当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Transcription in vivo directed by consensus sequences of E.coli promoters: their context heavily affects efficiencies and start sites.

Transcription in vivo directed by consensus sequences of E.coli promoters: their context heavily affects efficiencies and start sites.

Abstract：

:We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer linking them is AT or GC rich, or is as short as 14 bp or as large as 26 bp (standard size 17 bp). However, we find that the context influences transcription efficiency by as much as an order of magnitude, and is able to scatter transcription start sites over a region of as much as 30 bp, including start sites within a CH or even between the two sequences of the CH pair. The results demonstrate that, although the CH pair can be sufficient for directing transcription by E.coli RNAP, important determinants for promoter activity are at least in part contained in the context of the consensus sequences; they advocate a synergic interplay of signals borne by the CH pair and its context, extending over all parts of the promoter sequence. A two-step model is proposed, in which properly located consensus sequences provide RNAP with facilities required for stereospecific docking along the promoter sequence; the result would be a sharp change in the local environment of the double helix inducing local isothermal unwinding. The size of the loop (related to the AT constraint in the promoter) and the extend of the environmental change required for unwinding would determine the rate of transcriptionally competent complex formation, positioning and grouping of start sites.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Jacquet MA,Reiss C

doi

10.1093/nar/18.5.1137

subject

Has Abstract

pub_date

1990-03-11 00:00:00

pages

1137-43

issue

5

eissn

0305-1048

issn

1362-4962

journal_volume

18

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Genetic organization of the ribosomal transcription units of the yeast Saccharomyces carlsbergensis.

    abstract：:The genetic organization of the multiple ribosomal transcription units (RTUs) on the genome of the yeast Saccharomyces carlsbergensis was studied by electron microscopy of purified ribosomal DNA hybridized to 26S rRNA using the R-loop technique (Thomas, M., White, R.L. and Davis, R.W. (1973) Proc. Natl. Acad. Sci. U.S...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/5.8.2801

    authors： Meyerink JH,Retèl J,Raué HA,Planta RJ

    更新日期：1978-08-01 00:00:00

  • The yeast transcription factor genes YAP1 and YAP2 are subject to differential control at the levels of both translation and mRNA stability.

    abstract：:Two forms of post-transcriptional control direct differential expression of the Saccharomyces cerevisiae genes encoding the AP1-like transcription factors Yap1p and Yap2p. The mRNAs of these genes contain respectively one (YAP1 uORF) and two (YAP2 uORF1 and uORF2) upstream open reading frames. uORF-mediated modulation...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.5.1150

    authors： Vilela C,Linz B,Rodrigues-Pousada C,McCarthy JE

    更新日期：1998-03-01 00:00:00

  • SRPDB (Signal Recognition Particle Database).

    abstract：:Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogenetically-sup...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.1.169

    authors： Gorodkin J,Knudsen B,Zwieb C,Samuelsson T

    更新日期：2001-01-01 00:00:00

  • Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.

    abstract：:Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks223

    authors： Holub P,Lalakova J,Cerna H,Pasulka J,Sarazova M,Hrazdilova K,Arce MS,Hobor F,Stefl R,Vanacova S

    更新日期：2012-07-01 00:00:00

  • ProTox-II: a webserver for the prediction of toxicity of chemicals.

    abstract：:Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky318

    authors： Banerjee P,Eckert AO,Schrey AK,Preissner R

    更新日期：2018-07-02 00:00:00

  • Loss of EZH2 results in precocious mammary gland development and activation of STAT5-dependent genes.

    abstract：:Establishment and differentiation of mammary alveoli during pregnancy are controlled by prolactin through the transcription factors STAT5A and STAT5B (STAT5), which also regulate temporal activation of mammary signature genes. This study addressed the question whether the methyltransferase and transcriptional co-activ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv776

    authors： Yoo KH,Oh S,Kang K,Hensel T,Robinson GW,Hennighausen L

    更新日期：2015-10-15 00:00:00

  • General method of rapid Smith/Birnstiel mapping adds for gap closure in shotgun microbial genome sequencing projects: application to Pseudomonas putida KT2440.

    abstract：:A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/29.22.e110

    authors： Weinel C,Tümmler B,Hilbert H,Nelson KE,Kiewitz C

    更新日期：2001-11-15 00:00:00

  • Phospho.ELM: a database of phosphorylation sites--update 2011.

    abstract：:The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threoni...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkq1104

    authors： Dinkel H,Chica C,Via A,Gould CM,Jensen LJ,Gibson TJ,Diella F

    更新日期：2011-01-01 00:00:00

  • Ribosomal RNA cleavage, nuclease activation and 2-5A(ppp(A2'p)nA) in interferon-treated cells.

    abstract：:Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyt...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/9.7.1571

    authors： Wreschner DH,James TC,Silverman RH,Kerr IM

    更新日期：1981-04-10 00:00:00

  • Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing.

    abstract：:Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkx1003

    authors： Nguyen NTT,Vincens P,Roest Crollius H,Louis A

    更新日期：2018-01-04 00:00:00

  • Structure of the 70S ribosome from human pathogen Staphylococcus aureus.

    abstract：:Comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. Although the importance of such features may be less obvious within more closely rela...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkw933

    authors： Khusainov I,Vicens Q,Bochler A,Grosse F,Myasnikov A,Ménétret JF,Chicher J,Marzi S,Romby P,Yusupova G,Yusupov M,Hashem Y

    更新日期：2016-12-01 00:00:00

  • Global coordination in adaptation to gene rewiring.

    abstract：:Gene rewiring is a common evolutionary phenomenon in nature that may lead to extinction for living organisms. Recent studies on synthetic biology demonstrate that cells can survive genetic rewiring. This survival (adaptation) is often linked to the stochastic expression of rewired genes with random transcriptional cha...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1366

    authors： Murakami Y,Matsumoto Y,Tsuru S,Ying BW,Yomo T

    更新日期：2015-01-01 00:00:00

  • The relationship of potential G-quadruplex sequences in cis-upstream regions of the human genome to SP1-binding elements.

    abstract：:We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn078

    authors： Todd AK,Neidle S

    更新日期：2008-05-01 00:00:00

  • Gene organization of the small subunit of human calcium-activated neutral protease.

    abstract：:The gene for the small subunit of human calcium-activated neutral protease was isolated and sequenced. It is 11 kb long and comprises 11 exons. No TATA or CAT box was found upstream of the possible transcription initiation sites, but there are three so-called G-C box sequences and one G-C box-like sequence, which are ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.22.8805

    authors： Miyake S,Emori Y,Suzuki K

    更新日期：1986-11-25 00:00:00

  • Allosteric DNAzyme-based DNA logic circuit: operations and dynamic analysis.

    abstract：:Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky1245

    authors： Zheng X,Yang J,Zhou C,Zhang C,Zhang Q,Wei X

    更新日期：2019-02-20 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

  • Protein synthesis in rabbit reticulocytes: characteristics of CO-eIF-2 protein complex.

    abstract：:A high molecular weight reticulocyte protein factor, named Co-eIF-2, contains Co-eIF-2A, Co-eIF-2B, and Co-eIF-2C activities and stimulates Met-tRNAf binding to eIF-2 both in the presence and absence of Mg2+. Some characteristics of this stimulation in the absence of Mg2+ are: (1) Stimulation is most pronounced at low...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.20.6501

    authors： Bagchi MK,Banerjee AC,Roy R,Chakrabarty I,Gupta NK

    更新日期：1982-10-25 00:00:00

  • The non-autonomous retrotransposon SVA is trans-mobilized by the human LINE-1 protein machinery.

    abstract：:SINE-VNTR-Alu (SVA) elements are non-autonomous, hominid-specific non-LTR retrotransposons and distinguished by their organization as composite mobile elements. They represent the evolutionarily youngest, currently active family of human non-LTR retrotransposons, and sporadically generate disease-causing insertions. S...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkr863

    authors： Raiz J,Damert A,Chira S,Held U,Klawitter S,Hamdorf M,Löwer J,Strätling WH,Löwer R,Schumann GG

    更新日期：2012-02-01 00:00:00

  • Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development.

    abstract：:Intron retention (IR) has been proposed to modulate the delay between transcription and translation. Here, we provide an exhaustive characterization of IR in differentiated white blood cells from both the myeloid and lymphoid lineage where we observed highest levels of IR in monocytes and B-cells, in addition to previ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz1180

    authors： Ullrich S,Guigó R

    更新日期：2020-02-20 00:00:00

  • Single-cell paired-end genome sequencing reveals structural variation per cell cycle.

    abstract：:The nature and pace of genome mutation is largely unknown. Because standard methods sequence DNA from populations of cells, the genetic composition of individual cells is lost, de novo mutations in cells are concealed within the bulk signal and per cell cycle mutation rates and mechanisms remain elusive. Although sing...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt345

    authors： Voet T,Kumar P,Van Loo P,Cooke SL,Marshall J,Lin ML,Zamani Esteki M,Van der Aa N,Mateiu L,McBride DJ,Bignell GR,McLaren S,Teague J,Butler A,Raine K,Stebbings LA,Quail MA,D'Hooghe T,Moreau Y,Futreal PA,Stratton MR

    更新日期：2013-07-01 00:00:00

  • Displacement of a DNA binding protein by Dda helicase.

    abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkl369

    authors： Byrd AK,Raney KD

    更新日期：2006-05-31 00:00:00

  • Validation of kinetics similarity in qPCR.

    abstract：:Quantitative real-time PCR (qPCR) is the method of choice for specific and sensitive quantification of nucleic acids. However, data validation is still a major issue, partially due to the complex effect of PCR inhibition on the results. If undetected PCR inhibition may severely impair the accuracy and sensitivity of r...

    journal_title：Nucleic acids research

    pub_type： 杂志文章,评审

    doi：10.1093/nar/gkr778

    authors： Bar T,Kubista M,Tichopad A

    更新日期：2012-02-01 00:00:00

  • A revised secondary structure model for the 3'-end of hepatitis B virus pregenomic RNA.

    abstract：:The polymerase encoded by human hepatitis B virus, which has reverse transcriptase and RNase H activity, binds to its pregenomic RNA template in a two-step process involving a terminal redundancy. Both first strand and second strand DNA synthesis involve primer translocation and second strand synthesis involves a temp...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/24.17.3295

    authors： Kidd AH,Kidd-Ljunggren K

    更新日期：1996-09-01 00:00:00

  • DNA replication regulated by the priming promoter.

    abstract：:ColE1 derivative plasmids were constructed in which the natural promoter that primes replication or, in addition, the region coding for the RNA I control element had been deleted. In all of these molecules priming of the origin was effected by read-through transcription from constitutive or inducible (lacUV5) promoter...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/12.6.2641

    authors： Panayotatos N

    更新日期：1984-03-26 00:00:00

  • Dehydromonocrotaline generates sequence-selective N-7 guanine alkylation and heat and alkali stable multiple fragment DNA crosslinks.

    abstract：:Monocrotaline is a pyrrolizidine alkaloid known to cause toxicity in humans and animals. Its mechanism of biological action is still unclear although DNA crosslinking has been suggested to a play a role in its activity. In this study we found that an active metabolite of monocrotaline, dehydromonocrotaline (DHM), alky...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/26.23.5441

    authors： Pereira TN,Webb RI,Reilly PE,Seawright AA,Prakash AS

    更新日期：1998-12-01 00:00:00

  • BIOSMILE web search: a web application for annotating biomedical entities and relations.

    abstract：:BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn319

    authors： Dai HJ,Huang CH,Lin RT,Tsai RT,Hsu WL

    更新日期：2008-07-01 00:00:00

  • Construction of a chromosome-enriched HpaII library from flow-sorted wheat chromosomes.

    abstract：:We report here the first successful generation of a chromosome-enriched library from flow sorted plant chromosomes. Chromosomes with a characteristic DNA content (a peak) were sorted from a synchronized cell culture (TaKB1, derived from Triticum aestivum). A HpaII library was constructed from the sorted chromosomes an...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/20.8.1897

    authors： Wang ML,Leitch AR,Schwarzacher T,Heslop-Harrison JS,Moore G

    更新日期：1992-04-25 00:00:00

  • Specifically alkylated DNA fragments. Synthesis and physical characterization of d[CGC(O6Me)GCG] and d[CGT(O6Me)GCG].

    abstract：:Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.10.3393

    authors： Kuzmich S,Marky LA,Jones RA

    更新日期：1983-05-25 00:00:00

  • Site-specific fluorescence dynamics in an RNA 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function.

    abstract：:RNA thermometers control the translation of several heat shock and virulence genes by their temperature-sensitive structural transitions. Changes in the structure and dynamics of MiniROSE RNA, which regulates translation in the temperature range of 20-45°C, were studied by site specifically replacing seven adenine res...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1264

    authors： Narayan S,Kombrabail MH,Das S,Singh H,Chary KV,Rao BJ,Krishnamoorthy G

    更新日期：2015-01-01 00:00:00

  • 3did: a catalog of domain-based interactions of known three-dimensional structure.

    abstract：:The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Prote...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt887

    authors： Mosca R,Céol A,Stein A,Olivella R,Aloy P

    更新日期：2014-01-01 00:00:00