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Transcription Factors, General (6):
Recent article
Transcription Factors, General
Genes & Development (24)10 2010
Abstract
We report that PUMA (p53 up-regulated modulator of apoptosis), a key mediator of p53-dependent cell death, is regulated by a noncanonical, gene-specific mechanism. Using chromatin immunoprecipitation assays, we found that the first half of the PUMA locus (approximately 6 kb) is constitutively occupi...
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PMID: 20478995
PDF is available here.
PDF is available here.
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Human Molecular Genetics (18)12 2009
Abstract
We report the biochemical characterization of IGHMBP2 and the isolation of a modifier locus that rescues the phenotype and motor neuron degeneration of nmd mice. We find that a 166 kb BAC transgene derived from CAST/EiJ mice and containing tRNA genes and activator of basal transcription 1 (Abt1), a...
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PMID: 19299493
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)17 2008
Abstract
These results document that activation of the SNAT2 gene by the mammalian amino acid response pathway occurs independently of enhanced Mediator recruitment....
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PMID: 18757893
PDF is available here.
PDF is available here.
Genes & Development (22)14 2008
Abstract
We performed genome-wide location analysis of this factor. Under normal growth conditions, TFIIS was detected on Pol II-transcribed genes, and TFIIS occupancy was well correlated with that of Pol II, indicating that TFIIS recruitment is not restricted to NTP-depleted cells. Unexpectedly, TFIIS was a...
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PMID: 18628399
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)9 2008
Abstract
We report a comprehensive investigation of the regulatory mechanism of a heat-induced gene (hsp5) from Halobacterium salinarum. We demonstrated by mutation analysis that the sequences 5' and 3' to the core elements (TATA box and BRE) of the hsp5 promoter (P(hsp5)) did not significantly affect the ba...
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PMID: 18390887
PDF is available here.
PDF is available here.
Abstract
Molecular Cell (29)2 2008
Abstract
In a recent issue of Molecular Cell, two independent studies (Zhang et al., 2008; Zhao et al., 2008) provide compelling evidence that targeted deubiquitylation of histones is intimately linked to transcription activation, epigenetic regulation, and cancer progression.
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PMID: 18243109
PDF is available here.
PDF is available here.
Molecular Cell (29)1 2008
Abstract
We demonstrate that the 2 MDa GCN5 HAT-containing metazoan TFTC/STAGA complexes contain a histone H2A and H2B deubiquitinase activity. We have identified three additional subunits of TFTC/STAGA (ATXN7L3, USP22, and ENY2) that form the deubiquitination module. Importantly, we found that this module i...
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PMID: 18206972
PDF is available here.
PDF is available here.
Genes & Development (21)16 2007
Abstract
We determined the crystal structure of DiaA at 1.8 A resolution. DiaA forms a homotetramer consisting of a symmetrical pair of homodimers. Mutational analysis revealed that the DnaA-binding activity and formation of homotetramers are required for the stimulation of initiation by DiaA. DiaA tetramers...
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PMID: 17699754
PDF is available here.
PDF is available here.
Abstract
We examined a polymorphism (rs1864169) in the general transcription factor 2A1 (GTF2A1) gene as a test of the hypothesis that this transcription factor and IL-IB gene polymorphisms interact in the effects on the gastric cancer risk due to the possible biological relationship between the two genes. G...
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PMID: 17596959
PDF is available here.
PDF is available here.
Molecular Cell (26)1 2007
Abstract
We propose that this cavity constitutes the RNA polymerase-binding site, which becomes unmasked in RfaH only upon sequence-specific binding to the nontemplate DNA strand that triggers domain dissociation. Finally, we argue that RfaH binds to the beta' subunit coiled coil, the major target site for t...
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PMID: 17434131
PDF is available here.
PDF is available here.
Abstract
We provide experimental evidence (including protein-coimmunoprecipitation, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of...
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PMID: 17360575
PDF is available here.
PDF is available here.
Genetika (Moskva) (43)1 2007
Abstract
General transcription factors (GTFs) were tested for the presence on the promoter of the Drosophila melanogaster hsp70 gene in vivo. TBP, TBP-associated TAF proteins, TFIIB, TFIIF (RAP30), TFIIH (XPB), the TFTC complex (GCN5 and TRRAP), and a Mediator complex subunit (MEDI 3) were detected on the pr...
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PMID: 17333936
PDF is available here.
PDF is available here.
Molecular Cell (23)6 2006
Abstract
We show that the model activator GAL4-VP16 directs the ordered assembly of Mediator, histone acetyltransferases (HATs), and GTFs onto immobilized chromatin and naked DNA templates in vitro. Using purified proteins, we found that the Mediator regulates this assembly process by binding to p300 and TFI...
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PMID: 16973433
PDF is available here.
PDF is available here.
Nucleic Acids Research (34)10 2006
Abstract
We studied the recruitment of promoter-specific TFs, general TFs and epigenetic marks in activated promoters. H3-K4 di- and tri-methylation and H3-K79 di-methylation are present before induction. H3 acetylation is generally high before induction, and H4 acetylation shows a promoter-specific increase...
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PMID: 16757577
PDF is available here.
PDF is available here.
Abstract
We propose that an important role of some enhancers is to function as nucleation centres for the assembly of the pre-initiation complex to regulate the timing of gene activation during development, differentiation and the cell cycle....
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PMID: 16126390
PDF is available here.
PDF is available here.
Toxicology Letters (158)2 2005
Abstract
We previously reported that the molecular pro-inflammatory effects of welding fumes in vitro were caused by soluble transition metals via an oxidative stress-mediated mechanism. Herein, we tested the hypothesis that transition metals in welding fume drive the in vivo inflammatory response caused by...
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PMID: 16039403
PDF is available here.
PDF is available here.
Abstract
B200 cells are Ni(II)-transformed mouse BALB/c-3T3 fibroblasts displaying a malignant phenotype and increased resistance to Ni(II) toxicity. In an attempt to find genes whose expression has been altered by the transformation, the Atlas Mouse Stress/Toxicology cDNA Expression Array (Clontech Laborato...
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PMID: 15885260
PDF is available here.
PDF is available here.
BMC Genomics (6) 2005
Abstract
Several orthologs of general transcription factors associated with RNA polymerase II can be predicted among the hypothetical proteins of the P. falciparum genome using the two-dimensional Hydrophobic Cluster Analysis (HCA) together with profile-based search methods (PSI-BLAST). These predicted ortho...
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PMID: 16042788
PDF is available here.
PDF is available here.
Abstract
We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some genomes might be compensated by the presence of p...
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PMID: 15556475
PDF is available here.
PDF is available here.
Abstract
We recently identified a novel nuclear protein, activator of basal transcription 1 (ABT1), which binds TBP and DNA, and enhances Pol II-directed basal transcription. To better understand regulatory mechanisms for ABT1, we searched for ABT1-binding proteins using a yeast two-hybrid screening and isol...
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PMID: 15660422
PDF is available here.
PDF is available here.
Arthritis & Rheumatism (50)8 2004
Abstract
Systemic administration of Tat-srIkappaBalpha diminished infiltration of leukocytes into the site of inflammation. Analysis of the recruited inflammatory cells confirmed uptake of the inhibitor and reduction of the NF-kappaB activity. These cells exhibited elevated caspase activity, suggesting that...
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PMID: 15334484
PDF is available here.
PDF is available here.
Abstract
We mapped the location of the activation domain of Bcl10. This was done in the context of its interaction with TFIIB, as well as its ability to activate transcription as a fusion protein linked to the DNA-binding domain of Gal4 in the mammalian cells. Both approaches demonstrated that Bcl10 contains...
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PMID: 15207693
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (278)50 2003
Abstract
When RNA polymerase II (RNAP II) is forced to stall, elongation complexes (ECs) are observed to leave the active pathway and enter a paused state. Initially, ECs equilibrate between active and paused conformations, but with stalls of a long duration, ECs backtrack and become sensitive to transcript...
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PMID: 14506279
PDF is available here.
PDF is available here.
Molecular Cell (12)6 2003
Abstract
We show that recruitment of Htz1 to chromatin requires the SWR-C. Moreover, like Htz1 and Bdf1, the SWR-C promotes gene expression near silent heterochromatin....
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PMID: 14690608
PDF is available here.
PDF is available here.
Abstract
We identified in yeast several genes that contain internal poly(A) sites whose full-length mRNA formation is reduced by mutations in RNA polymerase II subunit RPB2, elongation factor SPT5, or TFIIS. RPB2 and SPT5 defects also promoted the utilization of upstream poly(A) sites for genes that contain...
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PMID: 14560031
PDF is available here.
PDF is available here.
Abstract
Abstract
We have diffused TFIIS into Pol II crystals and derived a model of the Pol II-TFIIS complex from X-ray diffraction data to 3.8 A resolution. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 A. Two essential and invariant acidic residues in...
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PMID: 12914699
PDF is available here.
PDF is available here.
Abstract
Bacterial GreA and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase. The structure of Escherichia coli core RNA polymerase bound to GreB was determined by cryo-electron microscopy and image processing of helical cr...
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PMID: 12914698
PDF is available here.
PDF is available here.
Abstract
Abstract
We describe the construction of a set of 20 Saccharomyces cerevisiae Gateway compatible vectors. These plasmids bear an URA3 or TRP1 selection marker. They are designed for expression without tag sequence or for C- or N-terminal protein tagging with 3HA (haemagglutinin), 13MYC, 4TAP (tandem affinity...
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PMID: 12794935
PDF is available here.
PDF is available here.
Journal of Bacteriology (185)11 2003
Abstract
We mapped the viral promoters and showed that the PM2 genome consists of three operons. Four new virus genes were assigned based on their function in transcription. Proteins P15 and P16 are shown to repress early transcription, and proteins P13 and P14 are shown to activate late transcription events...
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PMID: 12754225
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (278)21 2003
Abstract
We study the behavior of RNA polymerase when transcribing a template that contains two closely spaced lesions, one on each DNA strand. Similar DNA templates containing no CPD, or a single CPD on either the transcribed or the nontranscribed strand were used as controls. Using an in vitro transcriptio...
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PMID: 12646562
PDF is available here.
PDF is available here.
Journal of Biochemistry (133)4 2003
Abstract
We searched for factors that directly interact with S-II using a yeast two-hybrid system, and isolated a novel nuclear protein, FESTA. FESTA is expressed specifically in kidney and spleen, supporting our notion that S-II participates in gene-specific regulation. Two mRNA isoforms of FESTA encoding p...
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PMID: 12761297
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (278)10 2003
Abstract
These results suggest that cleavage, but not read-through, stimulation activity is responsible for all three biologic functions of S-II (i.e. suppression of 6-azauracil sensitivity, induction of the IMD2 gene, and suppression of temperature sensitivity of spt4 null mutant)....
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PMID: 12496271
PDF is available here.
PDF is available here.
Abstract
We have examined the localization and targeting of the RNA polymerase II (pol II) transcription elongation factor TFIIS in amphibian oocyte nuclei by immunofluorescence. Using a novel antibody against Xenopus TFIIS the major sites of immunostaining were found to be Cajal bodies, nuclear organelles t...
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PMID: 12631738
PDF is available here.
PDF is available here.
Abstract
We have characterized proteins that coimmunopurify with Spt5. Among these are the general elongation factors TFIIF and TFIIS as well as Spt6 and FACT, factors thought to regulate elongation through nucleosomes. Spt5 also coimmunopurified with the mRNA capping enzyme and cap methyltransferase, and sp...
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PMID: 12556496
PDF is available here.
PDF is available here.
European Journal of Biochemistry (269)21 2002
Abstract
We have previously reported that higher order complexes of mammalian pol II and general pol II transcription factors, referred to as pol II holoenzyme, also contain MCM proteins. In the present study we have analyzed in detail the interaction between MCM2 and pol II holoenzyme. N- and C- terminal de...
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PMID: 12392551
PDF is available here.
PDF is available here.
Abstract
To physically characterize the web of interactions connecting the Saccharomyces cerevisiae proteins suspected to be RNA polymerase II (RNAPII) elongation factors, subunits of Spt4/Spt5 and Spt16/Pob3 (corresponding to human DSIF and FACT), Spt6, TFIIF (Tfg1, -2, and -3), TFIIS, Rtf1, and Elongator (...
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PMID: 12242279
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1577)2 2002
Abstract
We discuss emerging genetic and biochemical evidence that points to a role of these factors not only in transcription initiation but also in elongation and possibly termination. In addition, we review phosphorylation events involving some of the general transcription factors (GTFs) and other regulat...
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PMID: 12213657
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1577)2 2002
Abstract
Transcript elongation by RNA polymerase is a dynamic process, capable of responding to a number of intrinsic and extrinsic signals. A number of elongation factors have been identified that enhance the rate or efficiency of transcription. One such class of factors facilitates RNA polymerase transcrip...
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PMID: 12213659
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1577)2 2002
Abstract
Chromatin forms a general, repeating barrier to elongation of transcripts by eukaryotic RNA polymerases. Recent studies of nucleosome structure and histone modifications reveal a set of likely mechanisms for control of elongation through chromatin. Genetic and biochemical studies of transcription ha...
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PMID: 12213658
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1577)2 2002
Abstract
RNA polymerase II is the eukaryotic enzyme that transcribes all the mRNA in the cell. Complex mechanisms of transcription and its regulation underlie basic functions including differentiation and morphogenesis. Recent evidence indicates the process of RNA chain elongation as a key step in transcript...
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PMID: 12213651
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1577)2 2002
Abstract
We examine the experimental evidence that defines promoter escape as a distinct stage in transcription, and point out areas where critical information is missing....
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PMID: 12213653
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1577)2 2002
Abstract
Promoter escape is the last stage of transcription initiation when RNA polymerase, having initiated de novo phosphodiester bond synthesis, must begin to relinquish its hold on promoter DNA and advance to downstream regions (DSRs) of the template. In vitro, this process is marked by the release of hi...
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PMID: 12213652
PDF is available here.
PDF is available here.
Abstract
We provide evidence for the involvement of RAD2, the S. cerevisiae counterpart of XPG, in promoting efficient RNA polymerase II transcription. Inactivation of RAD26, the S. cerevisiae counterpart of the human CSB gene, also causes a deficiency in transcription, and a synergistic decline in transcrip...
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PMID: 12110180
PDF is available here.
PDF is available here.
Nucleic Acids Research (30)11 2002
Abstract
We reconstituted transcription complexes in a highly purified pol II system on adenovirus Major-Late promoter constructs. We noted that these complexes have a high propensity for read-through upon GTP omission. Read-through occurred during the early stages at all registers analyzed. Addition of TFII...
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PMID: 12034815
PDF is available here.
PDF is available here.
Molecular Cell (9)4 2002
Abstract
We have systematically explored the in vivo occupancy of promoters and open reading frames by components of the RNA polymerase II transcription initiation and elongation apparatuses in yeast. RNA polymerase II, Mediator, and the general transcription factors (GTFs) were recruited to all promoters te...
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PMID: 11983171
PDF is available here.
PDF is available here.
DNA Sequence (13)1 2002
Abstract
We previously cloned the cDNA of the transcription factor TFIIS (SII) from Xenopus laevis and showed that its expression was not constant during Xenopus development. To investigate its regulation, we cloned the genomic DNA of Xenopus TFIIS, focusing on the 5'-promoter region. Here, we present the Xe...
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PMID: 12180138
PDF is available here.
PDF is available here.
Abstract
We demonstrated that the general RNA splicing factor RNPS1 is a specific PITSLRE p110 kinase interactor in vivo. This suggests that the PITSLRE family of protein kinases is involved in some aspect of RNA processing or transcription. Here we identify multiple transcriptional elongation factors, inclu...
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PMID: 11709559
PDF is available here.
PDF is available here.
Plant Cell Online (13)12 2001
Abstract
We use DNA microarrays to identify genes with altered expression levels in dst1 compared with the parental plants. In addition to verifying the increase in the transgene mRNA levels, which were used to isolate these mutants, we were able to identify new genes with altered mRNA abundance in dst1. RNA...
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PMID: 11752382
PDF is available here.
PDF is available here.
Abstract
We investigated relationships between three classes of these factors: (1) transcription elongation factors Spt4-Spt5, TFIIS, and Spt16; (2) the C-terminal heptapeptide repeat domain (CTD) of RNA polymerase II; and (3) protein kinases that phosphorylate the CTD and a phosphatase that dephosphorylates...
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PMID: 11606527
PDF is available here.
PDF is available here.
Abstract
We have characterized RNA polymerase II complexes halted from +16 to +49 on two templates which differ in the initial 20 nucleotides (nt) of the transcribed region. On a template with a purine-rich initial transcript, most complexes halted between +20 and +32 become arrested and cannot resume RNA sy...
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PMID: 11486021
PDF is available here.
PDF is available here.
Abstract
We designed a specific assay for transcriptional elongation in vivo that involves an artificial arrest (ARTAR) site designed from a thermodynamic theory of DNA-dependent transcriptional arrest in vitro. Transcriptional analysis and chromatin immunoprecipitation experiments indicate that the ARTAR si...
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PMID: 11390645
PDF is available here.
PDF is available here.
Nucleic Acids Research (29)13 2001
Abstract
We have employed a highly purified system to prepare pol II complexes stalled at very precise positions during the initial stage of transcript elongation. Using potassium permanganate we analyzed the open region ('transcription bubble') of complexes stalled between registers 15 and 35. We found that...
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PMID: 11433015
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (276)25 2001
Abstract
We investigated the possibility of cross-talk between SII and transcription factors TFIIF, ELL, and Elongin. These studies led to the discovery that TFIIF, ELL, and Elongin are all capable of inhibiting SII-induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediate...
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PMID: 11259417
PDF is available here.
PDF is available here.
Journal of Cell Biology (153)5 2001
Abstract
We report the identification of two ubiquitously expressed human proteins, stonin 1 and stonin 2, related to components of the endocytic machinery. The human stonins are homologous to the Drosophila melanogaster stoned B protein and exhibit a modular structure consisting of an NH(2)-terminal proline...
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PMID: 11381094
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1518)3 2001
Abstract
The promoter region of the Drosophila melanogaster TFIIS gene was characterized by transient expression assay. Serial deletion analysis of the promoter region showed that the promoter region between -112 and +113 is required for the efficient expression of the D. melanogaster TFIIS gene. The results...
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PMID: 11311940
PDF is available here.
PDF is available here.
Abstract
We demonstrate that deletion of the CTK1 gene, encoding the kinase subunit of RNA polymerase II carboxy-terminal domain kinase I (CTDK-I), is synthetically lethal when combined with deletion of PPR2 or ELP genes. The inviability of ctk1 elp3 double mutants can be rescued by expression of an Elp3 mut...
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PMID: 11311553
PDF is available here.
PDF is available here.
Abstract
We have assessed the contributions of some components of the RNA polymerase II (Pol II) transcription machinery to UV resistance in Saccharomyces cerevisiae. Deletion of the gene encoding the Pol II elongation factor TFIIS (SII) resulted in enhanced UV sensitivity, but only in the absence of global...
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PMID: 11254132
PDF is available here.
PDF is available here.