Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Deregulated expression of members of the myc oncogene family has been linked to the genesis of a wide range of cancers, whereas their normal expression is associated with growth, proliferation, differentiation, and apoptosis. Myc proteins are transcription factors that function within a network of transcriptional activators (Myc) and repressors (Mxd/Mad and Mnt), all of which heterodimerize with the bHLHZ protein Mad and bind E-box sequences in DNA. These transcription factors recruit coactivator or corepressor complexes that in turn modify histones. Myc, Mxd/Max, and Mnt proteins have been thought to act on a specific subset of genes. However, expression array studies and, most recently, genomic binding studies suggest that these proteins exhibit widespread binding across the genome. Here we demonstrate by immunostaining of Drosophila polytene chromosome that Drosophila Myc (dMyc) is associated with multiple euchromatic chromosomal regions. Furthermore, many dMyc-binding regions overlap with regions containing active RNA polymerase II, although dMyc can also be found in regions lacking active polymerase. We also demonstrate that the pattern of dMyc expression in nuclei overlaps with histone markers of active chromatin but not pericentric heterochromatin. dMyc binding is not detected on the X chromosome rDNA cluster (bobbed locus). This is consistent with recent evidence that in Drosophila cells dMyc regulates rRNA transcription indirectly, in contrast to mammalian cells where direct binding of c-Myc to rDNA has been observed. We further show that the dMyc antagonist dMnt inhibits rRNA transcription in the wing disc. Our results support the view that the Myc/Max/Mad network influences transcription on a global scale.
Cold Spring Harb Symp Quant Biol 2005
PMID:Genomic binding and transcriptional regulation by the Drosophila Myc and Mnt transcription factors. 1686 66

Foot-and-mouth disease virus (FMDV) is thought to evolve largely through genetic drift driven by the inherently error-prone nature of its RNA polymerase. There is, however, increasing evidence that recombination is an important mechanism in the evolution of these and other related picornoviruses. Here, we use an extensive set of recombination detection methods to identify 86 unique potential recombination events among 125 publicly available FMDV complete genome sequences. The large number of events detected between members of different serotypes suggests that horizontal flow of sequences among the serotypes is relatively common and does not incur severe fitness costs. Interestingly, the distribution of recombination breakpoints was found to be largely nonrandom. Whereas there are clear breakpoint cold spots within the structural genes, two statistically significant hot spots precisely separate these from the nonstructural genes. Very similar breakpoint distributions were found for other picornovirus species in the genera Enterovirus and Teschovirus. Our results suggest that genome regions encoding the structural proteins of both FMDV and other picornaviruses are functionally interchangeable modules, supporting recent proposals that the structural and nonstructural coding regions of the picornaviruses are evolving largely independently of one another.
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PMID:Recombination patterns in aphthoviruses mirror those found in other picornaviruses. 1697 23

Hypoxia plays an integral part in cardiac transplantation as prolonged graft preservation is an individual risk factor for the development of cardiac allograft vasculopathy (CAV). In this study we characterized the role of hypoxia-inducible factor-1 (HIF-1) during prolonged graft preservation, ischemia-reperfusion (I/R), acute rejection, and chronic rejection. Heart transplantations were performed from Dark Agouti (DA) to Wister-Furth (allo) or DA to DA (syn) rats, without immunosuppression (acute rejection model, harvested at day 5) or with cyclosporine (chronic rejection model, harvested at day 60). To study the effect of preservation on HIF-1 regulation, normal DA hearts were subjected to different cold ischemia times with or without 45 minutes of additional warm ischemia. The role of I/R was studied by harvesting syngrafts at different time points after reperfusion. Real-time reverse-transcriptase polymerase chain reaction quantified total HIF-1 mRNA, while enzyme-linked immunosorbent assay and immunohistochemistry quantified and localized HIF-1 protein. Our results show that HIF-1 nuclear immunoreactivity is increased during graft preservation and I/R leads to loss of nuclear HIF-1 immunoreactivity. Acute rejection induced HIF-1 in mRNA level. Our findings thus indicated that HIF-1 is activated during transplantation and suggested that manipulation of the HIF-1 pathway might reveal new therapeutic options to manage CAV.
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PMID:Effect of graft preservation and acute rejection on hypoxia-inducible factor-1 in rat cardiac allografts. 1717 75

Listeria monocytogenes is an important food-borne pathogen that can tolerate a wide range of stress conditions. However, its stress adaptation processes are still poorly understood. Real-time-based quantitative RT-PCR (qRT-PCR) provides a tool to probe gene expression changes underlying stress adaptation. But, a limitation to study mRNA levels by real-time qRT-PCR is that validated reference genes are required for normalization. Such genes are currently lacking for experimental models that may be applied to evaluate stress-related gene expression changes in L. monocytogenes. Therefore, five housekeeping genes (HKG) were studied as potential reference genes. Their expression stability was evaluated across 16 L. monocytogenes strains. Three experimental models designed to assess gene expression changes induced by cold, acid and high NaCl concentration stress adaptation were applied. The 16S rRNA gene was consistently the most stably expressed HKG across the different L. monocytogenes strains under all the experimental conditions. While the expressions of beta-glucosidase (bglA), Glyceraldehyde-3P-dehydrogenase (gap), RNA polymerase beta subunit (rpoB) and Ribosomal protein L4 (rplD) was stable amongst the different L. monocytogenes strains, they were prone to significant variations under the different stress adaptation models.
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PMID:Evaluation of housekeeping genes in Listeria monocytogenes as potential internal control references for normalizing mRNA expression levels in stress adaptation models using real-time PCR. 1726 45

The cold-water-fish pathogen Vibrio salmonicida expresses a functional bacterial luciferase but produces insufficient levels of its aliphatic-aldehyde substrate to be detectably luminous in culture. Our goals were to (i) better explain this cryptic bioluminescence phenotype through molecular characterization of the lux operon and (ii) test whether the bioluminescence gene cluster is associated with virulence. Cloning and sequencing of the V. salmonicida lux operon revealed that homologs of all of the genes required for luminescence are present: luxAB (luciferase) and luxCDE (aliphatic-aldehyde synthesis). The arrangement and sequence of these structural lux genes are conserved compared to those in related species of luminous bacteria. However, V. salmonicida strains have a novel arrangement and number of homologs of the luxR and luxI quorum-sensing regulatory genes. Reverse transcriptase PCR analysis suggests that this novel arrangement of quorum-sensing genes generates antisense transcripts that may be responsible for the reduced production of bioluminescence. In addition, infection with a strain in which the luxA gene was mutated resulted in a marked delay in mortality among Atlantic salmon relative to infection with the wild-type parent in single-strain challenge experiments. In mixed-strain competition between the luxA mutant and the wild type, the mutant was attenuated up to 50-fold. It remains unclear whether the attenuation results from a direct loss of luciferase or a polar disturbance elsewhere in the lux operon. Nevertheless, these findings document for the first time an association between a mutation in a structural lux gene and virulence, as well as provide a new molecular system to study Vibrio pathogenesis in a natural host.
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PMID:A novel lux operon in the cryptically bioluminescent fish pathogen Vibrio salmonicida is associated with virulence. 1727 25

The transcriptional coactivator peroxisome proliferator activated receptor gamma coactivator 1alpha (PGC-1alpha) can activate a number of transcription factors to regulate mitochondrial biogenesis and cell-specific responses to cold, fasting, and exercise. Recent studies indicate that PGC-1alpha knockout mice exhibit behavioral abnormalities and progressive vacuolization in various brain regions. To investigate the roles for PGC-1alpha in the nervous system, we evaluated the temporal and cell-specific expression of PGC-1alpha in the normal developing rat brain. Western blot of whole brain homogenates with a PGC-1alpha-specific antibody revealed that PGC-1alpha protein was most abundant in the embryonic and early postnatal forebrain and cerebellum. Using quantitative reverse-transcriptase polymerase chain reaction (RT-PCR), we determined that PGC-1alpha mRNA expression increased most markedly between postnatal days 3 (P3) and 14 in the cortex, striatum, and hippocampus. Immunohistochemical and immunofluorescence analyses of brain tissue indicated that while PGC-1alpha was found in most neuronal populations from embryonic day 15 to P3, it was specifically concentrated in GABAergic populations from P3 to adulthood. Interestingly, PGC-1alpha colocalized with the developmentally regulated chemoattractant reelin in the cortex and hippocampus, and the survival-promoting transcription factor myocyte enhancing factor 2 was highly concentrated in GABAergic populations in the striatum and cerebellum at times of PGC-1alpha expression. These results implicate PGC-1alpha as a regulator of metabolism and/or survival in GABAergic neurons during a phase of mitochondrial and synaptic changes in the developing brain and suggest that PGC-1alpha may be a good target for increasing metabolism in GABAergic populations in neurodevelopmental and neurodegenerative disorders.
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PMID:Localization of the transcriptional coactivator PGC-1alpha to GABAergic neurons during maturation of the rat brain. 1733 37

In recent years, the combinations of computational and molecular approaches have led to the identification of an increasing number of small, noncoding RNAs encoded by bacteria and their plasmids and phages. Most of the characterized small RNAs have been shown to operate at a posttranscriptional level, modulating mRNA stability or translation by base-pairing with the 5' regions of the target mRNAs. However, a subset of small RNAs has been found to regulate transcription. One example is the abundant 6S RNA that has been proposed to compete for DNA binding of RNA polymerase by mimicking the open conformation of promoter DNA. Other small RNAs affect transcription termination via base-pairing interactions with sequences in the mRNA. Here, we discuss current understanding and questions regarding the roles of small RNAs in regulating transcription.
Cold Spring Harb Symp Quant Biol 2006
PMID:Regulating bacterial transcription with small RNAs. 1738 6

We adapted the nuclear run-on method to measure changes in the rate of RNA polymerase II (pol II) transcription of repetitive elements and transposons in the female germ line of Drosophila melanogaster. Our data indicate that as little as an approximately 1.5-fold change in the rate of transcription can be detected by this method. Our nuclear run-on protocol likely measures changes in transcriptional elongation, because rates of transcription decline with time, consistent with a low rate of pol II re-initiation in the isolated nuclei. Surprisingly, we find that the retrotransposon gypsy and the repetitive sequence mst40 are silenced posttranscriptionally in fly ovaries.
Cold Spring Harb Symp Quant Biol 2006
PMID:Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germ line by nuclear run-on. 1738 14

Recent work in Arabidopsis has revealed a plant-specific RNA polymerase, pol IV, that is specialized for RNA interference (RNAi)-mediated, chromatin-based gene silencing. Two functionally diversified pol IV complexes have been identified: pol IVa is required to produce or amplify the small RNA trigger, whereas pol IVb, together with the plant-specific SWI/SNF-like chromatin remodeling factor DRD1, acts downstream from small RNA formation to induce de novo cytosine methylation of homologous DNA by an unknown mechanism. Retrotransposon long terminal repeats (LTRs) and other unannotated sequences that encode small RNAs are prime targets for DRD1/pol IVb-mediated cytosine methylation. In drd1 and pol IVb mutants, silent LTRs in euchromatin can be derepressed, resulting in enhanced transcription of adjacent genes or intergenic regions. In addition to mediating de novo methylation, some evidence suggests that DRD1 and pol IVb are also involved in a reciprocal process of active demethylation, perhaps in conjunction with DNA glycosylase domain-containing proteins such as ROS1. We speculate that DRD1/pol IV-dependent methylation/demethylation evolved in the plant kingdom as a means to facilitate rapid, reversible changes in gene expression, which might have adaptive significance for immobile plants growing in unpredictable environments.
Cold Spring Harb Symp Quant Biol 2006
PMID:RNA-directed DNA methylation and Pol IVb in Arabidopsis. 1738 27

In Arabidopsis thaliana, the pathway for transcriptional silencing via RNA-directed DNA methylation and chromatin modification involves two forms of nuclear RNA polymerase IV (pol IVa and pol IVb), RNA-DEPENDENT RNA POLYMERASE2 (RDR2), DICER-LIKE3 (DCL3), ARGONAUTE4 (AGO4), the chromatin remodeler, DRD1, and the de novo cytosine methyltransferase, DRM2. New insight into the order of events, as well as the spatial organization of this pathway within the nucleus, has come from the combined use of protein immunolocalization, RNA fluorescence in situ hybridization (RNA-FISH), DNA-FISH, and genetic analysis. New findings show that pol IVa, pol IVb, and DRD1 colocalize with DNA loci that are both the sources and targets of small interfering RNAs (siRNAs). However, RDR2-dependent doublestranded RNA production, dicing by DCL3, and loading of siRNAs into AGO4-containing RNA-induced silencing complexes (RISCs) appear to take place at a distant site, in an siRNA processing center located in the nucleolus. This siRNA processing center shares features of Cajal bodies, which are nucleolus-associated entities involved in the processing and trafficking of RNAs found in ribonucleoprotein (RNP) complexes that splice or modify mRNA, rRNA, or telomeres. Therefore, assembly and trafficking of chromatin-modifying RISCs may share similarities with other nuclear RNPs.
Cold Spring Harb Symp Quant Biol 2006
PMID:Cell biology of the Arabidopsis nuclear siRNA pathway for RNA-directed chromatin modification. 1738 29


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