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Transcriptional Elongation FactorsTranscription Elongation, GeneticTranscription, GeneticPositive Transcriptional Elongation Factor BRNA Polymerase IITranscription FactorsCyclin-Dependent Kinase 9Peptide Elongation FactorsTranscription Factors, GeneralCyclin TDNA-Directed RNA PolymerasesPeptide Chain Elongation, TranslationalMolecular Sequence DataPromoter Regions, GeneticNuclear ProteinsBase SequenceSaccharomyces cerevisiae ProteinsSaccharomyces cerevisiaeRNA, MessengerDichlororibofuranosylbenzimidazolePeptide Elongation Factor 1tat Gene Products, Human Immunodeficiency VirusProtein BindingGene Expression RegulationHeLa CellsMutationAmino Acid SequenceGene Products, tatChromatinHistonesTranscriptional ActivationBinding SitesDNA-Binding ProteinsPeptide Elongation Factor TuGene Expression Regulation, FungalCell LineTemplates, GeneticRepressor ProteinsTranscription Factors, TFIITrans-ActivatorsDNAIsatinChromosomal Proteins, Non-HistoneTerminator Regions, GeneticEscherichia coliPeptide Elongation Factor 2Chromatin ImmunoprecipitationSp1 Transcription FactorTranscription Initiation SiteRNAProtein Structure, TertiaryCell NucleusPlasmidsPhosphorylationHIV Long Terminal RepeatGene Expression Regulation, ViralSarcosineRNA Polymerase IModels, GeneticRNA-Binding ProteinsCloning, MolecularNucleosomesTATA-Box Binding ProteinSequence Homology, Amino AcidNucleic Acid ConformationGenes, ReporterModels, BiologicalUracilTransfectionRecombinant Fusion ProteinsFungal ProteinsTranscription Initiation, GeneticMethylationGene DeletionSignal TransductionTranscription Factor TFIIDElongation Factor 2 KinaseGene Expression Regulation, DevelopmentalCyclinsKineticsBacterial ProteinsRibonucleoproteins, Small NuclearGene Expression Regulation, BacterialGenes, FungalMultiprotein ComplexesCells, CulturedTranscription Factor TFIIHRNA, RibosomalRegulatory Sequences, Nucleic AcidCyclin-Dependent KinasesEscherichia coli ProteinsPhenotypePeptide Elongation Factor GReverse Transcriptase Polymerase Chain ReactionHIV-1TATA BoxSequence AlignmentChromatin Assembly and DisassemblyHistone-Lysine N-MethyltransferaseTranscription Factor AP-1
Transcriptional elongationFactorGenesInitiationBlock elongationProteinMRNAPerformed in vitroRegulatesFactors2001RegulationComplexProteinsChromatin modificationVitroModulateTerminationComplexesActinInterplayKineticsGenome-wide transcriptionLesionsMolecularVivoEfficient transcriptionAbstractTranscriptsFindingsNucleotidesNuclearCellularDrosophilaPromotersStabilityReplicationRNAPInterferenceInitial transcriptionExpression
Transcriptional elongation4
  • This gene encodes a nuclear protein that regulates transcriptional elongation and pre-mRNA splicing. (wikipedia.org)
  • 0.05 for all], demonstrating blocks to HIV transcriptional elongation, completion, and splicing. (nih.gov)
  • multiply-spliced transcripts, but the ratio of total to elongated transcripts was 6-fold lower than in blood CD4+ T cells (P = 0.016), suggesting less of a block to HIV transcriptional elongation in rectal CD4+ T cells. (nih.gov)
  • It functions as a positive regulator of RNA POLYMERASE II, increasing its rate of transcriptional elongation by suppressing transient pausing along the DNA template. (bvsalud.org)
Factor17
  • The target of alvocidib is the positive transcription elongation factor P-TEFb. (flavopiridolinhibitor.com)
  • Some studies suggest that it acts as a transcription factor, which means that it attaches (binds) to specific regions of DNA and helps control the activity of other genes, although the identity of these genes is unknown. (medlineplus.gov)
  • Biophysical Analysis of the N-Terminal Domain from the Human Protein Phosphatase 1 Nuclear Targeting Subunit PNUTS Suggests an Extended Transcription Factor TFIIS-Like Fold. (nih.gov)
  • In studies during the early 1990's, Gregg Semenza identified, and then in 1995 purified and cloned, a transcription factor that regulates these oxygen-dependent responses. (nobelprize.org)
  • Through the combined work of these three laureates it was thus demonstrated that the response by gene expression to changes in oxygen is directly coupled to oxygen levels in the animal cell, allowing immediate cellular responses to occur to oxygenation through the action of the HIF transcription factor. (nobelprize.org)
  • Microphthalmia-associated transcription factor (MITF) is a master transcription factor in melanogenesis. (frontiersin.org)
  • Gsn ) and is the archetypical transcription factor to study actin interplay with transcription. (jneurosci.org)
  • All organisms-bacteria, archaea, and eukaryotes-have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. (osti.gov)
  • This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. (osti.gov)
  • However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. (osti.gov)
  • In this paper, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the "σ-finger" of the bacterial transcription initiation factor σ. (osti.gov)
  • Cytoplasmic 5'-3' exonuclease Xrn1p is also a genome-wide transcription factor in yeast. (us.es)
  • Moreover, we find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. (nih.gov)
  • Under developmental conditions, the Tubulin beta-1 chain (β-Tubulin) was the most stable reference gene, followed by translation elongation factor (eEF2) and ribosomal protein S3 (RPS3). (lu.se)
  • WT-1, a zinc-finger transcription factor expressed in the metanephric mesenchyme, is essential for ureteric bud outgrowth. (medscape.com)
  • The glial cell line-derived neurotrophic factor (GDNF) from the metanephric mesenchyme binds to the C-ret receptor on the branching ureteric bud and is responsible for the branching and elongation of the ureteric bud. (medscape.com)
  • Transcription factors such as EMX-2, BF-2, fibroblast growth factor 7 (FGF 7), epithelial growth factor receptor (EGF-R), GDNF, retinoic acid receptor alpha, and beta 2 are involved in the branching of the ureteric bud. (medscape.com)
Genes15
  • Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. (harvard.edu)
  • Researchers] measured elongation rates ranging from 0.5 to 4 kb/min at ~1000 genes and within different regions of genes. (harvard.edu)
  • Strikingly, Pol II accelerates as it transcribes through the gene body, and a large amount of variation in elongation rates occurs between genes, and is associated with chromatin and exon density. (harvard.edu)
  • Mutations in any of the THO/TREX structural genes cause pleiotropic phenotypes such as transcription impairment, increased transcription-associated recombination, and mRNA export defects. (us.es)
  • In their native context, we observed that the chromatin landscape at and around the transcription regulatory region between the pair of bidirectional genes is modulated in concordance with transcriptional activity of each gene in the pair. (bvsalud.org)
  • We report that for the entire range of intergenic distance separating bidirectional genes , the expression profile of such genes (symmetric or asymmetric) matches the histone modification profile of marks associated with active transcription initiation and elongation. (bvsalud.org)
  • We demonstrate unique distribution of histone modification marks that correlate robustly with the transcription status of genes regulated by bidirectional promoters. (bvsalud.org)
  • We show that this is a genome-wide feature of highly expressed genes, by identifying a domain of ∼700 bp with high CpG content downstream of the transcription start site, correlating with high levels of transcription. (nih.gov)
  • This bi-genomic division is accompanied by profoundly different transcription regulatory system: whereas nDNA-encoded genes are transcribed individually by RNA polymerase 2 and the general nuclear transcription machinery, mtDNA transcription is long known to be regulated mainly by a dedicated RNA polymerase (POLRMT) and mtDNA-specific transcription factors (TFAM and TFB2) ( Shutt and Shadel 2010 ). (biorxiv.org)
  • However, as mtDNA transcription was mostly studied in vitro, little remains known about the mode and tempo of in vivo OXPHOS genes' transcription residing on the mtDNA. (biorxiv.org)
  • The coordinated transcription of genes involves the regulated release of RNA polymerase II (RNAPII) from promoter-proximal sites into active elongation. (nih.gov)
  • The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. (elifesciences.org)
  • These syndromes arise from mutations of genes critical for nucleotide-excision repair and RNA transcription. (medscape.com)
  • Cockayne syndrome group A or B ( CSA or CSB ) genes are required for transcription-coupled repair, a subpathway of nucleotide-excision repair. (medscape.com)
  • During nephrogenesis, multiple genes, transcription factors, and growth factors control the essential interaction between the ureteric bud and the metanephric mesenchyme. (medscape.com)
Initiation5
  • Abstract:) 'To dissect Pol II dynamics in mouse ES cells, [researchers] inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq [global run-on sequencing]. (harvard.edu)
  • Surprisingly, accurate detection of human mtDNA transcription initiation sites (TIS) in the heavy and light strands revealed a novel conserved transcription pausing site near the light strand TIS, upstream to the transcription-replication transition region. (biorxiv.org)
  • Translation happens in four stages: activation (make ready), initiation (start), elongation (make longer) and termination (stop). (easierwithpractice.com)
  • Transcription takes place in three steps: initiation, elongation, and termination. (easierwithpractice.com)
  • Transcription occurs in the three steps-initiation, elongation, and termination-all shown here. (easierwithpractice.com)
Block elongation2
  • We found that in a purified, reconstituted transcription system, these lesions block elongation by RNA pol II to different extents, depending on the type of lesion. (elsevierpure.com)
  • DNA lesions in transcribed strands block elongation and induce a strong transcriptional arrest. (nih.gov)
Protein8
  • Transcription elongation regulator 1, also known as TCERG1, is a protein which in humans is encoded by the TCERG1 gene. (wikipedia.org)
  • Hillman MA, Gecz J. Fragile XE-associated familial mental retardation protein 2 (FMR2) acts as a potent transcription activator. (medlineplus.gov)
  • The contributors discuss its normal functions in the control of cell growth, cell competition, pluripotency, and development, as well as the molecular basis for the effects of the MYC protein on transcription. (cshlpress.com)
  • Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription. (rndsystems.com)
  • It is also a vital medium in protein synthesis because it is the main molecules in DNA translation and transcription (wiki, translation) (wiki, transcription). (bartleby.com)
  • In Cockayne syndrome II, the defective CS group B protein, an SNF2-family DNA-dependent ATPase, is implicated in transcription elongation, transcription coupled repair, and DNA base excision repair. (medscape.com)
  • The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
  • Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
MRNA2
  • This work demonstrates that THO and Sub2 are required for efficient transcription elongation, providing further evidence for the coupling between transcription and mRNA metabolism and export. (us.es)
  • This transcription from DNA to mRNA happens by an RNA polymerase II. (bartleby.com)
Performed in vitro1
  • To assay the relevance of THO/TREX complex in transcription, we performed in vitro transcription elongation assays in mutant cell extracts using supercoiled DNA templates containing two G-less cassettes. (us.es)
Regulates2
  • Cdc42 regulates dendrite elongation, which is essential for melanosome transfer ( Luo, 2000 ). (frontiersin.org)
  • The variant histone H2A.Z regulates gene transcription, and deletion of the gene encoding H2A.Z strongly increases the requirement for SNF/SWI and SAGA. (sdbonline.org)
Factors4
  • The elongation factors Elongin and CSB, but not TFIIS, can also stimulate bypass of thymine glycol lesions, whereas Elongin, CSB and TFIIS can all enhance bypass of an 8-oxoguanine lesion. (elsevierpure.com)
  • By increasing the efficiency with which RNA pol II reads through oxidative lesions, elongation factors can contribute to transcriptional mutagenesis, an activity that could have implications for the generation or progression of human diseases. (elsevierpure.com)
  • BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. (rndsystems.com)
  • For example, the Lim1 and Pax2 transcription factors are essential for the formation of the mesonephric duct, from which the ureteric bud develops. (medscape.com)
20011
  • Liu, CH and Martin, CT, "Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase" (2001). (umass.edu)
Regulation1
  • The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation. (us.es)
Complex5
  • With these assays, we demonstrate that hpr1Δ, tho2Δ, and mft1Δ mutants of the THO complex and sub2 mutants show significant reductions in the efficiency of transcription elongation. (us.es)
  • In our model, the kinetic rates for the reaction pathway, calculated based on the stabilities of the transcription elongation complex (TEC), necessarily lead to sequence-dependent NTP incorporation rates. (psu.edu)
  • DNA Replication and RNA Transcription, although seemingly complex terms, hold within them concepts that are beautifully precise, methodical - true marvels of nature. (aboutdarwin.com)
  • The RNA polymerase II elongation complex. (reactome.org)
  • Transcription elongation complex stability: the topological lock. (umassmed.edu)
Proteins1
  • Gene expression is primarily controlled at the level of transcription, largely as a result of binding of proteins to specific sites on DNA. (easierwithpractice.com)
Chromatin modification1
  • Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions. (bvsalud.org)
Vitro2
  • In the present study, we investigated the impact of the oxidative lesions 8-oxoguanine, thymine glycol and 5-hydroxyuracil on RNA polymerase II (RNA pol II) transcription using a well-defined in vitro transcription system. (elsevierpure.com)
  • Finally, mtDNA transcription termination sites have been either mapped in-vitro, or were associated with MTERF binding sites ( Christianson and Clayton 1986 ), thus, again, limiting the capability to in-vivo map transcription terminations sites in diverse organisms. (biorxiv.org)
Modulate2
  • Thus, herein we provide first evidence that neuronal motility not only depends on cytoplasmic actin dynamics but also on the availability of actin to modulate nuclear functions such as gene transcription. (jneurosci.org)
  • These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure (Santisteban, 2000). (sdbonline.org)
Termination2
  • This study shows that CRISPRi mediates precise transcriptional pausing, which can be followed by transcription termination. (nature.com)
  • Analysis of non-human organisms enabled de novo mtDNA sequence assembly, as well as detection of previously unknown mtDNA TIS, pausing, and transcription termination sites with unprecedented accuracy. (biorxiv.org)
Complexes1
  • Nucleosomes impose a block to transcription that can be overcome in vivo by remodeling complexes such as SNF/SWI and histone modification complexes such as SAGA. (sdbonline.org)
Actin2
  • SRF controls gene transcription of various actin isoforms (e.g. (jneurosci.org)
  • Moreover these actin mutants affect neurite elongation, an actin function which by pharmacological actin interference was ambiguous. (jneurosci.org)
Interplay2
  • Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. (harvard.edu)
  • This interplay forms the foundation of processes like Replication and Transcription. (aboutdarwin.com)
Kinetics1
  • Simulated RNAP elongation kinetics is in good agreement with data from transcription gels and single-molecule studies. (psu.edu)
Genome-wide transcription1
  • Lastly, we offer a perspective on potentially using a sequence dependent KNM to predict genome-wide transcription error. (edu.sa)
Lesions1
  • The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but this is not sufficient to resume transcription. (nih.gov)
Molecular3
  • To understand the molecular mechanism of how productive bidirectional transcription is regulated, we focused on delineating the chromatin signature of bidirectional promoters. (bvsalud.org)
  • En: Methods in Molecular Biology. (us.es)
  • Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress. (nih.gov)
Vivo3
  • Moreover, enriched CpG levels correlate with increased RNA polymerase II elongation rates in vivo. (nih.gov)
  • Our approach paves the path towards in vivo, quantitative, reference sequence-free analysis of mtDNA transcription in all eukaryotes. (biorxiv.org)
  • These obstacles interfered with comparative in-vivo investigation of mtDNA transcription in diverse conditions, and hampered expanding the study of mtDNA nascent transcripts to organisms lacking an mtDNA reference sequence. (biorxiv.org)
Efficient transcription1
  • Interestingly, elevated CpG levels particularly at the 5' end of the gene promote efficient transcription. (nih.gov)
Abstract1
  • abstract = "Transcription elongation cycle (TEC) of RNA polymerase II (Pol II) is a process of adding a nucleoside triphosphate to the growing messenger RNA chain. (edu.sa)
Transcripts1
  • In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation . (bvsalud.org)
Findings2
  • These findings strongly imply that occurrence of these marks might signal the transcription machinery to drive maturation of antisense transcription from the bidirectional promoters. (bvsalud.org)
  • The findings were validated further using real-time quantitative reverse transcription PCR (RT-qPCR)-based target gene expression analysis. (lu.se)
Nucleotides1
Nuclear1
  • Suggesting the presence of a bypass activity, the block to elongation is alleviated when transcription is carried out in HeLa cell nuclear extracts. (elsevierpure.com)
Cellular1
  • However, as similar as they may appear to those newly introduced to these concepts, replication and transcription have unique roles to play in cellular activity. (aboutdarwin.com)
Drosophila1
  • Whereas mammals (chimpanzee, rhesus macaque, rat, and mouse) showed a human-like mtDNA transcription pattern, the invertebrate pattern (Drosophila and C. elegans) profoundly diverged. (biorxiv.org)
Promoters2
  • Testing of putative bidirectional promoters in this system demonstrates no measurable bias towards any one direction of transcription. (bvsalud.org)
  • Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. (rndsystems.com)
Stability1
  • We examine the impact that processes such as transcription and replication have on genome stability. (birmingham.ac.uk)
Replication1
  • Two such fundamental processes that keep the wheels of life turning are Replication and Transcription. (aboutdarwin.com)
RNAP2
  • We present a kinetic model for the sequence-dependent motion of RNA polymerase (RNAP) during transcription elongation. (psu.edu)
  • We thank Drs K. Adelman and T. J. Santangelo for purification of HA-tagged E. coli RNAP and the experimental transcription gel on the pKA2 template. (psu.edu)
Interference1
  • Overexpressing these mutant actins in mouse hippocampal neurons not only modulated growth-cone function but also neurite elongation, which was ambiguous by traditional pharmacological interference. (jneurosci.org)
Initial transcription1
Expression1