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Transcriptional Elongation Factors (1):
Recent article
Transcriptional Elongation Factors
EMBO Journal (29)23 2010
Abstract
We show that an N-terminal region of Spt6 (Spt6N) is responsible for interaction with Iws1. The crystallographic structures of Encephalitozoon cuniculi Iws1 and the Iws1/Spt6N complex reveal two conserved binding subdomains in Iws1. The first subdomain (one HEAT repeat; HEAT subdomain) is a putative...
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PMID: 21057455
PDF is available here.
PDF is available here.
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Biochemistry (New York) (75)5 2010
Abstract
We particularly focused on methylation of transcription factors and other nuclear nonhistone proteins. The methylated lysine residues serve as markers attracting nuclear "reader" proteins that possess different chromatin-modifying activities....
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PMID: 20632931
PDF is available here.
PDF is available here.
Abstract
médecine/sciences (26)2 2010
Abstract
Abstract
We show, using mammalian cells, that structure-specific recognition protein 1 (SSRP1) is a novel regulator of MT dynamics. SSRP1 colocalizes with the spindle and midbody MTs, and associates with MTs both in vitro and in vivo. Purified SSRP1 facilitates tubulin polymerization and MT bundling in vitro...
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PMID: 19995907
PDF is available here.
PDF is available here.
Acta Crystallographica Section F (66)Pt 1 2010
Abstract
RNA polymerase (RNAP) elongates RNA by iterative nucleotide-addition cycles (NAC). A specific structural state (or states) of RNAP may be the target of transcription elongation factors. Gfh1, a Thermus thermophilus Gre-family protein, inhibits NAC. To elucidate which RNAP structural state Gfh1 assoc...
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PMID: 20057074
PDF is available here.
PDF is available here.
Abstract
We use HeLa nuclear extracts to study two of these activities, poly(A) signal-dependent transcriptional pausing, which was originally proposed as a surveillance checkpoint, and poly(A) signal-dependent degradation (PDD) of unprocessed transcripts from weak poly(A) signals. We confirm directly, by me...
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PMID: 19926725
PDF is available here.
PDF is available here.
Abstract
We present clinical and laboratory findings in a patient who showed a small duplication in 4p16.3 associated with a subtle terminal deletion in the same chromosomal region. GTG-banding analyses, multiplex ligation-dependent probe amplification analyses, and studies by array-based comparative genomic...
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PMID: 19729912
PDF is available here.
PDF is available here.
Abstract
Abstract
We describe the application of these powerful techniques to study the dynamics of transcription elongation by RNA polymerase II from Saccharomyces cerevisiae....
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PMID: 19426807
PDF is available here.
PDF is available here.
Abstract
We describe experimental approaches for the isolation of RNAPII elongation complexes in vitro and the use of these complexes in the examination of the function of a variety of factors. The methods start with formation of elongation complexes on DNA templates immobilized to paramagnetic beads. Elonga...
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PMID: 19409997
PDF is available here.
PDF is available here.
Abstract
We describe a highly purified system that allows for efficient activator-dependent transcription by RNA polymerase II from the promoter through several contiguous nucleosomes on defined chromatin templates. The system contains natural or recombinant histones, chromatin assembly factors, the histone-...
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PMID: 19272450
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (284)28 2009
Abstract
Our in vitro and in vivo data demonstrate that ELL could also serve as a transcriptional factor to directly induce transcription of the thrombospondin-1 (TSP-1) gene. Experiments using ELL deletion mutants established that full-length ELL is required for the TSP-1 up-regulation and that the transact...
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PMID: 19447890
PDF is available here.
PDF is available here.
EMBO Reports (10)6 2009
Abstract
We identified SPT5-like, a plant-specific AGO4-interacting member of the nuclear SPT5 (Suppressor of Ty insertion 5) RNA polymerase (RNAP) elongation factor family that is characterized by the presence of a carboxy-terminal extension with more than 40 WG/GW motifs. Knockout SPT5-like mutants show a...
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PMID: 19343051
PDF is available here.
PDF is available here.
EMBO Journal (28)8 2009
Abstract
We performed a directed RNAi knock-down (KD) screen targeting 141 candidate transcription factors and identified multiple factors, including Spt6, that alter the induced Hsp70 transcript levels in Drosophila S2 cells. Spt6 is known to interact with both nucleosome structure and Pol II, and it has pr...
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PMID: 19279664
PDF is available here.
PDF is available here.
EMBO Journal (28)7 2009
Abstract
I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle. The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cel...
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PMID: 19214185
PDF is available here.
PDF is available here.
Mycological Research (113)Pt 4 2009
Abstract
We present a molecular phylogenetic analysis for two families within the Pleosporomycetidae (Dothideomycetes), the Hysteriaceae, and the Mytilinidiaceae, using four nuclear genes, the ribosomal LSU and SSU, transcription elongation factor 1 alpha and the second largest RNA polymerase II subunit. Mul...
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PMID: 19422072
PDF is available here.
PDF is available here.
Experimental Cell Research (315)2 2009
Abstract
The transcription rate of immediate early genes (IEGs) is controlled directly by transcription elongation factors at the transcription elongation step. Negative elongation factor (NELF) and 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB) sensitivity-inducing factor (DSIF) stall RNA polymerase...
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PMID: 19014935
PDF is available here.
PDF is available here.
Abstract
We report here the crystal structure of Saccharomyces cerevisiae Spt4 bound to the NGN domain of Spt5. This structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4. Mutations that disrupt this interaction disrupt the complex. Residues forming this piv...
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PMID: 19000817
PDF is available here.
PDF is available here.
Molecular BioSystems (4)11 2008
Abstract
We have called "nucleosome reorganization." The structures of two domains of FACT have been determined and they reveal multiple potential interaction sites. Roles for these binding sites in FACT function and regulation are discussed....
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PMID: 18931784
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)41 2008
Abstract
We found that a single N(2)-Et-dG lesion is a strong block to both mammalian RNAPII and two other multisubunit RNAPs, (yeast RNAPII and Escherichia coli RNAP), as well as to T7 RNAP. However, the mechanism of transcription blockage appears to differ between the multisubunit RNAPs and T7 RNAP. Specif...
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PMID: 18669632
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)41 2008
Abstract
We have taken several approaches to study Rtt106 in greater detail and have identified a previously unknown function of Rtt106. We found genetic interactions between rtt106Delta and mutations in genes encoding transcription elongation factors, including Spt6, TFIIS, and members of the PAF and yeast...
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PMID: 18708354
PDF is available here.
PDF is available here.
Molecular Microbiology (69)5 2008
Abstract
We describe the identification and characterization of two trypanosome homologues of transcription elongation factor TFIIS (TbTFIIS1 and TbTFIIS2-1). TFIIS has been shown to aid transcription elongation by relieving arrested pol II. Our phylogenetic analysis demonstrated the existence of four indepe...
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PMID: 18627464
PDF is available here.
PDF is available here.
Molecular Cell (31)5 2008
Abstract
We describe a mechanism by which nascent RNA inhibits transcriptional pausing. PutL RNA of bacteriophage HK022 suppresses transcription termination at downstream terminators and pausing within a nearby U-rich sequence. In vitro transcription and footprinting assays reveal that this pausing results f...
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PMID: 18775328
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.
Microbiology (154)Pt 7 2008
Abstract
I transcribes most rRNA, RNAP II transcribes mRNA, and RNAP III transcribes tRNA and 5S rRNA). The versatility of bacterial RNAP is dependent on both dynamic interactions with co-factors and the coding sequence of the template DNA, which allows RNAP to respond appropriately to the transcriptional ne...
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PMID: 18599813
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)25 2008
The membrane-bound GTPase Guf1 promotes mitochondrial protein synthesis under suboptimal conditions.
Abstract
We show that the yeast counterpart of LepA, Guf1, is located in the mitochondrial matrix and tightly associated with the inner membrane. It binds to mitochondrial ribosomes in a GTP-dependent manner. Mutants lacking Guf1 show cold- and heat-sensitive growth defects on non-fermentable carbon sources...
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PMID: 18442968
PDF is available here.
PDF is available here.
Abstract
We show the purification and characterization of the small subunit, hSpt4. We were able to purify the protein in a soluble form separately from the larger hSpt5 subunit. CD and NMR spectroscopy show that the purified protein hSpt4 exhibits an alpha/beta topology with a well defined tertiary structur...
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PMID: 18373978
PDF is available here.
PDF is available here.
Molecular Cell (30)4 2008
Abstract
We show that Ubp3 deubiquitylates RNAPII in yeast. Genetic characterization of ubp3 cells is consistent with a role in elongation, and Ubp3 can be purified with RNAPII, Def1, and the elongation factors Spt5 and TFIIF. This Ubp3 complex deubiquitylates both mono- and polyubiquitylated RNAPII in vitro...
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PMID: 18498751
PDF is available here.
PDF is available here.
Abstract
We report a potential third biological function of p53: as a transcriptional elongation factor. Using chromatin immunoprecipitation, we demonstrate that human p53 robustly associates with RNA polymerase II (Pol II), but neither Pol I- nor Pol III-transcribed regions in the budding yeast, Saccharomyc...
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PMID: 18026140
PDF is available here.
PDF is available here.
Molecular Cell (30)1 2008
Abstract
We isolate the H2AX-associated factors, which include FACT (Spt16/SSRP1), DNA-PK, and PARP1 from a human cell line. Our analyses demonstrate that the H2AX-associated factors efficiently promote both integration and dissociation of H2AX and this exchange reaction is mainly catalyzed by FACT among the...
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PMID: 18406329
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)12 2008
Abstract
We determined the solution structure of single-stranded transactivator responsive element (TAR) RNA-bound NELF-E RRM. This structure clearly shows that RNA binding to NELF-E RRM induces formation of a helix in the C-terminus. The RNA-bound form of NELF-E RRM is very similar to the RNA-bound form of...
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PMID: 18303858
PDF is available here.
PDF is available here.
Molecular Microbiology (67)6 2008
Abstract
We show that in contrast to the previously described decreased fimbriation observed in a ppGpp-deficient strain, DksA deficiency results in a hyperfimbriated state. In vivo assays show that the effect of DksA deficiency on the type 1 fimbriae occurs at the phase variation level because of elevated t...
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PMID: 18284577
PDF is available here.
PDF is available here.
Molecular Cell (29)1 2008
Abstract
We report that the N-CoR/HDAC1/3 complex specifically recruits a specific histone H2A ubiquitin ligase, 2A-HUB/hRUL138, to a subset of regulated gene promoters. 2A-HUB catalyzes monoubiquitination of H2A at lysine 119, functioning as a combinatoric component of the repression machinery required for...
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PMID: 18206970
PDF is available here.
PDF is available here.
Abstract
We identify direct target genes of Spt5 using fog(sk8) zebrafish mutant, which disrupts the foggy/spt5 gene. We identified that fog(sk8) and their wildtype siblings differentially express less than 5% of genes examined. These genes participate in diverse biological processes from stress response to...
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PMID: 18978947
PDF is available here.
PDF is available here.
Microbiology (62) 2008
Abstract
The elongation phase of transcription by RNA polymerase is highly regulated and modulated. Both general and operon-specific elongation factors determine the local rate and extent of transcription to coordinate the appearance of transcript with its use as a messenger or functional ribonucleoprotein o...
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PMID: 18729732
PDF is available here.
PDF is available here.
Biochemistry (77) 2008
Abstract
We discuss recent progress achieved by single-molecule studies, highlighting some of the unresolved questions and ongoing debates....
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PMID: 18410247
PDF is available here.
PDF is available here.
Genes & Development (22)1 2008
Abstract
We investigate RNAPII localization, distal gene co-association, and Hbb locus conformation during inhibition of transcription. Our results show distal active genes remain associated with RNAPII foci and each other in the absence of elongation. When initiation is inhibited, active genes dissociate fr...
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PMID: 18172162
PDF is available here.
PDF is available here.
BMC Cancer (8)1 2008
Abstract
Knockdown of TFIIS reduced cancer cell proliferation in breast, lung and pancreatic cancer cell lines. More specifically, TFIIS knockdown in the MCF7 breast cancer cell line induced cancer cell death and increased c-myc and p53 expression whereas TFIIS knockdown in the non-cancerous breast cell line...
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PMID: 18474089
PDF is available here.
PDF is available here.
Abstract
Here we show that depletion of the Ctr9 or Paf1 component of the Paf1 complex delays the loss of histones from the GAL1 gene upon induction. This delay in histone removal is accompanied by a decrease in association of RNA pol II with GAL1 and altered distribution of the polymerase along the locus. C...
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PMID: 18194564
PDF is available here.
PDF is available here.
Abstract
We report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface...
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PMID: 18160037
PDF is available here.
PDF is available here.
Abstract
I enzyme at 12 A resolution using cryo-electron microscopy (cryo-EM). Their study reveals that three subunits of Pol I perform functions in transcription elongation that are outsourced to the transcription factors TFIIF and TFIIS in the analogous Pol II transcription system....
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PMID: 18160031
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)50 2007
Abstract
When nucleoside triphosphate (NTP) substrates and alpha-amanitin are added to a human RNA polymerase II elongation complex simultaneously, the reaction becomes stalled in the core of the bond synthesis mechanism. The mode of stalling is influenced by NTP substrates at the active site and at downstre...
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PMID: 17875640
PDF is available here.
PDF is available here.
Abstract
We show the intrinsic RdRP activity of Pol II with only pure polymerase, an RNA template-product scaffold and nucleoside triphosphates (NTPs). Crystallography reveals the template-product duplex in the site occupied by the DNA-RNA hybrid during transcription. RdRP activity resides at the active site...
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PMID: 18004386
PDF is available here.
PDF is available here.
Biochemistry (Washington) (46)44 2007
Abstract
We propose entails polymerase molecules hyper forward translocating during the promoter escape transition. We discuss how certain features in the ITS, when combined with the N25 promoter, may lead to hyper forward translocation and abortive release at VLAT positions....
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PMID: 17929835
PDF is available here.
PDF is available here.
EMBO Reports (8)11 2007
Abstract
We report the GreB structure of Escherichia coli. The GreB monomers form a triangle with the tip of the amino-terminal CC of one molecule trapped within the hydrophobic cavity of the carboxy-terminal domain of a second molecule. This arrangement suggests an analogous model for recruitment to RNAP. I...
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PMID: 17917675
PDF is available here.
PDF is available here.
Abstract
We have used protein microarrays and autoantibodies from cancer patients to identify proteins that are aberrantly expressed in ovarian tissue. Sera from 30 cancer patients and 30 healthy individuals were used to probe microarrays containing 5,005 human proteins. Ninety-four antigens were identified...
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PMID: 17954908
PDF is available here.
PDF is available here.
Abstract
We provide direct evidence that the evolutionarily conserved transcription elongation factor TFIIS functions during preinitiation complex assembly. First, we identified TFIIS in a mass spectrometric screen of RNA polymerase II (Pol II) preinitiation complexes (PICs). Second, we show that the associa...
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PMID: 17913884
PDF is available here.
PDF is available here.
Abstract
We found that, in the absence of the Med31 Mediator subunit, yeast cells required the TFIIS polymerase II (Pol II)-binding domain but not its RNA cleavage stimulatory activity that is associated with its elongation function. We also found that the TFIIS Pol II-interacting domain was needed for the f...
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PMID: 17901206
PDF is available here.
PDF is available here.
Microbiology (153)Pt 10 2007
Abstract
Shigella flexneri 2a 2457T produces lipopolysaccharide (LPS) with two O-antigen (OAg) chain lengths: a short (S-OAg) controlled by WzzB and a very long (VL-OAg) determined by Wzz(pHS-2). This study demonstrates that the synthesis and length distribution of the S. flexneri OAg are under growth-phase-...
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PMID: 17906147
PDF is available here.
PDF is available here.
Abstract
We found that stably formed 300-nt long DNA-RNA hybrids in a negatively supercoiled transcription template reduced the efficiency of transcription elongation by half, providing a first experimental evidence that transcription elongation is impaired by R-loops in vitro....
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PMID: 17603014
PDF is available here.
PDF is available here.
Cancer Letters (253)2 2007
Abstract
FB1 is an important binding partner and a functional regulator of U19/EAF2, EAF1, and/or ELL....
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PMID: 17395368
PDF is available here.
PDF is available here.
Cell Cycle (6)15 2007
Abstract
Hexamethylene bis-acetamide inducible protein 1 (HEXIM1) is an inhibitor of positive transcription elongation factor b (P-TEFb) that has recently been shown to be involved in cancers, AIDS, cardiac hypertrophy and inflammation. It was first cloned from vascular smooth muscle cells (V...
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PMID: 17671421
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)30 2007
Abstract
We optimized a defined in vitro transcription system and compared results obtained with it to those obtained with a crude system. We found that controlling the function of TFIIF is a key aspect of RNA polymerase II elongation control. Before P-TEFb function, early elongation complexes under the cont...
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PMID: 17548348
PDF is available here.
PDF is available here.
Abstract
Treatment of wild type vaccinia virus infected cells with the anti-poxviral drug isatin-beta-thiosemicarbazone (IBT) induces the viral postreplicative transcription apparatus to synthesize longer-than-normal mRNAs through an unknown mechanism. Previous studies have shown that virus mutants resistant...
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PMID: 17336362
PDF is available here.
PDF is available here.
Abstract
Treatment of wild-type vaccinia virus infected cells with the anti-poxviral drug isatin-beta-thiosemicarbazone (IBT) induces the viral postreplicative transcription apparatus to synthesize longer-than-normal mRNAs through an unknown mechanism. Prior studies have shown that virus mutants resistant to...
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PMID: 17376501
PDF is available here.
PDF is available here.
Abstract
The multi-subunit Elongator complex was first identified by its association with an RNA polymerase II holoenzyme engaged in transcriptional elongation, and subsequent data have provided further evidence that the complex is involved in histone acetylation and transcription. However, most Elongator is...
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PMID: 17466506
PDF is available here.
PDF is available here.
Genes to Cells (12)5 2007
Abstract
We investigated the role of nascent transcript cleavage stimulation activity on the maintenance of transcriptional fidelity in yeast. In yeast, S-II is encoded by the DST1 gene. Disruption of the DST1 gene decreased transcriptional fidelity in cells. Mutations in the DST1 gene that reduce the S-II c...
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PMID: 17535246
PDF is available here.
PDF is available here.
Abstract
We identified and purified an activity, MSA-2, that confers extract-like Mediator responsiveness to our reconstituted system. Mass spectrometric analyses identified its two constituent polypeptides as hSpt5 and hSpt4, which also comprise the elongation factor DSIF. Mechanistically, MSA-2/DSIF acts b...
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PMID: 17404243
PDF is available here.
PDF is available here.
Abstract
We investigate the transcription dynamics of single RNAP II molecules from Saccharomyces cerevisiae against force and in the presence and absence of TFIIS, a transcription elongation factor known to increase transcription through nucleosomal barriers. Using a single-molecule dual-trap optical-tweeze...
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PMID: 17361130
PDF is available here.
PDF is available here.