Foreign transcriptional enhancers in yeast. I. Interactions of papovavirus transcriptional enhancers and a quiescent pseudopromoter on supercoiled plasmids.


:We have constructed simple test-plasmids to study transcriptional enhancers in yeast. In this paper the reporter-gene is a plasmid borne deletion-substitution derivative (his-del4) of the Saccharomyces cerevisiae HIS3 gene in which the native promoter has been replaced by a dormant, susceptible pseudopromoter. We investigate the function in yeast of foreign control elements, the polyomavirus enhancer and some of its derivatives, inserted in either orientation at the 3' or 5' ends of the reporter gene. The polyoma enhancer (and, although less thoroughly studied, the SV40 enhancer) will strongly activate transcription from latent start sites within the pseudo-promoter sequence. The rules we draw for the polyoma enhancer effect in yeast are, with a few interesting exceptions, remarkably similar to those discovered by experimentation in mammalian cells.


Nucleic Acids Res


Nucleic acids research


Ciaramella M,Sacco M,Pulitzer JF




Has Abstract


1988-09-26 00:00:00












  • Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA.

    abstract::Influenza viruses have a segmented viral RNA (vRNA) genome, which is replicated by the viral RNA-dependent RNA polymerase (RNAP). Replication initiates on the vRNA 3' terminus, producing a complementary RNA (cRNA) intermediate, which serves as a template for the synthesis of new vRNA. RNAP structures show the 3' termi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Robb NC,Te Velthuis AJ,Wieneke R,Tampé R,Cordes T,Fodor E,Kapanidis AN

    更新日期:2016-12-01 00:00:00

  • Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase by deletion mutagenesis.

    abstract::The integrase (IN) protein of human immunodeficiency virus type 1 (HIV-1) catalyzes site-specific cleavage of 2 bases from the viral long terminal repeat (LTR) sequence yet it binds DNA with little DNA sequence specificity. We have previously demonstrated that the C-terminal half of IN (amino acids 154-288) possesses ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Woerner AM,Marcus-Sekura CJ

    更新日期:1993-07-25 00:00:00

  • Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes.

    abstract::We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Nazarenko I,Pires R,Lowe B,Obaidy M,Rashtchian A

    更新日期:2002-05-01 00:00:00

  • Exposition of a family of RNA m(5)C methyltransferases from searching genomic and proteomic sequences.

    abstract::The Escherichia coli fmu gene product has recently been determined to be the 16S rRNA m(5)C 967 methyltransferase. As such, Fmu represents the first protein identified as an S -adenosyl-L-methionine (AdoMet)- dependent RNA m(5)C methyltransferase whose amino acid sequence is known. Using the amino acid sequence of Fmu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Reid R,Greene PJ,Santi DV

    更新日期:1999-08-01 00:00:00

  • A web-based genotyping resource for viral sequences.

    abstract::The Genotyping tool at the National Center for Biotechnology Information is a web-based program that identifies the genotype (or subtype) of recombinant or non-recombinant viral nucleotide sequences. It works by using BLAST to compare a query sequence to a set of reference sequences for known genotypes. Predefined ref...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rozanov M,Plikat U,Chappey C,Kochergin A,Tatusova T

    更新日期:2004-07-01 00:00:00

  • CAF-1-induced oligomerization of histones H3/H4 and mutually exclusive interactions with Asf1 guide H3/H4 transitions among histone chaperones and DNA.

    abstract::Anti-silencing function 1 (Asf1) and Chromatin Assembly Factor 1 (CAF-1) chaperone histones H3/H4 during the assembly of nucleosomes on newly replicated DNA. To understand the mechanism of histone H3/H4 transfer among Asf1, CAF-1 and DNA from a thermodynamic perspective, we developed and employed biophysical approache...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Liu WH,Roemer SC,Port AM,Churchill ME

    更新日期:2012-12-01 00:00:00

  • DnaG interacts with a linker region that joins the N- and C-domains of DnaB and induces the formation of 3-fold symmetric rings.

    abstract::Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Thirlway J,Turner IJ,Gibson CT,Gardiner L,Brady K,Allen S,Roberts CJ,Soultanas P

    更新日期:2004-06-01 00:00:00

  • Sequence requirement for specific interaction of an enhancer binding protein (EBP1) with DNA.

    abstract::Short DNA sequence motifs have been identified in viral and cellular enhancers which represent the binding sites for a variety of trans- acting factors. One such HeLa cell factor, EBP1, has been purified and shown to bind to sequences in the SV40 enhancer. The PRDII element in the human beta-interferon gene regulatory...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Clark L,Hay RT

    更新日期:1989-01-25 00:00:00

  • Physical map of Neurospora crassa mitochondrial DNA and its transcription unit for ribosomal RNA.

    abstract::A circular denaturation and restriction map of mitochondrial DNA from Neurospora crassa is presented. The map shows the position of all twelve fragments produced by restriction endonuclease Eco R I and the position of the largest Hin III fragment along the previously established map of AT-rich sequences. The two wild ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bernard U,Goldthwaite C,Küntzel H

    更新日期:1976-11-01 00:00:00

  • Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites.

    abstract::Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wang T,Tague N,Whelan SA,Dunlop MJ

    更新日期:2021-01-25 00:00:00

  • Histone modifications influence mediator interactions with chromatin.

    abstract::The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silence...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhu X,Zhang Y,Bjornsdottir G,Liu Z,Quan A,Costanzo M,Dávila López M,Westholm JO,Ronne H,Boone C,Gustafsson CM,Myers LC

    更新日期:2011-10-01 00:00:00

  • Global regulation of alternative splicing during myogenic differentiation.

    abstract::Recent genome-wide analyses have elucidated the extent of alternative splicing (AS) in mammals, often focusing on comparisons of splice isoforms between differentiated tissues. However, regulated splicing changes are likely to be important in biological transitions such as cellular differentiation, or response to envi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bland CS,Wang ET,Vu A,David MP,Castle JC,Johnson JM,Burge CB,Cooper TA

    更新日期:2010-11-01 00:00:00

  • Designating eukaryotic orthology via processed transcription units.

    abstract::Orthology is a widely used concept in comparative and evolutionary genomics. In addition to prokaryotic orthology, delineating eukaryotic orthology has provided insight into the evolution of higher organisms. Indeed, many eukaryotic ortholog databases have been established for this purpose. However, unlike prokaryotes...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Ho MR,Jang WJ,Chen CH,Ch'ang LY,Lin WC

    更新日期:2008-06-01 00:00:00

  • Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch.

    abstract::Applications of conditional gene expression, whether for therapeutic or basic research purposes, are increasingly requiring mammalian gene control systems that exhibit far tighter control properties. While numerous approaches have been used to improve the widely used Tet-regulatory system, many applications, particula...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Greber D,El-Baba MD,Fussenegger M

    更新日期:2008-09-01 00:00:00

  • DNA sequence of Rhizobium trifolii nodulation genes reveals a reiterated and potentially regulatory sequence preceding nodABC and nodFE.

    abstract::The Rhizobium trifolii nod genes required for host-specific nodulation of clovers are located on 14 kb of Sym (symbiotic) plasmid DNA. Analysis of the nucleotide sequence of a 3.7 kb portion of this region has revealed open reading frames corresponding to the nodABCDEF genes. A DNA sequencing technique, using primer e...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schofield PR,Watson JM

    更新日期:1986-04-11 00:00:00

  • Human protein reference database--2006 update.

    abstract::Human Protein Reference Database (HPRD) ( was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mishra GR,Suresh M,Kumaran K,Kannabiran N,Suresh S,Bala P,Shivakumar K,Anuradha N,Reddy R,Raghavan TM,Menon S,Hanumanthu G,Gupta M,Upendran S,Gupta S,Mahesh M,Jacob B,Mathew P,Chatterjee P,Arun KS,Sharma S,Chand

    更新日期:2006-01-01 00:00:00

  • Analysis of the autonomous replication behavior in human cells of the dihydrofolate reductase putative chromosomal origin of replication.

    abstract::Chinese hamster genomic DNA sequences from the region downstream of the dihydrofolate reductase (DHFR) gene reported to contain a chromosomal origin of bidirectional DNA replication (OBR-1) were tested for their ability to support autonomous DNA replication in human cells. A 13.3 kilobase fragment containing OBR-1 and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Caddle MS,Calos MP

    更新日期:1992-11-25 00:00:00

  • Actin and myosin contribute to mammalian mitochondrial DNA maintenance.

    abstract::Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding no...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Reyes A,He J,Mao CC,Bailey LJ,Di Re M,Sembongi H,Kazak L,Dzionek K,Holmes JB,Cluett TJ,Harbour ME,Fearnley IM,Crouch RJ,Conti MA,Adelstein RS,Walker JE,Holt IJ

    更新日期:2011-07-01 00:00:00

  • A G-tract element in apoptotic agents-induced alternative splicing.

    abstract::Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hai Y,Cao W,Liu G,Hong SP,Elela SA,Klinck R,Chu J,Xie J

    更新日期:2008-06-01 00:00:00

  • In vitro site-directed mutagenesis with synthetic DNA oligonucleotides yields unexpected deletions and insertions at high frequency.

    abstract::We have used in vitro site-directed mutagenesis with synthetic DNA oligonucleotides to introduce single nucleotide mutations in yeast mtDNA. In addition to the expected DNA alterations we also recovered with high frequency mutants with large deletions and insertions which arose through interaction with the synthetic D...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Osinga KA,Van der Bliek AM,Van der Horst G,Groot Koerkamp MJ,Tabak HF,Veeneman GH,Van Boom JH

    更新日期:1983-12-20 00:00:00

  • p53-mediated DNA renaturation can mimic strand exchange.

    abstract::The process of strand exchange is considered to be the hallmark of DNA recombination. Proteins known to carry out such exchange are believed to operate via one or the other of two mechanisms. RecA-like proteins promote the formation of a three-stranded or triplex synaptic intermediate in which strand exchange occurs, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jean D,Gendron D,Delbecchi L,Bourgaux P

    更新日期:1997-10-15 00:00:00

  • In vitro DNA dependent synthesis of globin RNA sequences from erythroleukemic cell chromatin.

    abstract::Murine erythroleukemic cells in culture accumulate cytoplasmic globin mRNA during differentiation induced by dimethyl sulfoxide (DMSO)1. Chromatin was prepared from DMSO induced erythroleukemic cells that were transcribing globin RNA in order to determine whether in vitro synthesis of globin RNA sequences was possible...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Reff ME,Davidson RL

    更新日期:1979-01-01 00:00:00

  • Importance of the reverse Hoogsteen base pair 54-58 for tRNA function.

    abstract::To elucidate the general constraints imposed on the structure of the D- and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions of these loops were randomized. Analysis of the nucleotide sequences of the selected clones...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zagryadskaya EI,Doyon FR,Steinberg SV

    更新日期:2003-07-15 00:00:00

  • Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes.

    abstract::Direct labeling of RNA is an expedient method for labeling large quantities (e.g. micrograms) of target RNA for microarray analysis. We have developed an efficient labeling system that uses T4 RNA ligase to attach a 3'-biotinylated donor molecule to target RNA. Microarray analyses indicate that directly labeled RNA is...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cole K,Truong V,Barone D,McGall G

    更新日期:2004-06-17 00:00:00

  • Genetic organization of alpha-bungarotoxins from Bungarus multicinctus (Taiwan banded krait): evidence showing that the production of alpha-bungarotoxin isotoxins is not derived from edited mRNAs.

    abstract::Two genomic DNAs with a size of approximately 2.8 kb, isolated from the liver of Bungarus multicinctus (Taiwan banded krait), encode the precursors of the long neurotoxins, alpha-Bgt(A31) and alpha-Bgt(V31), respectively. Both genes share virtually identical overall organization with three exons separated by two intro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chang L,Lin S,Huang H,Hsiao M

    更新日期:1999-10-15 00:00:00

  • Noncoding RNAs database (ncRNAdb).

    abstract::The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Szymanski M,Erdmann VA,Barciszewski J

    更新日期:2007-01-01 00:00:00

  • Induction of double-strand breaks by S1 nuclease, mung bean nuclease and nuclease P1 in DNA containing abasic sites and nicks.

    abstract::Defined DNA substrates containing discrete abasic sites or paired abasic sites set 1, 3, 5 and 7 bases apart on opposite strands were constructed to examine the reactivity of S1, mung bean and P1 nucleases towards abasic sites. None of the enzymes acted on the substrate containing discrete abasic sites. Under conditio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chaudhry MA,Weinfeld M

    更新日期:1995-10-11 00:00:00

  • Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE.

    abstract::Perturbation and time-course data sets, in combination with computational approaches, can be used to infer transcriptional regulatory networks which ultimately govern the developmental pathways and responses of cells. Here, we individually knocked down the four transcription factors PU.1, IRF8, MYB and SP1 in the huma...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Vitezic M,Lassmann T,Forrest AR,Suzuki M,Tomaru Y,Kawai J,Carninci P,Suzuki H,Hayashizaki Y,Daub CO

    更新日期:2010-12-01 00:00:00

  • 'Single addition' and 'transnucleotidation' reactions catalyzed by polynucleotide phosphorylase. Effect of enzymatic removal of inorganic phosphate during reaction.

    abstract::The reaction of the tetranucleotide, pA-A(2)-A, with 2'(3')-0-(alpha-methoxyethyl)uridine 5'-diphosphate, Mg(2+) ions, and M. luteus polynucleotide phosphorylase followed by mild acid treatment to remove the blocking groups results in a 49% yield of the desired single addition product, pA-A(3)-U, together with smaller...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sninsky JJ,Bennett GN,Gilham PT

    更新日期:1974-12-01 00:00:00

  • In vitro selection to identify determinants in tRNA for Bacillus subtilis tyrS T box antiterminator mRNA binding.

    abstract::The T box transcription antitermination regulatory system, found in Gram-positive bacteria, is dependent on a complex set of interactions between uncharged tRNA and the 5'-untranslated mRNA leader region of the regulated gene. One of these interactions involves the base pairing of the acceptor end of cognate tRNA with...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fauzi H,Jack KD,Hines JV

    更新日期:2005-05-06 00:00:00