Real-time observation of the initiation of RNA polymerase II transcription.

Abstract:

:Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.

journal_name

Nature

journal_title

Nature

authors

Fazal FM,Meng CA,Murakami K,Kornberg RD,Block SM

doi

10.1038/nature14882

subject

Has Abstract

pub_date

2015-09-10 00:00:00

pages

274-7

issue

7568

eissn

0028-0836

issn

1476-4687

pii

nature14882

journal_volume

525

pub_type

杂志文章

相关文献

NATURE文献大全
  • Channel opening and gating mechanism in AMPA-subtype glutamate receptors.

    abstract::AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid)-subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission throughout the central nervous system. Gated by the neurotransmitter glutamate, AMPA receptors are critical for synaptic strength, and dysregulation of AMPA receptor-mediated si...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature23479

    authors: Twomey EC,Yelshanskaya MV,Grassucci RA,Frank J,Sobolevsky AI

    更新日期:2017-09-07 00:00:00

  • Polymer-supported membranes as models of the cell surface.

    abstract::Lipid-bilayer membranes supported on solid substrates are widely used as cell-surface models that connect biological and artificial materials. They can be placed either directly on solids or on ultrathin polymer supports that mimic the generic role of the extracellular matrix. The tools of modern genetic engineering a...

    journal_title:Nature

    pub_type: 杂志文章,评审

    doi:10.1038/nature04164

    authors: Tanaka M,Sackmann E

    更新日期:2005-09-29 00:00:00

  • Prophylactic TNF blockade uncouples efficacy and toxicity in dual CTLA-4 and PD-1 immunotherapy.

    abstract::Combined PD-1 and CTLA-4-targeted immunotherapy with nivolumab and ipilimumab is effective against melanoma, renal cell carcinoma and non-small-cell lung cancer1-3. However, this comes at the cost of frequent, serious immune-related adverse events, necessitating a reduction in the recommended dose of ipilimumab that i...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-019-1162-y

    authors: Perez-Ruiz E,Minute L,Otano I,Alvarez M,Ochoa MC,Belsue V,de Andrea C,Rodriguez-Ruiz ME,Perez-Gracia JL,Marquez-Rodas I,Llacer C,Alvarez M,de Luque V,Molina C,Teijeira A,Berraondo P,Melero I

    更新日期:2019-05-01 00:00:00

  • Single stretch-activated ion channels in vascular endothelial cells as mechanotransducers?

    abstract::Endothelial cells line the inner surface of blood vessels and act as the main barrier to the passage of cells and large molecules from the blood stream to the tissues. Recent interest in the part played by the endothelium in regulating vascular tone has focused on the synthesis and secretion of prostacyclin and an end...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/325811a0

    authors: Lansman JB,Hallam TJ,Rink TJ

    更新日期:1987-02-26 00:00:00

  • Sensitivity of coccolithophores to carbonate chemistry and ocean acidification.

    abstract::About one-third of the carbon dioxide (CO(2)) released into the atmosphere as a result of human activity has been absorbed by the oceans, where it partitions into the constituent ions of carbonic acid. This leads to ocean acidification, one of the major threats to marine ecosystems and particularly to calcifying organ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature10295

    authors: Beaufort L,Probert I,de Garidel-Thoron T,Bendif EM,Ruiz-Pino D,Metzl N,Goyet C,Buchet N,Coupel P,Grelaud M,Rost B,Rickaby RE,de Vargas C

    更新日期:2011-08-03 00:00:00

  • Retinoblastoma-protein-dependent cell-cycle inhibition by the tumour suppressor p16.

    abstract::D-type cyclins, in association with the cyclin-dependent kinases Cdk4 or Cdk6, promote progression through the G1 phase of the cell cycle by phosphorylating the retinoblastoma protein (RB). The activities of Cdk4 and Cdk6 are constrained by inhibitors such as p16, the product of the CDKN2 gene on human chromosome 9p21...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/375503a0

    authors: Lukas J,Parry D,Aagaard L,Mann DJ,Bartkova J,Strauss M,Peters G,Bartek J

    更新日期:1995-06-08 00:00:00

  • Bird song: superfast muscles control dove's trill.

    abstract::Bird songs frequently contain trilling sounds that demand extremely fast vocalization control. Here we show that doves control their syrinx, a vocal organ that is unique to birds, by using superfast muscles. These muscles, which are similar to those that operate highly specialist acoustic organs such as the rattle of ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/431146a

    authors: Elemans CP,Spierts IL,Müller UK,Van Leeuwen JL,Goller F

    更新日期:2004-09-09 00:00:00

  • Distinct aspects of neuronal differentiation encoded by frequency of spontaneous Ca2+ transients.

    abstract::Stimulation of transient increases in intracellular calcium (Cai2+) activates protein kinases, regulates transcription and influences motility and morphology. Developing neurons generate spontaneous Cai2+ transients, but their role in directing neuronal differentiation and the way in which they encode information are ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/375784a0

    authors: Gu X,Spitzer NC

    更新日期:1995-06-29 00:00:00

  • Immune clearance of highly pathogenic SIV infection.

    abstract::Established infections with the human and simian immunodeficiency viruses (HIV and SIV, respectively) are thought to be permanent with even the most effective immune responses and antiretroviral therapies only able to control, but not clear, these infections. Whether the residual virus that maintains these infections ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature12519

    authors: Hansen SG,Piatak M Jr,Ventura AB,Hughes CM,Gilbride RM,Ford JC,Oswald K,Shoemaker R,Li Y,Lewis MS,Gilliam AN,Xu G,Whizin N,Burwitz BJ,Planer SL,Turner JM,Legasse AW,Axthelm MK,Nelson JA,Früh K,Sacha JB,Estes JD

    更新日期:2013-10-03 00:00:00

  • Long-range correlations in nucleotide sequences.

    abstract::DNA sequences have been analysed using models, such as an n-step Markov chain, that incorporate the possibility of short-range nucleotide correlations. We propose here a method for studying the stochastic properties of nucleotide sequences by constructing a 1:1 map of the nucleotide sequence onto a walk, which we term...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/356168a0

    authors: Peng CK,Buldyrev SV,Goldberger AL,Havlin S,Sciortino F,Simons M,Stanley HE

    更新日期:1992-03-12 00:00:00

  • Adjuvant-free IgG responses induced with antigen coupled to antibodies against class II MHC.

    abstract::The generation of strong serological responses to protein antigens in experimental animals usually requires the use of potent adjuvants, most of which cannot be used in human or veterinary vaccines because of deleterious side effects. Attempting to circumvent this problem, we have assessed an adjuvant-free antigen-del...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/327059a0

    authors: Carayanniotis G,Barber BH

    更新日期:1987-05-07 00:00:00

  • Visible-frequency hyperbolic metasurface.

    abstract::Metamaterials are artificial optical media composed of sub-wavelength metallic and dielectric building blocks that feature optical phenomena not present in naturally occurring materials. Although they can serve as the basis for unique optical devices that mould the flow of light in unconventional ways, three-dimension...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature14477

    authors: High AA,Devlin RC,Dibos A,Polking M,Wild DS,Perczel J,de Leon NP,Lukin MD,Park H

    更新日期:2015-06-11 00:00:00

  • Coherent spin manipulation without magnetic fields in strained semiconductors.

    abstract::A consequence of relativity is that in the presence of an electric field, the spin and momentum states of an electron can be coupled; this is known as spin-orbit coupling. Such an interaction opens a pathway to the manipulation of electron spins within non-magnetic semiconductors, in the absence of applied magnetic fi...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature02202

    authors: Kato Y,Myers RC,Gossard AC,Awschalom DD

    更新日期:2004-01-01 00:00:00

  • Solar eclipses of Phobos and Deimos observed from the surface of Mars.

    abstract::The small martian satellites Phobos and Deimos orbit in synchronous rotation with inclinations of only 0.01 degrees and 0.92 degrees , respectively, relative to the planet's equatorial plane. Thus, an observer at near-equatorial latitudes on Mars could occasionally observe solar eclipses by these satellites (see ref. ...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature03437

    authors: Bell JF 3rd,Lemmon MT,Duxbury TC,Hubbard MY,Wolff MJ,Squyres SW,Craig L,Ludwinski JM

    更新日期:2005-07-07 00:00:00

  • Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis.

    abstract::A fundamental tenet of classical mendelian genetics is that allelic information is stably inherited from one generation to the next, resulting in predictable segregation patterns of differing alleles. Although several exceptions to this principle are known, all represent specialized cases that are mechanistically rest...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature03380

    authors: Lolle SJ,Victor JL,Young JM,Pruitt RE

    更新日期:2005-03-24 00:00:00

  • Detection of carbonates in dust shells around evolved stars.

    abstract::Carbonates on large Solar System bodies like Earth and Mars (the latter represented by the meteorite ALH84001) form through the weathering of silicates in a watery (CO3)2- solution. The presence of carbonates in interplanetary dust particles and asteroids (again, represented by meteorites) is not completely understood...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/415295a

    authors: Kemper F,Jäger C,Waters LB,Henning T,Molster FJ,Barlow MJ,Lim T,de Koter A

    更新日期:2002-01-17 00:00:00

  • Formation of accumbens GluR2-lacking AMPA receptors mediates incubation of cocaine craving.

    abstract::Relapse to cocaine use after prolonged abstinence is an important clinical problem. This relapse is often induced by exposure to cues associated with cocaine use. To account for the persistent propensity for relapse, it has been suggested that cue-induced cocaine craving increases over the first several weeks of absti...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature06995

    authors: Conrad KL,Tseng KY,Uejima JL,Reimers JM,Heng LJ,Shaham Y,Marinelli M,Wolf ME

    更新日期:2008-07-03 00:00:00

  • A role for branchpoints in splicing in vivo.

    abstract::The nucleotides immediately surrounding intron/exon junctions of genes transcribed by RNA polymerase B can be derived from 'consensus' sequences for donor and acceptor splice sites by only a few base changes. Studies in vivo have underlined the importance of these junction nucleotides for splicing. In higher eukaryote...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/315430a0

    authors: Rautmann G,Breathnach R

    更新日期:1985-05-30 00:00:00

  • In situ observation of incompressible Mott-insulating domains in ultracold atomic gases.

    abstract::The observation of the superfluid to Mott insulator phase transition of ultracold atoms in optical lattices was an enabling discovery in experimental many-body physics, providing the first tangible example of a quantum phase transition (one that occurs even at zero temperature) in an ultracold atomic gas. For a trappe...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature08244

    authors: Gemelke N,Zhang X,Hung CL,Chin C

    更新日期:2009-08-20 00:00:00

  • The evolution of lncRNA repertoires and expression patterns in tetrapods.

    abstract::Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lnc...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature12943

    authors: Necsulea A,Soumillon M,Warnefors M,Liechti A,Daish T,Zeller U,Baker JC,Grützner F,Kaessmann H

    更新日期:2014-01-30 00:00:00

  • Extracellular domains mediating epsilon subunit interactions of muscle acetylcholine receptor.

    abstract::Ligand-gated ion channels, a major class of cell-surface proteins, have a pseudosymmetric structure with five highly homologous subunits arranged around a central ion pore. The correct assembly of each channel, whose subunit composition varies with cell type and stage of development, requires specific recognition betw...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/352064a0

    authors: Yu XM,Hall ZW

    更新日期:1991-07-04 00:00:00

  • Ceramic-metal composites for heat exchangers in concentrated solar power plants.

    abstract::The efficiency of generating electricity from heat using concentrated solar power plants (which use mirrors or lenses to concentrate sunlight in order to drive heat engines, usually involving turbines) may be appreciably increased by operating with higher turbine inlet temperatures, but this would require improved hea...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-018-0593-1

    authors: Caccia M,Tabandeh-Khorshid M,Itskos G,Strayer AR,Caldwell AS,Pidaparti S,Singnisai S,Rohskopf AD,Schroeder AM,Jarrahbashi D,Kang T,Sahoo S,Kadasala NR,Marquez-Rossy A,Anderson MH,Lara-Curzio E,Ranjan D,Henry A,Sandhag

    更新日期:2018-10-01 00:00:00

  • ATM stabilizes DNA double-strand-break complexes during V(D)J recombination.

    abstract::The ATM (ataxia-telangiectasia mutated) protein kinase mediates early cellular responses to DNA double-strand breaks (DSBs) generated during metabolic processes or by DNA-damaging agents. ATM deficiency leads to ataxia-telangiectasia, a disease marked by lymphopenia, genomic instability and an increased predisposition...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature04866

    authors: Bredemeyer AL,Sharma GG,Huang CY,Helmink BA,Walker LM,Khor KC,Nuskey B,Sullivan KE,Pandita TK,Bassing CH,Sleckman BP

    更新日期:2006-07-27 00:00:00

  • Hypothalamic regulation of sleep and circadian rhythms.

    abstract::A series of findings over the past decade has begun to identify the brain circuitry and neurotransmitters that regulate our daily cycles of sleep and wakefulness. The latter depends on a network of cell groups that activate the thalamus and the cerebral cortex. A key switch in the hypothalamus shuts off this arousal s...

    journal_title:Nature

    pub_type: 杂志文章,评审

    doi:10.1038/nature04284

    authors: Saper CB,Scammell TE,Lu J

    更新日期:2005-10-27 00:00:00

  • Effect of cell history on response to helix-loop-helix family of myogenic regulators.

    abstract::In multinucleated heterokaryons formed from the fusion of differentiated muscle cells to either hepatocytes or fibroblasts, muscle-specific gene expression is activated, liver-specific gene expression is repressed, and there are changes in the location of the Golgi apparatus. An understanding of the regulatory mechani...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/344454a0

    authors: Schäfer BW,Blakely BT,Darlington GJ,Blau HM

    更新日期:1990-03-29 00:00:00

  • Kondo resonance in a single-molecule transistor.

    abstract::When an individual molecule, nanocrystal, nanotube or lithographically defined quantum dot is attached to metallic electrodes via tunnel barriers, electron transport is dominated by single-electron charging and energy-level quantization. As the coupling to the electrodes increases, higher-order tunnelling and correlat...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature00790

    authors: Liang W,Shores MP,Bockrath M,Long JR,Park H

    更新日期:2002-06-13 00:00:00

  • Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-kappaB.

    abstract::Protein modification by the conjugation of ubiquitin moieties--ubiquitination--plays a major part in many biological processes, including cell cycle and apoptosis. The enzymes that mediate ubiquitin-conjugation have been well-studied, but much less is known about the ubiquitin-specific proteases that mediate de-ubiqui...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/nature01811

    authors: Brummelkamp TR,Nijman SM,Dirac AM,Bernards R

    更新日期:2003-08-14 00:00:00

  • Single-species models for many-species food webs.

    abstract::Most species live in species-rich food webs; yet, for a century, most mathematical models for population dynamics have included only one or two species. We ask whether such models are relevant to the real world. Two-species population models of an interacting consumer and resource collapse to one-species dynamics when...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/417541a

    authors: Murdoch WW,Kendall BE,Nisbet RM,Briggs CJ,McCauley E,Bolser R

    更新日期:2002-05-30 00:00:00

  • No extreme bipolar glaciation during the main Eocene calcite compensation shift.

    abstract::Major ice sheets were permanently established on Antarctica approximately 34 million years ago, close to the Eocene/Oligocene boundary, at the same time as a permanent deepening of the calcite compensation depth in the world's oceans. Until recently, it was thought that Northern Hemisphere glaciation began much later,...

    journal_title:Nature

    pub_type: 历史文章,杂志文章

    doi:10.1038/nature06053

    authors: Edgar KM,Wilson PA,Sexton PF,Suganuma Y

    更新日期:2007-08-23 00:00:00

  • DNA mismatches reveal conformational penalties in protein-DNA recognition.

    abstract::Transcription factors recognize specific genomic sequences to regulate complex gene-expression programs. Although it is well-established that transcription factors bind to specific DNA sequences using a combination of base readout and shape recognition, some fundamental aspects of protein-DNA binding remain poorly und...

    journal_title:Nature

    pub_type: 杂志文章

    doi:10.1038/s41586-020-2843-2

    authors: Afek A,Shi H,Rangadurai A,Sahay H,Senitzki A,Xhani S,Fang M,Salinas R,Mielko Z,Pufall MA,Poon GMK,Haran TE,Schumacher MA,Al-Hashimi HM,Gordân R

    更新日期:2020-11-01 00:00:00