crp mRNA at the same level as did the native crp gene, suggesting that the mRNA stabilization effect is probably a general nature of rho-independent terminators.

Bacterial Proteins↗

PubMed2005

HIV-1 Cis Enhancing Sequence (CES) enhances CTE-dependent Gag expression.

In order to export intron-containing RNA from nucleus, retroviruses use either viral trans-acting factors or constitutive cellular factors interacting with cis-elements in their intron-containing RNA. We have previously identified a Cis Enhancing Sequence (CES) in HIV-1 env region that could co-operate with Rev and RRE to enhance Gag expression by promoting RNA stabilization and exportation. In this study, we found that CES could function in a Rev-independent manner by co-operating with a Constitutive Transport Element (CTE) of Mason-Pfizer monkey viruses (MPMV). RRE and CTE promote intron-containing RNA exportation through different pathways. The fact that CES could function in both pathways of RNA export suggested that CES might function at a common step either up- or downstream to Rev/RRE or CTE functions. Known hnRNP-A1-binding sites as well as other 3 highly conserved sequences in the CES were found to be required for its activity.

Animals↗

PubMed2004

Epidermal growth factor-mediated inhibition of follicle-stimulating hormone-stimulated StAR gene expression in porcine granulosa cells is associated with reduced histone H3 acetylation.

Steroidogenic acute regulatory protein (StAR) mediates cholesterol transport into the mitochondria and is essential for ovarian steroidogenesis. Epidermal growth factor (EGF) has been reported to inhibit FSH-stimulated differentiation in porcine granulosa cells. Previous studies have demonstrated FSH stimulates StAR mRNA accumulation and gene promoter activation in granulosa cells. Treatment of granulosa cells with FSH (5 ng/ml, 6 h) increased StAR mRNA, whereas coaddition of EGF (10 ng/ ml) significantly reduced (P < 0.05) FSH-stimulated mRNA accumulation by 62.7% +/- 13.9%. Under these same conditions, FSH-stimulated cAMP accumulation in cultures was unaltered by coincubation with EGF. RNA stability studies showed that cotreatment with FSH and EGF did not alter the StAR mRNA half-life compared with FSH alone, t(1/2) = 1.9-3.8 and 2.7-4.1 h, respectively. EGF significantly inhibited (P < 0.05) FSH-stimulated StAR heterogeneous nuclear RNA levels by 47.6% +/- 6.8 %, implicating a repressive effect on transcription. Surprisingly, EGF (1-50 ng/ml) did not affect FSH stimulation of a 1423-base pair StAR gene promoter-luciferase construct in transient transfection assays in porcine granulosa cells. To evaluate FSH and EGF effects on the endogenous StAR gene, chromatin immunoprecipitation assays were performed in combination with real-time polymerase chain reaction. FSH increased histone H3 acetylation (lysines 9, 14) within the proximal region of the StAR gene promoter and coincubation with EGF blocked this effect. Dimethylation (lysine 9) of histone H3 was not influenced by treatments. In conclusion, EGF repression of FSH-stimulated StAR transcription in porcine granulosa cells is accompanied by reductions in histone H3 acetylation associated with the StAR gene promoter.

Acetylation↗

PubMed1996

Regulation of the Mel 1a melatonin receptor mRNA and protein levels in the ovine pars tuberalis: evidence for a cyclic adenosine 3',5'-monophosphate-independent Mel 1a receptor coupling and an autoregulatory mechanism of expression.

The Mel 1a receptor gene has recently been cloned and sequenced, and its product has been found to represent a new class of the G protein-coupled receptor superfamily. A unique aspect of its endogenous hormonal ligand, melatonin, is the prolonged duration (16 h) required to initiate appropriate photoperiodic responses in the animal. This study provides the first data on the transcriptional and translational regulation of this receptor in primary cultures of its native tissue, the pars tuberalis of the ovine pituitary. Using RNAse protection assays we show Mel 1a mRNA expression is rapidly induced through changes in intracellular cAMP levels. Forskolin enhances Mel 1a mRNA expression, whereas melatonin reverses this effect. RNA stability is also a factor, as Mel 1a mRNA expression decreases rapidly in the presence of actinomycin D. Although the expression of receptor protein is sensitive to forskolin stimulation, the lag between induction of mRNA and protein suggests that other factors (e.g. RNA splicing) contribute to functional receptor expression. Furthermore we observed that both mRNA and receptor protein levels increase spontaneously during primary culture, and these rises could be blocked by melatonin. A spontaneous rise in Mel 1a mRNA can also occur in serum-depleted cultures. In the absence of corresponding changes in cAMP, these results suggest not only that the Mel 1a receptor can autoregulate its own expression by an undefined pathway, but also they provide the first evidence that melatonin can act via a cAMP-independent signal transduction pathway to repress transcription in this tissue.

Animals↗

PubMed2000

Retinal lesions induce differential changes in the expression of flip and flop isoforms of the glutamate receptor subunit GluR1 in the chick optic tectum.

A sensitive RNase protection assay was employed to determine the levels of mRNA encoding the GluR1 subunit flip and flop isoforms in the chick optic tectum and forebrain. We found that the flip GluR1 mRNA predominates in the forebrain, whereas the flop variant is more strongly expressed in the optic tectum. A temporal analysis of GluR1 variants in the embryonic and adult chick brain revealed that the flip isoform is more highly expressed at E12 than at P15-21, whereas mRNA levels of the flop isoform are higher at P15-21 than at E12. To study the effect of deafferentation on GluR1 expression, unilateral retinal lesions were performed. Two days later the mRNA levels of GluR1 flip and flop variants were decreased in the deafferented tectum, especially for the flop isoform. However, 7 days after the lesion, the mRNA levels of both GluR1 isoforms were increased, especially for the flip isoform. These results reveal an important control of the retinal input upon the expression of the different GluR1 isoforms. Furthermore, they indicate a differential spatial and temporal regulation of the flip and flop splice variants, suggesting the existence of a mechanism regulating differential splicing or possibly differential RNA stability.

Aging↗

PubMed2000

The sense of naturally transcribed antisense RNAs in plants.

Naturally occurring antisense transcripts are well documented in mammals and prokaryotes but little is known about their existence and effects in plants. Generally, antisense RNAs are believed to control gene expression negatively by annealing to the complementary sequences of the sense transcript. The resulting double-stranded RNAs are thought either to affect RNA stability, transcription and/or translation directly, or to generate a signal for gene silencing and defense against viruses.

Gene Expression Regulation, Plant↗

PubMed1994

Differential transcription of plastome-encoded genes in the mesophyll and bundle-sheath chloroplasts of the monocotyledonous NADP-malic enzyme-type C4 plants maize and Sorghum.

The transcription of plastome-encoded genes in mesophyll and bundle-sheath chloroplasts of the monocotyledonous NADP-malic enzyme-type C4 species Zea mays L. (maize) and Sorghum bicolor (L.) Moench. was investigated. RNA accumulation and transcription were assayed starting from isolated mesophyll and bundle-sheath chloroplasts and using quantitative northern and run-on transcription analysis. Determination of the mesophyll to bundle-sheath ratios of transcript abundance in maize and Sorghum chloroplasts showed that the mRNAs of the plastome-encoded photosystem II genes analysed (psbA, psbB, psbD, psbH and psbE/F) varied from 2.5- to 4.0-fold (maize) and 3.1- to 5.2-fold (Sorghum), respectively. The rbcL transcript, in contrast, was more abundant in bundle-sheath chloroplasts of both species, about 3-fold in maize and more than 10-fold in Sorghum. On the other hand, transcripts of genes encoding the 16S ribosomal RNA (r16) and subunits of photosystem I (psaA) and the cytochrome b/f complex (petB, petA) accumulated to similar levels in both types of chloroplasts. Determination of absolute transcript levels for rbcL and psbA in chloroplasts from maize and Sorghum demonstrated that for both genes, the mesophyll to bundle-sheath differences in transcript abundance were more pronounced in Sorghum. Measurements of the transcriptional activities of rbcL and psbA showed that the transcription rate of rbcL is higher in bundle-sheath chloroplasts while psbA is more actively transcribed in mesophyll chloroplasts. The differences in the transcription rates between the two chloroplast types were again more pronounced in Sorghum, thus reflecting the differences between maize and Sorghum in the relative levels of the rbcL and psbA transcripts. However, although transcription rate and mRNA abundance are correlated, they did not exactly match one another. This indicates additional regulation of transcript abundance at the level of RNA stability.

Chloroplasts↗

PubMed2000

The end of the (DNA) line.

Telomerases contain an essential RNA subunit (TER), as well as an essential protein reverse transcriptase subunit (TERT). The RNA subunit includes a short template region that is copied into telomeric DNA, but otherwise it is large and divergent. However, phylogenetic studies have revealed a conserved core secondary structure for TER. Much of the divergence can be accounted for by the acquisition of different types of RNA domains that function in RNA stabilization. Some of the nontemplate portions of TER, which include regions in the conserved core, are important for aspects of telomerase enzymatic activity independent of their role in telomerase assembly. Mutational studies indicate that telomerase enzyme function results from a collaboration of both protein and RNA functional groups contributed by TERT and TER.

DNA↗

PubMed2004

Quantitative monitoring of BCR--ABL transcript--suggestion of a simplified approach considering inaccuracy of measurement and calibration.

According to standard-protocols, real time quantitative RT-PCR (RQ-PCR) for quantification of BCR-ABL fusion transcripts in CML patients is performed with the construction of a standard curve for each run, each sample is analyzed at least in duplicate and 10-40 ml peripheral blood are processed. This approach is appropriate for a research laboratory, but is not suitable for a routine laboratory setting. We show that the calibration curve based on the common 5 dilution standards (between 10 and 10(6) copies) is strongly influenced by the large variability of the measurements below 100 copies of the gene. In other words, including a standard with 10 copies is a source of error, which cannot be reduced through the construction of a standard curve with each run. Adding additional dilutions between 10 and 100 copies to the standard curve, the variance of the obtained curve is much reduced. As a conclusion, it is unnecessary to construct a calibration curve with each run since only negligible inaccuracy of calibration is added to the inaccuracy of measurement. Running of the samples in duplicate seems unnecessary since the inaccuracy of the method can be correctly estimated. Finally, we propose a standardized collection and isolation of total RNA from only 2.5 ml blood using an integrated system, which allows RNA stabilization for up to 5 days and provides snapshots of BCR-ABL fusion transcripts with higher accuracy than with non-stabilized blood samples.

Calibration↗

PubMed1985

Multiple-level caerulein control of the gene expression of secretory proteins in the rat pancreas.

Continuous intravenous infusion of caerulein (0.25 micrograms X kg-1 X h-1) has recently been reported [Schick, J., Kern, H. & Scheele, G. (1984) J. Cell Biol. 99, 1569-1574] to enhance significantly the synthesis of both trypsinogen and chymotrypsinogen and to decrease that of amylase in the rat pancreas. With a view to achieving a better understanding of the mechanisms underlying caerulein modulation of pancreatic gene expression, the relative levels of active mRNA corresponding to these proteins were determined in caerulein-stimulated animals and compared to those of controls infused with a 0.9% NaCl solution. For this purpose, the translation products synthesized in vitro in a rabbit reticulocyte lysate translation system were measured. Prolonged caerulein infusion had less pronounced effects on mRNA levels as determined by the relative synthesis of translation products than on individual secretory proteins. No changes in mRNA levels were observed during 6 h of hormonal stimulation, whereas a 7-fold increase in the ratio of trypsinogen to amylase synthesis was obtained previously. After 24 h of caerulein infusion, only a slight change in active mRNA coding for amylase (1.7-fold) and serine protease zymogens (1.4-fold) occurred as compared to 14-fold and 2-fold variations in the synthesis rates of the corresponding proteins. These findings indicate that caerulein exerts a predominantly translational control on the biosynthesis of pancreatic amylase, trypsinogen and chymotrypsinogen even after 24 h of hormonal stimulation. However, additional control at a transcriptional or post-transcriptional level (i.e. via messenger RNA stability) may well take place.

Amylases↗

PubMed2000

Both increased stability and transcription contribute to the induction of the urokinase plasminogen activator receptor (uPAR) message by hypoxia.

Both hypoxia and overexpression of the urokinase plasminogen activator receptor (uPAR) are associated with a poor clinical outcome in human cancers. Hypoxia has been shown to induce uPAR expression in breast cancer cells and to increase their invasion through Matrigel, a phenomenon which can be blocked using an anti-uPAR antibody. We examined expression of uPAR mRNA in MCF7 human breast carcinoma cells under hypoxia and found that an increase in the level of the message could be detected at 1% oxygen but was most marked at 0.2 or 0.05% oxygen with an induction of 9- to 20-fold over baseline. To determine whether changes in RNA stability contributed to this dramatic increase, we used actinomycin D to inhibit transcription and found that the half-life of the message was much longer under hypoxic conditions (approximately 10 h) than during reoxygenation (approximately 2 h). Transient transfections using a luciferase reporter construct containing 2 kbp of the mouse uPAR promoter showed that promoter activity increased up to 5-fold after exposure to 0.2% oxygen. Thus, hypoxic induction of the uPAR message in MCF7 cells is due to both mRNA stabilization and increased transcriptional activation.

Animals↗

PubMed1989

Downregulation of cell growth and cell cycle regulated genes during chick osteoblast differentiation with the reciprocal expression of histone gene variants.

Expression of cell cycle (core and H1 histone) and cell growth (c-myc and c-fos) regulated genes was examined in primary cultures of chick calvarial osteoblasts during a developmental sequence associated with the progressive maturation of the osteoblast in a bonelike mineralized extracellular matrix. We have identified a transition point early in the developmental sequence which occurs when proliferation ceases and expression of genes related to the differentiated phenotype of osteoblasts is initiated. During this transition period, cellular levels of RNA transcripts from core and H1 histone genes and the c-myc and c-fos protooncogenes decrease in a parallel and coordinate manner. The decline in histone gene transcription that accompanies the loss of accumulated histone mRNA indicates that the downregulation of histone gene expression is at least, in part, transcriptionally mediated. In contrast, persistence of c-myc and c-fos transcription following completion of the proliferation period, when the mRNAs are no longer present at detectable levels, suggests that the initial downregulation of protooncogene expression is controlled at the level of messenger RNA stability. Thus, two types of signaling mechanisms are operative in the down-regulation of cell proliferation genes during osteoblast differentiation--one that impinges on regulatory sequences that influence the interactions of transcription factors with cis-acting promoter elements and a second that modulates messenger RNA turnover. Of significance, downregulation of the cell cycle regulated histone genes is accompanied by a reciprocal increase in the expression of a structurally distinct subset of the histone genes that are not coupled with DNA replication during the period of expression of osteoblast phenotype markers.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1992

Gene expression in Leishmania: analysis of essential 5' DNA sequences.

A major unanswered question in Kinetoplastida parasites is the mechanism of regulating gene expression. Using a transfection system, we have previously shown that the intergenic region of the alpha-tubulin gene of Leishmania enriettii contained sequences required for gene expression. The goal of the work reported here was to determine whether the Leishmania-derived sequences were providing transcriptional control signals or functioning at a post-transcriptional level, most likely in trans-splicing. The chloramphenicol acetyltransferase (cat) gene was used as the reporter gene and was stably introduced into L. enriettii as part of an extrachromosomal element by transfection. We show here that the production of cat mRNA was dramatically dependent on the presence of the intergenic region 5' to the cat gene. The intergenic region could be substituted by a smaller fragment (222 base pairs) that contained the trans-splice acceptor site and an adjacent polypyrimidine tract. This native fragment could be replaced by a synthetic polypyrimidine tract containing an AG site. The native and the synthetic fragments had unidirectional activity. No effect on transcription of the cat gene by the wild-type fragment or the synthetic polypyrimidine was detected. The results indicate that both regions contain signals that affect RNA stability, probably sequences involved in trans-splicing.

Animals↗

PubMed1991

Specific binding of chloroplast proteins in vitro to the 3' untranslated region of spinach chloroplast petD mRNA.

A detailed analysis of RNA-protein complex formation in the 3' untranslated region of spinach chloroplast petD mRNA has been carried out. Five chloroplast proteins that interact with petD RNA in this region, which contains an inverted repeat sequence capable of forming a hairpin structure, have been identified. A 33-kDa protein recognizes specifically the double-stranded stem of the hairpin structure; mutations that disrupt base pairing at the base of the stem reduce or eliminate protein binding. A 57-kDa protein recognizes specifically an AU-rich sequence motif that is highly conserved in petD genes of different higher plant species. The 57-kDa protein and possibly the 33-kDa protein form stable complexes with petD RNA in vitro and may interact with each other. In addition, their interaction with petD RNA is highly sensitive to heparin. The three other proteins, of 100, 32, and 28 kDa, display little sequence or structural binding specificity apart from their preference for uridine-rich sequences. They also interact with the 3' untranslated regions of other chloroplast RNAs such as those of psbA and rbcL. The functions of these proteins in the regulation of petD gene expression, including possible roles in transcription termination and RNA stability, are discussed.

Base Composition↗

PubMed2001

Ribozyme gene therapy: applications for molecular medicine.

RNA enzymes--ribozymes--are being developed as treatments for a variety of diseases ranging from inborn metabolic disorders to viral infections and acquired diseases such as cancer. Ribozymes can be used both to downregulate and to repair pathogenic genes. In some instances, short-term exogenous delivery of stabilized RNA is desirable, but many treatments will require viral-mediated delivery to provide long-term expression of the therapeutic catalyst. Current gene therapy applications employ variations on naturally occurring ribozymes, but in vitro selection has provided new RNA and DNA catalysts, and research on trans-splicing and RNase P has suggested ways to harness the endogenous ribozymes of the cell for therapeutic purposes.

Acquired Immunodeficiency Syndrome↗

PubMed1990

Identification of a potential RNA intermediate for transposition of the LINE-like element I factor in Drosophila melanogaster.

The I factor, a transposable element related to mammalian LINEs, controls the I-R system of hybrid dysgenesis in Drosophila melanogaster. It transposes at high frequency in the germ-line of the female progeny of crosses between females of the reactive class of strains and males of the inducer class. The structure and DNA sequence of the I factor suggest that it transposes by reverse transcription of an RNA intermediate. Northern blot and S1 mapping experiments show that a full-length RNA of the I factor is synthesized specifically in the conditions of which I factors transpose. This RNA has all characteristics of a transposition intermediate. It is only found in the ovaries of dysgenic females suggesting that I factor activity is restricted to this tissue because of regulation at the level of the initiation of transcription or RNA stability.

Animals↗

PubMed1996

Mutational analysis of RNA structures and sequences postulated to affect 3' processing of M1 RNA, the RNA component of Escherichia coli RNase P.

When the rnpB gene encoding M1 RNA, the RNA component of Escherichia coli RNase P, is transcribed, the primary M1 RNA transcript (pM1 RNA) is produced and subsequently processed at the 3' end to generate the mature M1 RNA. To study features of pM1 RNA thought to be involved in RNA processing, systematic mutations were introduced in sequence elements and secondary structures surrounding the processing site using p23 RNA, a truncated pM1 RNA transcribed from the internally deleted rnpB gene, as a model substrate and the processing of its mutant derivatives was analyzed in vivo and in vitro. Neither the alteration of two bases forming the processing site nor the disruption of secondary structures surrounding the site significantly affected the processing efficiency although the secondary structures were required for maintaining RNA stability. In contrast, mutations at the rne-dependent site, GAUUU, immediately 3' to the processing site inhibited the processing and the extent of the inhibition varied with the altered sequences. Furthermore, the processing of the mutants of the rne-dependent site as well as wild-type p23 RNA was inhibited in an E. coli rnets strain at the nonpermissive temperature.

Base Sequence↗

PubMed1992

Interleukin-1 down-regulates gene and surface expression of interleukin-1 receptor type I by destabilizing its mRNA whereas interleukin-2 increases its expression.

The interleukin-1 receptor type I (IL-1RtI) plays an important role in the biological effects of IL-1, but regulation of its surface and gene expression remains unknown. We found that occupancy of 2-15% of the IL-1 surface receptor results in dramatic down-regulation of IL-1RtI both at the mRNA and cell surface level in murine D10S cells, a subline of T-helper type 2 cells. At these low occupancy levels (3 x 10(-12) to 3 x 10(-13) M), the reduction in IL-1RtI surface expression appears at 24 hr and continues to 48 and 72 hr. At the mRNA level, low occupancy of the IL-1R results in decreased IL-1RtI mRNA stability; steady state half-life of the IL-1RtI mRNA is reduced from 6 to 1 hr after exposure to 3 x 10(-12) M IL-1. This down-regulation of IL-1RtI by IL-1 is blocked by cycloheximide, suggesting de novo protein synthesis is necessary for decreased RNA stability. Low concentrations of human IL-1 beta, murine and rabbit IL-1 alpha or beta similarly down-regulated IL-1RtI, whereas low concentrations of human IL-1 alpha failed to reduce the receptor surface expression, despite inducing a full proliferative response. We also observed that the effect of IL-1 on this down-regulation was not through protein kinase C (PKC), since PMA rapidly increased IL-1RtI mRNA levels within 30 min and persisted for 24 hr. IL-2 up-regulated IL-1RtI in D10S cells at both mRNA and protein levels. These results demonstrate that low occupancy of IL-1 receptors induces down-regulation of IL-1RtI surface as well as mRNA expression. The regulation of IL-1RtI gene expression may be one of the mechanisms by which IL-1-mediated events are controlled.

Animals↗