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At least 613 records · Page 34Linked to original sources
PubMed2003

Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP.

Repeated rounds of polyploidy have been commonplace in the lineages leading to modern eukaryotic genomes, giving rise to widespread gene duplication. Genes duplicated by polyploidy, or "homoeologs," may continue to be expressed at equal levels following polyploidization or their expression may be dramatically altered. In this report, we describe how SSCP analysis of RT-PCR products can be used to evaluate the expression status (presence and relative quantity) of highly similar homoelogous gene pairs from an allotetraploid genome. This cDNA-SSCP approach was used to evaluate transcript abundance in "synthetic tetraploid" mRNA pools (i.e., mixtures of diploid products) and three natural homoeologous gene pairs expressed in tetraploid cotton (Gossypium hirsutum) ovules. Results from replicated tests show that cDNA-SSCP reliably separates duplicated transcripts with 99% sequence identity. Most significantly, the method yields quantitative estimates of transcript ratios in template pools that range from equimolar to approximately 100:1.

DNA, Complementary↗
PubMed2005

Anti-apoptotic effects of L-glutamine-mediated transcriptional modulation of the heat shock protein 72 during heat shock.

BACKGROUND & AIMS: During physiologic stress, L-glutamine becomes conditionally essential. Its deficiency results in altered epithelial barrier competence, bacterial translocation, and decreased survival. L-glutamine may attenuate these effects by modulating heat shock protein expression, a well-described effect in vitro. We sought to characterize L-glutamine-dependent transcriptional regulation in heat-shocked intestinal cells and to determine its physiologic relevance. METHODS: IEC-18 and H4 intestinal cells were used. Heat shock protein 72 (Hsp72) gene expression was determined by Northern blotting and luciferase assays. Heat shock factor-1 (HSF-1) activation was assessed by electromobility shift assay, Western blotting, and HSF-1 minimal promoters. Phosphorylation and trimerization of HSF-1 were determined by immunoprecipitation and native nonreducing gradient polyacrylamide gel electrophoresis (PAGE). Camptothecin-induced apoptosis was monitored using caspase-3 and poly (ADP-ribose) polymerase [PARP]-specific antibodies and DNA Elisa +/- Hsp72 siRNA. RESULTS: L-glutamine specifically augmented Hsp72 transcript abundance and HSF-1 DNA binding during heat shock. No glutamine-dependent differences in HSF-1 phosphorylation, trimerization, nuclear localization during heat shock, or HSF-1 minimal promoter activity were observed. Nevertheless, the presence of L-glutamine was an important determinant of wild-type Hsp72 promoter transcriptional activation. Reduced Hsp72 was associated with increased camptothecin-induced caspase-3 and PARP cleavage in glutamine-deficient cells. siRNA treated cells were less resistant to camptothecin. CONCLUSIONS: Taken together, the data suggest that glutamine does not affect the classical pathway of HSF-1 activation and that glutamine-dependent upstream trans -factor binding elsewhere in the Hsp72 promoter or coactivator recruitment may determine Hsp72 abundance. L-glutamine potentiation of Hsp72 is associated with increased epithelial resistance to apoptotic injury.

Apoptosis↗
PubMed1983

Post-transcriptional control of human cytomegalovirus gene expression.

During the immediate-early, early, and late phases of human cytomegalovirus infection in human fibroblasts, transcripts accumulated, respectively, from approximately 20, 75, and 90% of the sequences on the genome. Not all of the sequences which accumulated during the immediate-early and early phases were represented on polysomes, however. Four transcripts synthesized in cycloheximide-treated cells were studied in detail. A 2.2-kb transcript (0.713-0.733 map units) represented 95% of the polysome-associated RNA in cycloheximide-treated cells and was the first to be detected on polysomes at 2 hr postinfection in untreated cells. A second, less abundant, transcript of 5.2 kb (0.670-0.733 map units) was also found on polysomes in cycloheximide-treated cells, and preliminary evidence suggested that this transcript may be spliced during processing. A 3.25-kb transcript (0.190-0.217 map units) was identified also as a minor polysome-associated species of RNA. One transcript of 4.8 kb (0.630-0.670) remained associated with the nucleus and was not processed into mRNA in cycloheximide-treated cells. Differential stability between the various transcripts was observed, the 2.2-kb transcript being the most stable. The results showed that in human cytomegalovirus-infected cells controls exist at the level of transcript accumulation, transport into the cytoplasm, preferential association with polysomes, and relative stability of RNAs.

Cell Line↗
PubMed2004

Spinal cord molecular profiling provides a better understanding of amyotrophic lateral sclerosis pathogenesis.

Research efforts in amyotrophic lateral sclerosis (ALS) have not yet provided a comprehensive explanation of the disease pathogenesis, which is emerging as a complex interaction between multiple factors. Gene expression studies traditionally based on single mRNA specie analysis have recently progressed to allow entire transcriptional profiles of affected tissues to be obtained through array-based methods. This experimental approach has significantly improved our understanding of the molecular changes occurring in ALS, although its limitations in the detection of low-abundance transcripts in tissues with a high level of complexity are becoming increasingly recognized. In this paper, experimental findings based on an expression study in post-mortem spinal cord from sporadic ALS individuals will be discussed in light of recently published data using array analysis in an animal model of the disease. Previous expression data obtained using conventional techniques are also compared. Through the analysis of the information arising from ALS post-mortem and animal model tissues studies, we have identified a pattern of molecular events in which factors implicated in the immune response, cytoprotection and growth-differentiation are differentially regulated in a time-dependent way from early to advanced stages of disease progression.

Amyotrophic Lateral Sclerosis↗
PubMed2001

Cold tolerance and proline metabolic gene expression in Drosophila melanogaster.

Treatment of Drosophila melanogaster adults with an inhibitor of protein synthesis led to a decrease in intrinsic cold-shock tolerance, but no difference in the rapid cold hardening response, which is apparent only if a period at 4 degrees C precedes the cold stress. Increases in energy reserves, including proline, were found in lines of flies selected for resistance to chilling injury. Since an increase in proline levels has been associated with overwintering in insects, and for salt and cold tolerance in plants, an RNase protection assay was developed to assess changes in transcript abundance for two genes encoding enzymes important for proline metabolism, pyrroline 5-carboxylate reductase and proline oxidase. The mRNA levels did not change in response to low temperature, but the high level of pyrroline 5-carboxylate reductase transcript is consistent with the interpretation that a large proline pool is important for Drosophila metabolism and survival during cold stress.

Journal Article↗
PubMed2006

The expression of cell proliferation-related genes in early developing flowers is affected by a fruit load reduction in tomato plants.

Changes in photoassimilate partitioning between source and sink organs significantly affect fruit development and size. In this study, a comparison was made of tomato plants (Solanum lycopersicum L.) grown under a low fruit load (one fruit per truss, L1 plants) and under a standard fruit load (five fruits per truss, L5 plants), at morphological, biochemical, and molecular levels. Fruit load reduction resulted in increased photoassimilate availability in the plant and in increased growth rates in all plant organs analysed (root, stem, leaf, flower, and fruit). Larger flower and fruit size in L1 plants were correlated with higher cell number in the pre-anthesis ovary. This was probably due to the acceleration of the flower growth rate since other flower developmental parameters (schedule and time-course) remained otherwise unaffected. Using RT-PCR, it was shown that the transcript levels of CYCB2;1 (cyclin) and CDKB2;1 (cyclin-dependent kinase), two mitosis-specific genes, strongly increased early in developing flower buds. Remarkably, the transcript abundance of CYCD3;1, a D-type cyclin potentially involved in cell cycle regulation in response to mitogenic signals, also increased by more than 5-fold at very early stages of L1 flower development. By contrast, transcripts from fw2.2, a putative negative regulator of cell division in tomato fruit, strongly decreased in developing flower bud, as confirmed by in situ hybridization studies. Taken together, these results suggest that changes in carbohydrate partitioning could control fruit size through the regulation of cell proliferation-related genes at very early stages of flower development.

Cell Cycle Proteins↗
PubMed1996

Stability of the human dystrophin transcript in muscle.

The human dystrophin gene has 79 exons spanning >2300 kb making it the largest known gene. In previous studies we showed that approximately 16 h are required to transcribe the gene in myogenic cultures [Tennyson, C.N., Klamut, H.J. and Worton, R.G. (1995) Nature Genet. 9, 184-190]. To estimate the half-life of the dystrophin mRNA, the decay of the transcript was monitored by quantitative RT-PCR in cultured human fetal myotubes following exposure to actinomycin D. Results from this analysis indicated that the half-life of the dystrophin mRNA is 15.6 +/- 2.8 h in these cultures. Transcript accumulation profiles were predicted using a mathematical model which incorporated the measured half-life. The modeled accumulation profiles were consistent with observed profiles supporting the half-life measured using actinomycin D. The kinetic model was then used to predict the relative amount of nascent and mature dystrophin transcript at steady state. Measurements by quantitative RT-PCR indicated that in adult skeletal muscle tissue the concentration of mature dystrophin mRNA is 5-10 molecules per nucleus, demonstrating, as expected, that it is a low abundance transcript. Furthermore the ratio of nascent to mature dystrophin transcript indicated that dystrophin synthesis may not be at steady state in the adult skeletal muscle we tested. Alternatively, the kinetics of transcript production in skeletal muscle tissue may be different from those observed in cultured fetal myogenic cells.

Adult↗
PubMed1999

The involvement of gRNA-binding protein gBP21 in RNA editing-an in vitro and in vivo analysis.

RNA editing in the parasitic organism Trypanosoma brucei is characterised by the insertion and deletion of uridylate residues into otherwise incomplete primary transcripts. The processing reaction is a required pathway for the expression of most mitochondrial genes and proceeds by a cascade of enzyme-catalysed steps. RNA editing involves one or more macromolecular ribonucleoprotein complexes which are likely to interact with additional components as the reaction proceeds. Here we examined the involvement of the gRNA-binding polypeptide gBP21, a protein which has been demonstrated to be associated with active RNA editing complexes. We show that in vitro RNA editing can be suppressed by the addition of a gBP21-specific antibody or by immunodepletion of the protein. By creating a gBP21 knockout mutant we analysed the requirement for the protein in vivo. gBP21(-) trypanosomes are viable as bloodstream stage cells and contain edited mRNAs. However, the knockout mutant is not capable of differentiating from the bloodstream to the insect life cycle stage in vitro. Moreover, mutant cells are characterised by a low mitochondrial transcript abundance. Together, these data establish that gBP21 contributes a non-essential function to the RNA editing reaction and further suggest that the protein is involved in additional mitochondrial processes which impact a larger pool of mitochondrial transcripts.

Animals↗
PubMed2005

Cauliflower mosaic virus, a compatible pathogen of Arabidopsis, engages three distinct defense-signaling pathways and activates rapid systemic generation of reactive oxygen species.

We analyzed expression of marker genes for three defense pathways during infection by Cauliflower mosaic virus (CaMV), a compatible pathogen of Arabidopsis (Arabidopsis thaliana), using luciferase reporter transgenes and directly by measuring transcript abundance. Expression of PR-1, a marker for salicylic acid signaling, was very low until 8 d postinoculation and then rose sharply, coinciding with the rise in virus levels. In contrast, as early as 2 h postinoculation, transcriptional up-regulation of GST1-a marker for reactive oxygen species-and PDF1.2-a marker for jasmonic acid/ethylene defense signaling-was detectable in the virus-inoculated leaf and systemically. In parallel with the activation of GST1, H(2)O(2) accumulated locally and systemically in virus- but not mock-inoculated plants. However, in plants inoculated with infectious CaMV DNA rather than virus particles, the onset of systemic luciferase activity was delayed by 24 to 48 h, suggesting that virion structural proteins act as the elicitor. This phenomenon, which we term the rapid systemic response, preceded virus movement from the inoculated leaf; therefore, the systemic signal is not viral. Systemic, but not local, H(2)O(2) accumulation was abolished in rbohDF double mutants and in etr1-1 and ein2-1 mutants, implicating NADPH oxidase and ethylene signaling in the generation and transduction of the response. Ethylene, but not rbohDF mutants, also showed reduced susceptibility to CaMV, whereas in NahG transgenics, virus levels were similar to wild type. These findings implicate reactive oxygen species and ethylene in signaling in response to CaMV infection, but suggest that salicylic acid does not play an effective role.

Arabidopsis↗
PubMed2000

Increased insulin-like growth factor binding protein-4 expression after partial hepatectomy in the rat.

The insulin-like growth factor (IGF) binding proteins (IGFBPs) are important regulators of cell growth produced by different tissues. The IGFBPs regulate cell growth by modulating the activity and bioavailability of IGFs. The evidence that IGFBP-1 is a liver-specific immediate-early gene highly induced after 70% partial hepatectomy (PHx) suggests a role for the IGF-IGFBP system in hepatic regeneration. In this work we analyzed the effect of PHx on the expression of IGFBP-4, which is highly produced by the liver and very abundant in rat serum. Our results show a marked increase in hepatic IGFBP-4 mRNA levels 6-12 h after PHx and no significant change in sham-operated control animals. A parallel rise in IGFBP-4 transcript abundance was observed in the kidneys of PHx rats but not in sham-operated animals. Moreover, ligand blot analysis demonstrated that serum IGFBP-4 levels began to increase 12-24 h after surgery, consistent with the rise in the corresponding mRNA. This enhancement in IGFBP-4 production after PHx could be part of a fine regulatory mechanism to modulate IGF activity during liver regeneration.

Animals↗
PubMed1998

Regulation of nitrate reductase transcript levels by glutamine accumulating in the leaves of a ferredoxin-dependent glutamate synthase-deficient gluS mutant of Arabidopsis thaliana, and by glutamine provided via the roots.

The regulation by glutamine of the leaf transcript level corresponding to the Arabidopsis thaliana (L.) Heynh. nitrate reductase gene nia2 was examined using a novel approach: we took advantage of the ability of a ferredoxin-dependent glutamate synthase-deficient gluS mutant of A. thaliana to accumulate glutamine in the leaves when illuminated under conditions that favour photorespiration. The accumulation of glutamine in gluS mutant leaves and the concomitant decline in the leaf glutamate pool were not correlated with a reduction in the foliar nia2 transcript level. This result indicates that glutamine may not exert a negative control of the leaf nia2 transcript pool. The pattern of diurnal nia2 mRNA oscillation did not change upon illumination of the gluS mutant in air, although the leaf glutamine level remained high during the diurnal cycle. The amplitude of the diurnal fluctuation in nia2 transcript abundance, therefore, does not seem to depend on the size of the leaf glutamine pool (which normally fluctuates in opposite phase). This result also appears to argue against a role of glutamine as an effective repressor of nia2 transcript accumulation. The application of a solution containing 100 mM glutamine to the roots of A. thaliana resulted in an increase in the leaf glutamine level and in a decrease in the leaf nia2 transcript level. Net CO2 uptake and chlorophyll fluorescence quenching by attached leaves of A. thaliana were determined as a control of the physiological status of the plants and remained unaffected by the glutamine treatment. However, there was a decrease in the foliar nitrate level. The negative effect on the nia2 transcript pool exerted by exogeneous glutamine may, therefore, be explained as a result of the down-regulation of nitrate-uptake permeases in the roots by glutamine.

Amino Acid Oxidoreductases↗
PubMed1999

Distamycin A selectively inhibits Acanthamoeba RNA synthesis and differentiation.

The effects of distamycin A on Acanthamoeba transcription, growth and differentiation were determined. Distamycin A inhibits transcription both in vitro and in vivo and can displace from DNA the transcription activator TATA binding protein promoter binding factor (TPBF). Inhibition in vivo is surprisingly selective for large rRNA precursors, 5S rRNA, profilin, S-adenosylmethionine synthetase, and extendin. Transcription from the TATA binding protein (TBP), TPBF, protein disulfide isomerase, tubulin and RNA polymerase II large subunit genes is only slightly inhibited. Moreover the rate of 5S rRNA transcription eventually recovers and exceeds that of untreated cells, while profilin transcription remains inhibited. Distamycin A inhibition is accompanied by a complex pattern of alterations to steady state levels of mRNAs. Actin, profilin and S-adenosylmethionine synthetase mRNAs are degraded, whereas mRNA encoding TBP is increased slightly in abundance. Transcription inhibition is accompanied by cessation of growth and severe morphological changes to Acanthamoeba, which are consistent with loss of production of mRNA encoding cytoskeletal proteins. Distamycin A also prevents starvation-induced differentiation of Acanthamoeba, in part due to complete prevention of cellulose production and cell wall formation.

Acanthamoeba↗
PubMed2003

Quantification of gene transcription and enzyme activity for functionally important proteolytic enzymes during early development in the Pacific oyster Crassostrea gigas.

Gene transcripts and enzyme activities were quantified for a selection of functionally important aminopeptidases at 2-day intervals throughout the first 72 days of development in the Pacific oyster Crassostrea gigas. Leucine aminopeptidase (LAP) and cathepsin B (CathB) gene transcripts were quantified using fluorogenic ('real time') PCR. LAP and CathB gene transcripts were detected at all time points. The proportion of CathB transcripts remained essentially constant and low throughout development (Ct<35). The proportion of LAP transcripts was often similar (Ct<30), but with a distinct peak in transcript abundance at day 19 (Ct approximately 23). CathB and cathepsin D (CathD) enzyme activities were measured biochemically. Whilst CathD activity peaked at day 19, LAP and CathB activities both peaked at day 24. The closely coupled increase in transcript and enzyme activity for LAP indicates regulation at the transcriptional level. Alternatively, the peak in enzyme activity for CathB without enhanced transcriptional activity suggests post-transcriptional regulation. Similar mechanisms of regulation for LAP and CathB have been observed in both plants and mammals, indicating widespread conservation.

Animals↗
PubMed2005

Divergent transcriptional enhancer factor-1 regulates the cardiac troponin T promoter.

MCAT elements are essential for cardiac gene expression during development. Avian transcriptional enhancer factor-1 (TEF-1) proteins are muscle-enriched and contribute to MCAT binding activities. However, direct activation of MCAT-driven promoters by TEF-1-related proteins has not been uniformly achieved. Divergent TEF (DTEF)-1 is a unique member of the TEF-1 multigene family with abundant transcripts in the heart but not in skeletal muscle. Herein we show that DTEF-1 proteins are highly expressed in the heart. Protein expression is activated at very early stages of chick embryogenesis (Hamburger-Hamilton stage 4, 16-18 h), after which DTEF-1 becomes abundant in the sinus venosus and is expressed in the trabeculated ventricular myocardium and ventricular outflow tracts. By chromatin immunoprecipitation, DTEF-1 interacts with the cardiac troponin T (cTnT) promoter in vivo. DTEF-1 also interacts with MEF- 2 by coimmunoprecipitation and independently or cooperatively (with MEF-2) trans-activates the cTnT promoter. DTEF-1 isoforms do not activate the cTnT promoter in fibroblasts or skeletal muscle. DTEF-1 expression occurs very early in chick embryogenesis (16-18 h), preceding sarcomeric protein expression, and it activates cardiac promoters. As such, DTEF-1 may be an early marker of the myocardial phenotype. DTEF-1 trans-activates the cTnT promoter in a tissue-specific fashion independent of AT-rich, MEF-2, or GATA sites. The observed spatial pattern suggests decreasing levels of expression from the cardiac inlet to the ventricular outflow tracts, which may mark a cardiogenic or differentiation pathway that parallels the direction of flow through the developing chick heart.

Amino Acid Motifs↗
PubMed2001

Thyroid hormone receptor expression in rat placenta.

The expression of c- erbAalpha and -beta encoded thyroid hormone receptors (TR) was investigated in rat placenta between 16 and 21 days of gestation (dg), and in fetal liver and brain at 16 dg, using semi-quantitative RT-PCR and nuclear 3,5,3'-triiodothyronine (T(3)) binding. TRalpha1, TRbeta1, c- erbAalpha 2 and c- erbAalpha 3 mRNA abundance was unchanged in placenta between 16 and 21 dg, as was the dissociation constant (K(d)) of T(3) binding. The maximal T(3) binding capacity (B(max)) in placenta doubled over this period, suggesting placental TR binding activity is post-transcriptionally regulated. Transcript abundance in tissues at 16 dg can be summarized: TRalpha1, placenta=fetal liver fetal brain; c- erbAalpha 2 and alpha3, placenta=fetal liver<fetal brain; TRbeta2; none detected. T(3)binding in fetal liver and brain exhibited equivalent K(d) and B(max), the K(d) being less than 50 per cent of that in placenta, though B(max) was unchanged. The higher K(d)in placenta may reflect tissue-specific patterns of TR modification. In conclusion, rat placenta expresses significant levels of c- erbAalpha and -beta transcripts and protein, providing a possible mechanism of action for T(3) of maternal and fetal origin in this tissue.

Animals↗
PubMed1990

Presence and transcription of intracisternal A-particle-related sequences in CHO cells.

We have characterized sequences expressed in Chinese hamster ovary (CHO) cells which are related to the intracisternal A-particle (IAP) genes of mice and Syrian hamsters. Several cDNA clones homologous to Syrian hamster IAP probes have been isolated and used to evaluate the abundance and expression of these retroviruslike sequences. DNA blot analysis with homologous Chinese hamster IAP probes revealed that IAP-related sequences are present in CHO cell DNA at moderately repetitive levels (approximately 300 copies per haploid genome). Sequence analysis has revealed the existence of at least two distinct families of IAP-related sequences in CHO cell DNA. Family I sequences exhibit identical 4.5-kilobase-pair internal deletions relative to complete IAP genomes of mice or Syrian hamsters, but family II sequences showed no major sequence discontinuities relative to the IAP genes of other species. Both families are expressed as abundant cytoplasmic RNA in CHO cells, but only family II sequences produce abundant transcripts of a size consistent with that of a full-length IAP RNA. Intact gag, pol, or env open reading frames were not present in sequences of either family, although incomplete open reading frames spanning putative p27 and protease regions of IAP genes were observed.

Amino Acid Sequence↗
PubMed1986

Expression of the major heat shock gene of Drosophila melanogaster in Saccharomyces cerevisiae.

A copy of the gene which encodes the major heat shock protein (hsp70) of D. melanogaster was integrated in both orientations into the genome of S. cerevisiae at the leu2 locus. The level of transcript from the D. melanogaster gene was measured under both normal conditions and conditions which are known to give rise to the heat shock response in S. cerevisiae. In both orientations the D. melanogaster gene gave rise to an abundant transcript in uninduced cells. The level of this transcript was increased transiently on heat shock, peaking after about 30 min at the elevated temperature. The average induction observed was around 5-fold. Although the D. melanogaster gene is heat inducible in S. cerevisiae, the transcripts are initiated at several sites which lie between 10 and 40 base pairs downstream of the initiation site in D. melanogaster. Thus, the transcriptional apparatus of S. cerevisiae appears to recognize the promoter and regulatory elements of the D. melanogaster major heat shock gene, although the manner in which transcription is initiated differs between the two species.

Animals↗
PubMed2000

Control of ovine hepatic growth hormone receptor and insulin-like growth factor I by thyroid hormones in utero.

By use of RNase protection assays, hepatic growth hormone receptor (GHR) and insulin-like growth factor I (IGF-I) mRNA abundances were measured in sheep fetuses after experimental manipulation of fetal plasma thyroid hormone concentrations by fetal thyroidectomy (TX) and exogenous infusion of triiodothyronine (T(3)) and cortisol. TX abolished the normal prepartum rise in hepatic GHR abundance but had little effect on hepatic GHR gene expression at 127-130 days (term 145 +/- 2 days). By contrast, it upregulated basal IGF-I expression in immature fetal liver by increasing both Class 1 and Class 2 transcript abundance but had no further effects on IGF-I gene mRNA levels at 142-145 days. Raising plasma T(3) to prepartum values by exogenous infusion of either T(3) or cortisol into immature intact fetuses prematurely raised hepatic GHR and IGF-I mRNA abundances to values similar to those seen in intact fetuses at 142-145 days. In TX fetuses, cortisol infusion increased hepatic GHR mRNA but not total IGF-I mRNA abundance at 127-130 days. These findings show that thyroid hormones have an important role in the regulation of hepatic GHR and IGF-I gene expression in fetal sheep during late gestation and suggest that T(3) mediates the maturational effects of cortisol on the hepatic somatotropic axis close to term.

Animals↗