Search results for "Transcription factor II D"

showing 8 items of 18 documents

What do you mean by transcription rate?

2013

mRNA synthesis in all organisms is performed by RNA polymerases, which work as nanomachines on DNA templates. The rate at which their product is made is an important parameter in gene expression. Transcription rate encompasses two related, yet different, concepts: the nascent transcription rate, which measures the in situ mRNA production by RNA polymerase, and the rate of synthesis of mature mRNA, which measures the contribution of transcription to the mRNA concentration. Both parameters are useful for molecular biologists, but they are not interchangeable and they are expressed in different units. It is important to distinguish when and where each one should be used. We propose that for fu…

GeneticsTranscription GeneticGeneral transcription factorPromoterE-boxRNA polymerase IIBiologyGeneral Biochemistry Genetics and Molecular BiologyCell biologychemistry.chemical_compoundTerminator (genetics)chemistryYeastsRNA polymerasebiology.proteinRNA MessengerTranscription factor II DTranscriptomeRNA polymerase II holoenzymeBioEssays
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Reiterative transcription initiation from galP2 promoter of Escherichia coli

2000

The expression of gal operon in Escherichia coli is driven by two promoters, P1 and P2 separated by 5 bp. The transcription initiated from the P2 generates a large amount of abortive transcripts to produce a comparable amount of full-length transcript as P1 in vitro. In this study, we investigated the source of the abortive transcripts by employing a quantitative potassium permanganate footprinting method that determines the extent of open promoter complex formation. The extents of open promoter complex formation at the two gal promoters were about the same during the given reaction time while the amount of transcription initiation determined by in vitro transcription assay showed a conside…

Models MolecularCyclic AMP Receptor ProteinTranscription GeneticDNA FootprintingBiophysicsRNA polymerase IIBiochemistryAbortive initiationchemistry.chemical_compoundPotassium PermanganateStructural BiologyRNA polymeraseEscherichia coliGeneticsPromoter Regions GeneticbiologyGeneral transcription factorPromoterDNA-Directed RNA PolymerasesTemplates GeneticMolecular biologyKineticschemistrybiology.proteinRNATranscription factor II FTranscription factor II DCarrier ProteinsTranscription factor II BBiochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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The transcription reinitiation properties of RNA polymerase III in the absence of transcription factors

2007

AbstractTranscription reinitiation by RNA polymerase (Pol) III proceeds through facilitated recycling, a process by which the terminating Pol III, assisted by the transcription factors TFIIIB and TFIIIC, rapidly reloads onto the same transcription unit. To get further insight into the Pol III transcription mechanism, we analyzed the kinetics of transcription initiation and reinitiation of a simplified in vitro transcription system consisting only of Pol III and template DNA. The data indicates that, in the absence of transcription factors, first-round transcription initiation by Pol III proceeds at a normal rate, while facilitated reinitiation during subsequent cycles is compromised.

RNA polymerase IIISaccharomyces cerevisiae ProteinsTranscription GeneticvirusesShort CommunicationMolecular Sequence DataRNA polymerase IISaccharomyces cerevisiaeBiochemistryRNA polymerase IIITranscription Factor TFIIIBTranscription Factors TFIIIGene Expression Regulation FungalMolecular BiologyTFIIIBBase SequencebiologyGeneral transcription factorG-less cassetteCell BiologyMolecular biologyTranscription preinitiation complexbiology.proteinTranscription reinitiationTranscription factor II FTranscription factor II ETranscription factor II DTranscription factor II BCellular and Molecular Biology Letters
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Rtp1p Is a Karyopherin-Like Protein Required for RNA Polymerase II Biogenesis

2013

The assembly and nuclear transport of RNA polymerase II (RNA pol II) are processes that require the participation of many auxiliary factors. In a yeast genetic screen, we identified a previously uncharacterized gene, YMR185w (renamed RTP1), which encodes a protein required for the nuclear import of RNA pol II. Using protein affinity purification coupled to mass spectrometry, we identified interactions between Rtp1p and members of the R2TP complex. Rtp1p also interacts, to a different extent, with several RNA pol II subunits. The pattern of interactions is compatible with a role for Rtp1p as an assembly factor that participates in the formation of the Rpb2/Rpb3 subassembly complex and its bi…

Saccharomyces cerevisiae ProteinsActive Transport Cell NucleusRNA polymerase IISaccharomyces cerevisiaeKaryopherinsBiologyGene Expression Regulation FungalTranscriptional regulationRNA polymerase IProtein Interaction MapsMolecular BiologyRNA polymerase II holoenzymeR2TP complexGeneticsNuclear cap-binding protein complexArticlesCell BiologyPhosphoproteinsUp-RegulationCell biologyNuclear Pore Complex Proteinsbiology.proteinRNA Polymerase IITranscription factor II DCarrier ProteinsGene DeletionSmall nuclear RNATranscription Factors
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The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors.

2010

In order to study the intragenic profiles of active transcription, we determined the relative levels of active RNA polymerase II present at the 3'- and 5'-ends of 261 yeast genes by run-on. The results obtained indicate that the 3'/5' run-on ratio varies among the genes studied by over 12 log(2) units. This ratio seems to be an intrinsic characteristic of each transcriptional unit and does not significantly correlate with gene length, G + C content or level of expression. The correlation between the 3'/5' RNA polymerase II ratios measured by run-on and those obtained by chromatin immunoprecipitation is poor, although the genes encoding ribosomal proteins present exceptionally low ratios in …

Saccharomyces cerevisiae ProteinsbiologyGeneral transcription factorTranscription GeneticGenes FungalRNA-dependent RNA polymeraseRNA polymerase IISaccharomyces cerevisiaeGene Regulation Chromatin and EpigeneticsMolecular biologyTranscripció genèticaMutationGeneticsRNA polymerase Ibiology.proteinRNATranscription factor II FRNA Polymerase IITranscription factor II DTranscriptional Elongation FactorsTranscription factor II BRNA polymerase II holoenzymeOligonucleotide Array Sequence AnalysisNucleic acids research
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Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle

2015

The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution following a new biotin-based genomic run-on (BioGRO) technique. Compared with conventional profiling with chromatin immunoprecipitation, the analysis of the BioGRO profiles in Saccharomyces cerevisiae shows that RNA polymerase II has unique activity profiles at both gene ends, which are highly dependent on positioned nucleosomes. This is the first demonstration of the in vivo infl…

Transcription factoriesSaccharomyces cerevisiae ProteinsTranscription Elongation GeneticTranscription GeneticRNA polymerase II28Saccharomyces cerevisiaeBiology03 medical and health scienceschemistry.chemical_compoundTranscripció genèticaRNA polymeraseGeneticsRNA polymerase IRNA polymerase II holoenzyme9030304 developmental biologyGenetics0303 health sciencesGeneral transcription factorGene regulation Chromatin and Epigenetics030302 biochemistry & molecular biologyRNA Polymerase IIIGenomicsNucleosomesCell biologychemistryTranscription Termination Geneticbiology.proteinRNARNA Polymerase IIGenome FungalTranscription factor II DSmall nuclear RNA
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A complete set of nascent transcription rates for yeast genes

2010

The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) a…

Transcription factoriesSaccharomyces cerevisiae ProteinsTranscription GeneticRNA StabilityGenes FungalDNA transcriptionlcsh:MedicineYeast and Fungal ModelsRNA polymerase IISaccharomyces cerevisiaeBiologyBiochemistryGenètica molecularchemistry.chemical_compoundSaccharomycesModel OrganismsMolecular cell biologyTranscripció genèticaGene Expression Regulation FungalRNA polymeraseGeneticsRNA MessengerRNA synthesislcsh:ScienceBiologyRNA polymerase II holoenzymeGeneticsMultidisciplinaryGeneral transcription factorGene Expression Profilinglcsh:RPromoterGenomicsChromatinFunctional GenomicsNucleic acidsGenòmicaRNA processingchemistrybiology.proteinRNAlcsh:QRNA Polymerase IIGene expressionTranscription factor II DTranscription factor II BResearch Article
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Casein kinase 2 inhibits HomolD-directed transcription by Rrn7 in Schizosaccharomyces pombe.

2014

In Schizosaccharomyces pombe, ribosomal protein gene (RPG) promoters contain a TATA analogue element called the HomolD box. The HomolD-binding protein Rrn7 forms a complex with the RNA polymerase II machinery. Despite the importance of ribosome biogenesis to cell survival, the mechanisms involved in the regulation of transcription of eukaryotic RPGs are unknown. In this study, we identified Rrn7 as a new substrate of the pleiotropic casein kinase 2 (CK2), which is a regulator of basal transcription. Recombinant Rrn7 from S. pombe, which is often used as a model organism for studying eukaryotic transcription, interacted with CK2 in vitro and in vivo. Furthermore, CK2-mediated phosphorylation…

animal structuresbiologyGeneral transcription factorfungiEukaryotic transcriptionResponse elementRNA polymerase IIE-boxPromoterCell BiologyBiochemistryMolecular biologyCell biologyembryonic structuresTAF2Schizosaccharomycesbiology.proteinSchizosaccharomyces pombe ProteinsTranscription factor II DPhosphorylationCasein Kinase IIMolecular BiologyPol1 Transcription Initiation Complex ProteinsProtein BindingThe FEBS journal
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