A conformational change in TFIIB is required for activator-mediated assembly of the preinitiation complex.

Abstract:

:TFIIB plays a pivotal role during assembly of the RNA polymerase II transcription preinitiation complex. TFIIB is composed of two domains that engage in an intramolecular interaction that can be disrupted by the VP16 activation domain. In this study, we describe a novel human TFIIB derivative harbouring two point mutations in the highly conserved N-terminal charged cluster domain. This mutant, TFIIB R53E:R66E, exhibits an enhanced affinity in its intramolecular interaction when compared with wild-type TFIIB. Consistent with this, the mutant displays a significantly reduced affinity for VP16. However, its ability to complex with TATA-binding protein at a model promoter is equivalent to that of wild-type TFIIB. Furthermore, this TFIIB derivative is able to support high order preinitiation complex assembly in the absence of an activator. Strikingly though, an activator fails to recruit the TFIIB mutant to the promoter. Taken together, our results show that a TFIIB conformational change is critical for the formation of activator-dependent transcription complexes.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Glossop JA,Dafforn TR,Roberts SG

doi

10.1093/nar/gkh504

keywords:

subject

Has Abstract

pub_date

2004-03-22 00:00:00

pages

1829-35

issue

5

eissn

0305-1048

issn

1362-4962

pii

32/5/1829

journal_volume

32

pub_type

杂志文章
  • Nucleotide sequence of satellite DNA contained in the eliminated genome of Ascaris lumbricoides.

    abstract::Several restriction endonuclease fragments isolated from highly repetitive satellite DNA of the chromatin eliminating nematode Ascaris lumbricoides var. suum have been cloned. Each type of restriction fragment corresponds to a different variant of the same related ancestral sequence. These variants differ by small del...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.23.7493

    authors: Müller F,Walker P,Aeby P,Neuhaus H,Felder H,Back E,Tobler H

    更新日期:1982-12-11 00:00:00

  • Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

    abstract::Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn470

    authors: Li JT,Zhang Y,Kong L,Liu QR,Wei L

    更新日期:2008-09-01 00:00:00

  • Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells.

    abstract::When designed to cleave a target RNA in trans, the hammerhead ribozyme contains two antisense flanks which form helix I and helix III by pairing with the complementary target RNA. The sequences forming helix II are contained on the ribozyme strand and represent a major structural component of the hammerhead structure....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.19.3951

    authors: Homann M,Tabler M,Tzortzakaki S,Sczakiel G

    更新日期:1994-09-25 00:00:00

  • Light-activated RNA interference using double-stranded siRNA precursors modified using a remarkable regiospecificity of diazo-based photolabile groups.

    abstract::Diazo-based precursors of photolabile groups have been used extensively for modifying nucleic acids, with the intention of toggling biological processes with light. These processes include transcription, translation and RNA interference. In these cases, the photolabile groups have been typically depicted as modifying ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp415

    authors: Shah S,Jain PK,Kala A,Karunakaran D,Friedman SH

    更新日期:2009-07-01 00:00:00

  • Characterization of a novel T lymphocyte protein which binds to a site related to steroid/thyroid hormone receptor response elements in the negative regulatory sequence of the human immunodeficiency virus long terminal repeat.

    abstract::We have previously identified a T lymphocyte protein which binds to a site within the LTR of the human immunodeficiency virus type 1 (HIV-1) and exerts an inhibitory effect on virus gene expression. The palindromic site (site B) recognized by this protein is related to the palindromic binding sites of members of the s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.20.5429

    authors: Orchard K,Lang G,Collins M,Latchman D

    更新日期:1992-10-25 00:00:00

  • Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases.

    abstract::We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn1008

    authors: Ryu GM,Song P,Kim KW,Oh KS,Park KJ,Kim JH

    更新日期:2009-03-01 00:00:00

  • Multitarget-ribozyme directed to cleave at up to nine highly conserved HIV-1 env RNA regions inhibits HIV-1 replication--potential effectiveness against most presently sequenced HIV-1 isolates.

    abstract::Several mono-, di-, tetra-, penta- and nonaribozymes were developed. These multitarget-ribozymes were targeted to cleave HIV-1 env RNA at up to nine different conserved sites. Each multitarget-ribozyme consisted of a chain of up to nine hammerhead motifs, each flanked by a different targeting sequence. The multitarget...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.17.4581

    authors: Chen CJ,Banerjea AC,Harmison GG,Haglund K,Schubert M

    更新日期:1992-09-11 00:00:00

  • G-quadruplex formation at the 3' end of telomere DNA inhibits its extension by telomerase, polymerase and unwinding by helicase.

    abstract::Telomere G-quadruplex is emerging as a promising anti-cancer target due to its inhibition to telomerase, an enzyme expressed in more than 85% tumors. Telomerase-mediated telomere extension and some other reactions require a free 3' telomere end in single-stranded form. G-quadruplex formation near the 3' end of telomer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr164

    authors: Wang Q,Liu JQ,Chen Z,Zheng KW,Chen CY,Hao YH,Tan Z

    更新日期:2011-08-01 00:00:00

  • Mutation detection using immobilized mismatch binding protein (MutS).

    abstract::An accurate and highly sensitive mutation detection assay has been developed. The assay is based on the detection of mispaired and unpaired bases by immobilized mismatch binding protein (Escherichia coli MutS). The assay can detect most mismatches and all single base substitution mutations, as well as small addition o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.19.3944

    authors: Wagner R,Debbie P,Radman M

    更新日期:1995-10-11 00:00:00

  • InParanoid 6: eukaryotic ortholog clusters with inparalogs.

    abstract::The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm1020

    authors: Berglund AC,Sjölund E,Ostlund G,Sonnhammer EL

    更新日期:2008-01-01 00:00:00

  • Superhelical stress restrained in plasmid DNA during repair synthesis initiated by the UvrA, B and C proteins in vitro.

    abstract::Purified UvrA, UvrB, UvrC, UvrD, PolA and Lig proteins from Escherichia coli have been used to assess the effect of nucleotide excision repair on the conformation of native negatively supercoiled plasmid DNA in an in vitro test system. The analysis of labeled reaction products on specific gel systems suggests that the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.24.10337

    authors: Backendorf C,Olsthoorn R,van de Putte P

    更新日期:1989-12-25 00:00:00

  • Alternatively spliced p53 RNA in transformed and normal cells of different tissue types.

    abstract::The alternatively spliced RNA species of tumor suppressor gene p53, containing an additional 96 bases derived from intron 10, is present at approximately 25 to 30% the level of regularly spliced p53 RNA in both normal epidermal and carcinoma cells. The presence of this alternatively spliced RNA in 10T1/2 fibroblast ce...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.8.1979

    authors: Han KA,Kulesz-Martin MF

    更新日期:1992-04-25 00:00:00

  • DNA unwinding and protein displacement by superfamily 1 and superfamily 2 helicases.

    abstract::DNA helicases are required for virtually every aspect of DNA metabolism, including replication, repair, recombination and transcription. A comprehensive description of these essential biochemical processes requires detailed understanding of helicase mechanisms. These enzymes are ubiquitous, having been identified in v...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/gkl501

    authors: Mackintosh SG,Raney KD

    更新日期:2006-01-01 00:00:00

  • ASD: a comprehensive database of allosteric proteins and modulators.

    abstract::Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1022

    authors: Huang Z,Zhu L,Cao Y,Wu G,Liu X,Chen Y,Wang Q,Shi T,Zhao Y,Wang Y,Li W,Li Y,Chen H,Chen G,Zhang J

    更新日期:2011-01-01 00:00:00

  • Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog.

    abstract::The specific recognition of homopurine-homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gng031

    authors: Nagatsugi F,Sasaki S,Miller PS,Seidman MM

    更新日期:2003-03-15 00:00:00

  • MLL fusion proteins link transcriptional coactivators to previously active CpG-rich promoters.

    abstract::Mixed-lineage leukemia (MLL) maintains the expression of cellular memory genes during development, while leukemic MLL fusion proteins aberrantly maintain expression of hematopoietic stem cell program genes such as HOXA9 to cause leukemia. However, the molecular mechanism of gene activation is unclear. Here we show tha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1394

    authors: Okuda H,Kawaguchi M,Kanai A,Matsui H,Kawamura T,Inaba T,Kitabayashi I,Yokoyama A

    更新日期:2014-04-01 00:00:00

  • Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid.

    abstract::Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.8.3427

    authors: Sano T,Uyeda I,Shikata E,Ohno T,Okada Y

    更新日期:1984-04-25 00:00:00

  • Stabilization of RNA stacking by pseudouridine.

    abstract::The effect of the modified nucleoside pseudouridine (psi) on RNA structure was compared with uridine. The extent of base stacking in model RNA oligonucleotides was measured by 1H NMR, UV, and CD spectroscopy. The UV and CD results indicate that the model single-stranded oligoribonucleotides AAUA and AA psi A form stac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.24.5020

    authors: Davis DR

    更新日期:1995-12-25 00:00:00

  • Structural motifs in the RNA encoded by the early nodulation gene enod40 of soybean.

    abstract::The plant gene enod40 is highly conserved among legumes and also present in various non-legume species. It is presumed to play a central regulatory role in the Rhizobium-legume interaction, being expressed well before the initiation of cortical cell divisions resulting in nodule formation. Two small peptides encoded b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg721

    authors: Girard G,Roussis A,Gultyaev AP,Pleij CW,Spaink HP

    更新日期:2003-09-01 00:00:00

  • The mouse beta-globin locus control region: hypersensitive sites 3 and 4.

    abstract::The human beta-globin LCR plays a key role in the transcriptional regulation of the beta-globin locus and comprises four erythroid specific DNase I hypersensitive sites, designated 5'HS1-4. We have now isolated genomic clones containing 5'HS3 and 5'HS4 of the mouse beta-globin LCR. 5'HS3 and 5'HS4 are located 15 kb an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.21.5797

    authors: Jiménez G,Gale KB,Enver T

    更新日期:1992-11-11 00:00:00

  • Streamlining effects of extra telomeric repeat on telomeric DNA folding revealed by fluorescence-force spectroscopy.

    abstract::A human telomere ends in a single-stranded 3' tail, composed of repeats of T2AG3. G-quadruplexes (GQs) formed from four consecutive repeats have been shown to possess high-structural and mechanical diversity. In principle, a GQ can form from any four repeats that are not necessarily consecutive. To understand the dyna...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz906

    authors: Mitra J,Ha T

    更新日期:2019-12-02 00:00:00

  • Nucleotide sequence of the 3'-terminal tRNA-like structure in barley stripe mosaic virus genome.

    abstract::This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is show...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.9.4001

    authors: Kozlov YuV,Rupasov VV,Adyshev DM,Belgelarskaya SN,Agranovsky AA,Mankin AS,Morozov SYu,Dolja VV,Atabekov JG

    更新日期:1984-05-11 00:00:00

  • PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

    abstract::Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gni142

    authors: Brohede J,Dunne R,McKay JD,Hannan GN

    更新日期:2005-09-30 00:00:00

  • Polynucleotide:adenosine glycosidase activity of ribosome-inactivating proteins: effect on DNA, RNA and poly(A).

    abstract::Ribosome-inactivating proteins (RIP) are a family of plant enzymes for which a unique activity was determined: rRNAN-glycosidase at a specific universally conserved position, A4324in the case of rat ribosomes. Recently we have shown that the RIP from Saponaria officinalis have a much wider substrate specificity: they ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/25.3.518

    authors: Barbieri L,Valbonesi P,Bonora E,Gorini P,Bolognesi A,Stirpe F

    更新日期:1997-02-01 00:00:00

  • Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil.

    abstract::Archaeal family-B DNA polymerases bind tightly to deaminated bases and stall replication on encountering uracil in template strands, four bases ahead of the primer-template junction. Should the polymerase progress further towards the uracil, for example, to position uracil only two bases in front of the junction, 3'-5...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1364

    authors: Richardson TT,Wu X,Keith BJ,Heslop P,Jones AC,Connolly BA

    更新日期:2013-02-01 00:00:00

  • Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate.

    abstract::Diethyl pyrocarbonate reacts with the single-stranded loops of cruciform structures with great selectivity. Adenine bases are carbethoxylated, as a result of which the backbone may be cleaved with piperidine, and the level of chemical modification at each base may be determined. We have studied the ColE1 and (A-T)34 c...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.10.3995

    authors: Furlong JC,Lilley DM

    更新日期:1986-05-27 00:00:00

  • Identification of a methylated oligoribonucleotide as a potent inhibitor of HIV-1 reverse transcription complex.

    abstract::Upon HIV-1 infection of a target cell, the viral reverse transcriptase (RT) copies the genomic RNA to synthesize the viral DNA. The genomic RNA is within the incoming HIV-1 core where it is coated by molecules of nucleocapsid (NC) protein that chaperones the reverse transcription process. Indeed, the RT chaperoning pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr117

    authors: Grigorov B,Bocquin A,Gabus C,Avilov S,Mély Y,Agopian A,Divita G,Gottikh M,Witvrouw M,Darlix JL

    更新日期:2011-07-01 00:00:00

  • Nucleotide sequence and expression of a Pseudomonas savastanoi cytokinin biosynthetic gene: homology with Agrobacterium tumefaciens tmr and tzs loci.

    abstract::The nucleotide sequence of a Pseudomonas trans-zeatin producing gene (ptz) from the pCK1 plasmid of Pseudomonas syringae pv. savastanoi strain 1006 has been determined. This gene confers upon E. coli the ability to synthesize and secrete several cytokinins including trans-zeatin, iso-pentenyladenine and their respecti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.6.2555

    authors: Powell GK,Morris RO

    更新日期:1986-03-25 00:00:00

  • Finding approximate gene clusters with Gecko 3.

    abstract::Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw843

    authors: Winter S,Jahn K,Wehner S,Kuchenbecker L,Marz M,Stoye J,Böcker S

    更新日期:2016-11-16 00:00:00

  • ArchDB: automated protein loop classification as a tool for structural genomics.

    abstract::The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh002

    authors: Espadaler J,Fernandez-Fuentes N,Hermoso A,Querol E,Aviles FX,Sternberg MJ,Oliva B

    更新日期:2004-01-01 00:00:00