Dynamic mechanism for the transcription apparatus orchestrating reliable responses to activators.

Abstract:

:The transcription apparatus (TA) is a huge molecular machine. It detects the time-varying concentrations of transcriptional activators and initiates mRNA transcripts at appropriate rates. Based on the general structural organizations of the TA, we propose how the TA dynamically orchestrates transcriptional responses. The activators rapidly cycle in and out of a clamp-like space temporarily formed between the enhancer and the Mediator, with the concentration of activators encoded as their temporal occupancy rate (R(TOR)) within the space. The entry of activators into this space induces allostery in the Mediator, resulting in a facilitated circumstance for transcriptional reinitiation. The reinitiation rate is much larger than the cycling rate of activators, thereby R(TOR) guiding the amount of transcripts. Based on this mechanism, stochastic simulations can qualitatively reproduce and interpret multiple features of gene expression, e.g., transcriptional bursting is not mere noise as traditionally believed, but rather the basis of reliable transcriptional responses.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Wang Y,Liu F,Wang W

doi

10.1038/srep00422

subject

Has Abstract

pub_date

2012-01-01 00:00:00

pages

422

issn

2045-2322

journal_volume

2

pub_type

杂志文章
  • Survival of pancreatic cancer patients is negatively correlated with age at diagnosis: a population-based retrospective study.

    abstract::In this population-based retrospective study, we aimed to investigate the association between age at diagnosis and prognosis of pancreatic cancer (PC) patients using data from the National Cancer Institute's Surveillance, Epidemiology, and the End Results database. Different factors for stratification, like race, sex,...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-64068-3

    authors: Wang H,Liu J,Xia G,Lei S,Huang X,Huang X

    更新日期:2020-04-27 00:00:00

  • Transaminase levels reflect disease severity in children ventilated for respiratory syncytial virus (RSV) bronchiolitis.

    abstract::Bronchiolitis, often caused by respiratory syncytial virus (RSV), is the commonest cause of hospitalisation in infancy. Serum transaminases are sometimes raised in children with bronchiolitis. We tested the hypothesis that raised transaminases are associated with increased disease severity in children ventilated for b...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-20292-6

    authors: Thorburn K,Fulton C,King C,Ramaneswaran D,Alammar A,McNamara PS

    更新日期:2018-01-29 00:00:00

  • Mesoscale structures in amorphous silks from a spider's orb-web.

    abstract::Of the 7-8 silk fibers making up an orb-web only the hierarchical structural organization of semicrystalline radial fibers -composed of major ampullate silk- has been studied in detail, given its fascinating mechanical features. While major ampullate silk's nanofibrillar morphology is well established, knowhow on meso...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-74638-0

    authors: Riekel C,Burghammer M,Rosenthal M

    更新日期:2020-10-23 00:00:00

  • Cerium oxide nanoparticles display antilipogenic effect in rats with non-alcoholic fatty liver disease.

    abstract::Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease worldwide, ranging from steatosis to non-alcoholic steatohepatitis (NASH). Recently, cerium oxide nanoparticles (CeO2NPs) have emerged as a new antioxidant agent with hepatoprotective properties in experimental liver disease. T...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-49262-2

    authors: Carvajal S,Perramón M,Oró D,Casals E,Fernández-Varo G,Casals G,Parra M,González de la Presa B,Ribera J,Pastor Ó,Morales-Ruíz M,Puntes V,Jiménez W

    更新日期:2019-09-06 00:00:00

  • Cyclin Y inhibits plasticity-induced AMPA receptor exocytosis and LTP.

    abstract::Cyclin Y (CCNY) is a member of the cyclin protein family, known to regulate cell division in proliferating cells. Interestingly, CCNY is expressed in neurons that do not undergo cell division. Here, we report that CCNY negatively regulates long-term potentiation (LTP) of synaptic strength through inhibition of AMPA re...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep12624

    authors: Cho E,Kim DH,Hur YN,Whitcomb DJ,Regan P,Hong JH,Kim H,Ho Suh Y,Cho K,Park M

    更新日期:2015-07-29 00:00:00

  • Relationship between Lipoprotein (a) and cognitive function - Results from the Berlin Aging Study II.

    abstract::It has been suggested that an age-related loss of cognitive function might be driven by atherosclerotic effects associated with altered lipid patterns. However, the relationship between Lipoprotein (a) [Lp(a)] and healthy cognitive aging has not yet been sufficiently investigated. For the current analysis we used the ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-66783-3

    authors: Röhr F,Bucholtz N,Toepfer S,Norman K,Spira D,Steinhagen-Thiessen E,Lill CM,Bertram L,Demuth I,Buchmann N,Düzel S

    更新日期:2020-06-30 00:00:00

  • Principled BCI Decoder Design and Parameter Selection Using a Feedback Control Model.

    abstract::Decoders optimized offline to reconstruct intended movements from neural recordings sometimes fail to achieve optimal performance online when they are used in closed-loop as part of an intracortical brain-computer interface (iBCI). This is because typical decoder calibration routines do not model the emergent interact...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44166-7

    authors: Willett FR,Young DR,Murphy BA,Memberg WD,Blabe CH,Pandarinath C,Stavisky SD,Rezaii P,Saab J,Walter BL,Sweet JA,Miller JP,Henderson JM,Shenoy KV,Simeral JD,Jarosiewicz B,Hochberg LR,Kirsch RF,Bolu Ajiboye A

    更新日期:2019-06-20 00:00:00

  • A microfluidic device for measuring cell migration towards substrate-bound and soluble chemokine gradients.

    abstract::Cellular locomotion is a central hallmark of eukaryotic life. It is governed by cell-extrinsic molecular factors, which can either emerge in the soluble phase or as immobilized, often adhesive ligands. To encode for direction, every cue must be present as a spatial or temporal gradient. Here, we developed a microfluid...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36440

    authors: Schwarz J,Bierbaum V,Merrin J,Frank T,Hauschild R,Bollenbach T,Tay S,Sixt M,Mehling M

    更新日期:2016-11-07 00:00:00

  • Numerical research on the anisotropic transport of thermal neutron in heterogeneous porous media with micron X-ray computed tomography.

    abstract::The anisotropic transport of thermal neutron in heterogeneous porous media is of great research interests in many fields. In this paper, it is the first time that a new model based on micron X-ray computed tomography (CT) has been proposed to simultaneously consider both the separation of matrix and pore and the distr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep27488

    authors: Wang Y,Yue W,Zhang M

    更新日期:2016-06-08 00:00:00

  • Graphene-protected copper and silver plasmonics.

    abstract::Plasmonics has established itself as a branch of physics which promises to revolutionize data processing, improve photovoltaics, and increase sensitivity of bio-detection. A widespread use of plasmonic devices is notably hindered by high losses and the absence of stable and inexpensive metal films suitable for plasmon...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05517

    authors: Kravets VG,Jalil R,Kim YJ,Ansell D,Aznakayeva DE,Thackray B,Britnell L,Belle BD,Withers F,Radko IP,Han Z,Bozhevolnyi SI,Novoselov KS,Geim AK,Grigorenko AN

    更新日期:2014-07-01 00:00:00

  • Micro-gun based on laser pulse propulsion.

    abstract::This paper proposes a novel "micro-gun" structure for laser pulse propulsion. The "micro-bullets" (glass microspheres) are irradiated by a laser pulse with a 10 ns duration in a dynamic process. Experimental parameters such as the microsphere diameter and the laser pulse energy are varied to investigate their influenc...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-16400-7

    authors: Yu H,Li H,Cui L,Liu S,Yang J

    更新日期:2017-11-24 00:00:00

  • Control strategies of 3-cell Central Pattern Generator via global stimuli.

    abstract::The study of the synchronization patterns of small neuron networks that control several biological processes has become an interesting growing discipline. Some of these synchronization patterns of individual neurons are related to some undesirable neurological diseases, and they are believed to play a crucial role in ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep23622

    authors: Lozano Á,Rodríguez M,Barrio R

    更新日期:2016-03-29 00:00:00

  • Novel characteristics of energy spectrum for 3D Dirac oscillator analyzed via Lorentz covariant deformed algebra.

    abstract::We investigate the Lorentz-covariant deformed algebra for Dirac oscillator problem, which is a generalization of Kempf deformed algebra in 3 + 1 dimension of space-time, where Lorentz symmetry are preserved. The energy spectrum of the system is analyzed by taking advantage of the corresponding wave functions with expl...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep03221

    authors: Betrouche M,Maamache M,Choi JR

    更新日期:2013-11-14 00:00:00

  • OSM-9 and an amiloride-sensitive channel, but not PKD-2, are involved in mechanosensation in C. elegans male ray neurons.

    abstract::Mechanotransduction is crucial for touch sensation, hearing, proprioception, and pain sensing. In C. elegans, male ray neurons have been implicated to be involved in the mechanosensation required for mating behavior. However, whether ray neurons directly sense mechanical stimulation is not yet known, and the underlyin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-25542-1

    authors: Zhang H,Yue X,Cheng H,Zhang X,Cai Y,Zou W,Huang G,Cheng L,Ye F,Kang L

    更新日期:2018-05-08 00:00:00

  • The origin of rare alkali metals in geothermal fluids of southern Tibet, China: A silicon isotope perspective.

    abstract::Geothermal waters from the Semi, Dagejia and Kawu hot springs in the Shiquanhe-Yarlung Zangbo geothermal field of southern Tibet (China) are highly enriched in rare alkali metals (RAM). However, the enrichment mechanism is still hotly debated. Here, we report the first silicon isotope data of these geothermal waters t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44249-5

    authors: Wang W,Wei HZ,Jiang SY,Tan HB,Eastoe CJ,Williams-Jones AE,Hohl SV,Wu HP

    更新日期:2019-05-27 00:00:00

  • Quantifying the Pathway and Predicting Spontaneous Emulsification during Material Exchange in a Two Phase Liquid System.

    abstract::Kinetic restriction of a thermodynamically favourable equilibrium is a common theme in materials processing. The interfacial instability in systems where rate of material exchange is far greater than the mass transfer through respective bulk phases is of specific interest when tracking the transient interfacial area, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14638-9

    authors: Spooner S,Rahnama A,Warnett JM,Williams MA,Li Z,Sridhar S

    更新日期:2017-10-30 00:00:00

  • Chemical signatures and new drug targets for gametocytocidal drug development.

    abstract::Control of parasite transmission is critical for the eradication of malaria. However, most antimalarial drugs are not active against P. falciparum gametocytes, responsible for the spread of malaria. Consequently, patients can remain infectious for weeks after the clearance of asexual parasites and clinical symptoms. H...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep03743

    authors: Sun W,Tanaka TQ,Magle CT,Huang W,Southall N,Huang R,Dehdashti SJ,McKew JC,Williamson KC,Zheng W

    更新日期:2014-01-17 00:00:00

  • Active structural acoustic illusions.

    abstract::We present active manipulation of the structural vibrations of an elastic body to generate an acoustic illusion. The resultant illusion misrepresents the nature, size and number of objects in the exterior acoustic domain. We demonstrate our technique, herein termed active structural acoustic illusion, using an elastic...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-66398-8

    authors: Eggler D,Kessissoglou N

    更新日期:2020-06-17 00:00:00

  • Design methodology for a confocal imaging system using an objective microlens array with an increased working distance.

    abstract::In this study, a design methodology for a multi-optical probe confocal imaging system was developed. To develop an imaging system that has the required resolving power and imaging area, this study focused on a design methodology to create a scalable and easy-to-implement confocal imaging system. This system overcomes ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep33278

    authors: Choi W,Shin R,Lim J,Kang S

    更新日期:2016-09-12 00:00:00

  • Compact Shielding of Graphene Monolayer Leads to Extraordinary SERS-Active Substrate with Large-Area Uniformity and Long-Term Stability.

    abstract::Surface-enhanced Raman scattering (SERS) can significantly boost the inherently weak Raman scattering signal and provide detailed structural information and binding nature of the molecules on the surface. Despite the long history of this technology, SERS has yet to become a sophisticated analytical tool in practical a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep17167

    authors: Liu X,Wang J,Wu Y,Fan T,Xu Y,Tang L,Ying Y

    更新日期:2015-11-30 00:00:00

  • Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression.

    abstract::Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42310-x

    authors: Kehlmaier C,Zhang X,Georges A,Campbell PD,Thomson S,Fritz U

    更新日期:2019-04-09 00:00:00

  • ZFP226 is a novel artificial transcription factor for selective activation of tumor suppressor KIBRA.

    abstract::KIBRA has been suggested as a key regulator of the hippo pathway, regulating organ size, cell contact inhibition as well as tissue regeneration and tumorigenesis. Recently, alterations of KIBRA expression caused by promotor methylation have been reported for several types of cancer. Our current study aimed to design a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-22600-6

    authors: Schelleckes K,Schmitz B,Lenders M,Mewes M,Brand SM,Brand E

    更新日期:2018-03-09 00:00:00

  • Time dynamics of quantum coherence and monogamy in a non-Markovian environment.

    abstract::The time evolution of the distribution and shareability of quantum coherence of a tripartite system in a non-Markovian environment is examined. The total coherence can be decomposed into various contributions, ranging from local, global bipartite and global tripartite, which characterize the type of state. We identify...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39027-2

    authors: Radhakrishnan C,Chen PW,Jambulingam S,Byrnes T,Ali MM

    更新日期:2019-02-20 00:00:00

  • Assessing the effect on the generation of environmentally persistent free radicals in hydrothermal carbonization of sewage sludge.

    abstract::Environmentally persistent free radicals (EPFRs) have attracted increasing research interest in recent years. Herein, the generation of EPFRs during the hydrothermal carbonization of sewage sludge (SS) was studied. First, the surface morphology, functional groups, constituent elements and free radicals were characteri...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-53781-3

    authors: Zhu Y,Wei J,Liu Y,Liu X,Li J,Zhang J

    更新日期:2019-11-19 00:00:00

  • Natural Erosion of Sandstone as Shape Optimisation.

    abstract::Natural arches, pillars and other exotic sandstone formations have always been attracting attention for their unusual shapes and amazing mechanical balance that leave a strong impression of intelligent design rather than the result of a stochastic process. It has been recently demonstrated that these shapes could have...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17777-1

    authors: Ostanin I,Safonov A,Oseledets I

    更新日期:2017-12-11 00:00:00

  • DNA methylation landscape of ocular tissue relative to matched peripheral blood.

    abstract::Epigenetic variation is implicated in a range of non-communicable diseases, including those of the eye. However, investigating the role of epigenetic variation in central tissues, such as eye or brain, remains problematic and peripheral tissues are often used as surrogates. In this study, matched human blood and eye t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46330

    authors: Hewitt AW,Januar V,Sexton-Oates A,Joo JE,Franchina M,Wang JJ,Liang H,Craig JE,Saffery R

    更新日期:2017-04-13 00:00:00

  • Associations between adipose tissue volume and small molecules in plasma and urine among asymptomatic subjects from the general population.

    abstract::Obesity is one of the major risk factor for cardiovascular and metabolic diseases. A disproportional accumulation of fat at visceral (VAT) compared to subcutaneous sites (SAT) has been suspected as a key detrimental event. We used non-targeted metabolomics profiling to reveal metabolic pathways associated with higher ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-58430-8

    authors: Otto L,Budde K,Kastenmüller G,Kaul A,Völker U,Völzke H,Adamski J,Kühn JP,Krumsiek J,Artati A,Nauck M,Friedrich N,Pietzner M

    更新日期:2020-01-30 00:00:00

  • A comparative analysis using flowmeter, laser-Doppler |spectrophotometry, and indocyanine green-videoangiography for detection of vascular stenosis in free flaps.

    abstract::The effects of gradual vascular occlusion on the blood supply of perfused areas are poorly described. Information relating to the comparison of flap monitoring techniques is lacking. Varying stenotic conditions (0%, 25%, 50%, 75% and 100%) were generated on purpose at the A. and V. femoralis in the rat model. Analyses...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-57777-2

    authors: Mücke T,Hapfelmeier A,Schmidt LH,Fichter AM,Kanatas A,Wolff KD,Ritschl LM

    更新日期:2020-01-22 00:00:00

  • Magnetic anisotropy, unusual hysteresis and putative "up-up-down" magnetic structure in EuTAl4Si2 (T = Rh and Ir).

    abstract::We present detailed investigations on single crystals of quaternary EuRhAl4Si2 and EuIrAl4Si2. The two compounds order antiferromagnetically at TN1 = 11.7 and 14.7 K, respectively, each undergoing two magnetic transitions. The magnetic properties in the ordered state present a large anisotropy despite Eu(2+)being an S...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep12021

    authors: Maurya A,Thamizhavel A,Dhar SK,Bonville P

    更新日期:2015-07-09 00:00:00

  • Novel Programmable Shape Memory Polystyrene Film: A Thermally Induced Beam-power Splitter.

    abstract::Micro/nanophotonic structures that are capable of optical wave-front shaping are implemented in optical waveguides and passive optical devices to alter the phase of the light propagating through them. The beam division directions and beam power distribution depend on the design of the micro/nanostructures. The ultimat...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep44333

    authors: Li P,Han Y,Wang W,Liu Y,Jin P,Leng J

    更新日期:2017-03-09 00:00:00