Antisense-induced ribosomal frameshifting.

Abstract:

:Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2 fusion protein. Such programmed frameshifting is commonly utilized as a gene expression mechanism in viruses that infect eukaryotic cells and in a subset of cellular genes. RNA secondary structures, consisting of pseudoknots or stem-loops, located downstream of the shift site often act as cis-stimulators of frameshifting. Here, we demonstrate for the first time that antisense oligonucleotides can functionally mimic these RNA structures to induce +1 ribosomal frameshifting when annealed downstream of the frameshift site, UCC UGA. Antisense-induced shifting of the ribosome into the +1 reading frame is highly efficient in both rabbit reticulocyte lysate translation reactions and in cultured mammalian cells. The efficiency of antisense-induced frameshifting at this site is responsive to the sequence context 5' of the shift site and to polyamine levels.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Henderson CM,Anderson CB,Howard MT

doi

10.1093/nar/gkl531

subject

Has Abstract

pub_date

2006-01-01 00:00:00

pages

4302-10

issue

15

eissn

0305-1048

issn

1362-4962

pii

gkl531

journal_volume

34

pub_type

杂志文章
  • Complementarity-directed RNA dimer-linkage promotes retroviral recombination in vivo.

    abstract::Retroviral particles contain a dimeric RNA genome, which serves as template for the generation of double-stranded DNA by reverse transcription. Transfer between RNA strands during DNA synthesis is governed by both sequence similarity between templates and structural features of the dimeric RNA. A kissing hairpin, beli...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh159

    authors: Mikkelsen JG,Rasmussen SV,Pedersen FS

    更新日期:2004-01-09 00:00:00

  • Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals.

    abstract::We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar struc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa629

    authors: Cabaj MK,Dominiak PM

    更新日期:2020-09-04 00:00:00

  • Multivariate curve resolution: a powerful tool for the analysis of conformational transitions in nucleic acids.

    abstract::A successful application is reported of the multivariate curve resolution alternating least-squares method (MCR-ALS) for the analysis of nucleic acid melting and salt-induced transitions. Under conditions where several structures co-exist in a conformational equilibrium, MCR-ALS analysis of the UV and circular dichroi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnf091

    authors: Jaumot J,Escaja N,Gargallo R,González C,Pedroso E,Tauler R

    更新日期:2002-09-01 00:00:00

  • PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.

    abstract::PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw415

    authors: Sriyudthsak K,Mejia RF,Arita M,Hirai MY

    更新日期:2016-07-08 00:00:00

  • Pharos: Collating protein information to shed light on the druggable genome.

    abstract::The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Genome (IDG) program was initiated in 2014, has the goal of developing experimental...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1072

    authors: Nguyen DT,Mathias S,Bologa C,Brunak S,Fernandez N,Gaulton A,Hersey A,Holmes J,Jensen LJ,Karlsson A,Liu G,Ma'ayan A,Mandava G,Mani S,Mehta S,Overington J,Patel J,Rouillard AD,Schürer S,Sheils T,Simeonov A,Sklar L

    更新日期:2017-01-04 00:00:00

  • A cis-encoded sRNA, Hfq and mRNA secondary structure act independently to suppress IS200 transposition.

    abstract::IS200 is found throughout Enterobacteriaceae and transposes at a notoriously low frequency. In addition to the transposase protein (TnpA), IS200 encodes an uncharacterized Hfq-binding sRNA that is encoded opposite to the tnpA 5'UTR. In the current work we asked if this sRNA represses tnpA expression. We show here that...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv584

    authors: Ellis MJ,Trussler RS,Haniford DB

    更新日期:2015-07-27 00:00:00

  • Targeted mutagenesis of DNA with alkylating RecA assisted oligonucleotides.

    abstract::Site-specific mutation was demonstrated in a shuttle vector system using nitrogen mustard-conjugated oligodeoxyribonucleotides (ODNs). Plasmid DNA was modified in vitro by ODNs containing all four DNA bases in the presence of Escherichia coli RecA protein. Up to 50% of plasmid molecules were alkylated in the targeted ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.24.e38

    authors: Singer MJ,Podyminogin MA,Metcalf MA,Reed MW,Brown DA,Gamper HB,Meyer RB,Wydro RM

    更新日期:1999-12-15 00:00:00

  • Cloning the gyrA gene of Bacillus subtilis.

    abstract::We have isolated an eight kilobase fragment of Bacillus subtilis DNA by specific integration and excision of a plasmid containing a sequence adjacent to ribosomal operon rrn O. The genetic locus of the cloned fragment was verified by linkage of the integrated vector to nearby genetic markers using both transduction an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.15.6307

    authors: Lampe MF,Bott KF

    更新日期:1984-08-10 00:00:00

  • DmTTF, a novel mitochondrial transcription termination factor that recognises two sequences of Drosophila melanogaster mitochondrial DNA.

    abstract::Using a combination of bioinformatic and molecular biology approaches a Drosophila melanogaster protein, DmTTF, has been identified, which exhibits sequence and structural similarity with two mitochondrial transcription termination factors, mTERF (human) and mtDBP (sea urchin). Import/processing assays indicate that D...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg272

    authors: Roberti M,Polosa PL,Bruni F,Musicco C,Gadaleta MN,Cantatore P

    更新日期:2003-03-15 00:00:00

  • Crystal structure of the 5hmC specific endonuclease PvuRts1I.

    abstract::PvuRts1I is a prototype for a larger family of restriction endonucleases that cleave DNA containing 5-hydroxymethylcytosine (5hmC) or 5-glucosylhydroxymethylcytosine (5ghmC), but not 5-methylcytosine (5mC) or cytosine. Here, we report a crystal structure of the enzyme at 2.35 Å resolution. Although the protein has bee...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku186

    authors: Kazrani AA,Kowalska M,Czapinska H,Bochtler M

    更新日期:2014-05-01 00:00:00

  • Ensembl 2018.

    abstract::The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1098

    authors: Zerbino DR,Achuthan P,Akanni W,Amode MR,Barrell D,Bhai J,Billis K,Cummins C,Gall A,Girón CG,Gil L,Gordon L,Haggerty L,Haskell E,Hourlier T,Izuogu OG,Janacek SH,Juettemann T,To JK,Laird MR,Lavidas I,Liu Z,Lovel

    更新日期:2018-01-04 00:00:00

  • Action of pancreatic DNase: requirements for activation of DNA as a template-primer for DNA polymerase.

    abstract::Pancreatic DNase requires both Ca2+ and Mg2+ for its activity as measured by formation of an activated DNA template for in vitro DNA polymerase alpha assay and by the hyperchromic shift. Mn2+ can partially satisfy the Mg2+ requirement of the DNase for activation of DNA but the resulting template is only 50% as active ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.8.2641

    authors: Baril E,Mitchener J,Lee L,Baril B

    更新日期:1977-08-01 00:00:00

  • Function of TFIIIC, RNA polymerase III initiation factor, in activation and repression of tRNA gene transcription.

    abstract::Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC d...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky656

    authors: Ciesla M,Skowronek E,Boguta M

    更新日期:2018-10-12 00:00:00

  • CAG*CTG repeat instability in cultured human astrocytes.

    abstract::Cells of the central nervous system (CNS) are prone to the devastating consequences of trinucleotide repeat (TNR) expansion. Some CNS cells, including astrocytes, show substantial TNR instability in affected individuals. Since astrocyte enrichment occurs in brain regions sensitive to neurodegeneration and somatic TNR ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl614

    authors: Farrell BT,Lahue RS

    更新日期:2006-01-01 00:00:00

  • Packaging of DNA by shell crosslinked nanoparticles.

    abstract::We demonstrate compaction of DNA with nanoscale biomimetic constructs which are robust synthetic analogs of globular proteins. These constructs are approximately 15 nm in diameter, shell crosslinked knedel-like (SCKs) nanoparticles, which are prepared by covalent stabilization of amphiphilic di-block co-polymer micell...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.14.2966

    authors: Thurmond KB 2nd,Remsen EE,Kowalewski T,Wooley KL

    更新日期:1999-07-15 00:00:00

  • A novel RNA molecular signature for activation of 2'-5' oligoadenylate synthetase-1.

    abstract::Human 2'-5' oligoadenylate synthetase-1 (OAS1) is central in innate immune system detection of cytoplasmic double-stranded RNA (dsRNA) and promotion of host antiviral responses. However, the molecular signatures that promote OAS1 activation are currently poorly defined. We show that the 3'-end polyuridine sequence of ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1289

    authors: Vachon VK,Calderon BM,Conn GL

    更新日期:2015-01-01 00:00:00

  • HuD binds to three AU-rich sequences in the 3'-UTR of neuroserpin mRNA and promotes the accumulation of neuroserpin mRNA and protein.

    abstract::Neuroserpin is an axonally secreted serine protease inhibitor expressed in the nervous system that protects neurons from ischemia-induced apoptosis. Mutant neuroserpin forms have been found polymerized in inclusion bodies in a familial autosomal encephalopathy causing dementia, or associated with epilepsy. Regulation ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/30.10.2202

    authors: Cuadrado A,Navarro-Yubero C,Furneaux H,Kinter J,Sonderegger P,Muñoz A

    更新日期:2002-05-15 00:00:00

  • A nucleobase-binding pocket in a viral RNA-dependent RNA polymerase contributes to elongation complex stability.

    abstract::The enterovirus 71 (EV71) 3Dpol is an RNA-dependent RNA polymerase (RdRP) that plays the central role in the viral genome replication, and is an important target in antiviral studies. Here, we report a crystal structure of EV71 3Dpol elongation complex (EC) at 1.8 Å resolution. The structure reveals that the 5'-end gu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz1170

    authors: Shi W,Ye HQ,Deng CL,Li R,Zhang B,Gong P

    更新日期:2020-02-20 00:00:00

  • Intracellular receptor-type transcription factor, LasR, contains a highly conserved amphipathic region which precedes the putative helix-turn-helix DNA binding motif.

    abstract::We have cloned and sequenced the lasR gene, which is involved in the transcriptional activation of several pathogenic factors, from Pseudomonas aeruginosa IFO3455 and PA103. These clones were predicted to be an open reading frame of 239 amino acids as reported for the PAO1 strain. There is only a single base change re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.18.3706

    authors: Fukushima J,Ishiwata T,Kurata M,You Z,Okuda K

    更新日期:1994-09-11 00:00:00

  • EVEREST: a collection of evolutionary conserved protein domains.

    abstract::Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several systems that identify protein domains and classify them into families. EVEREST, recently described in Portugaly et al. (2006) BMC Bioinformatic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl850

    authors: Portugaly E,Linial N,Linial M

    更新日期:2007-01-01 00:00:00

  • R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.

    abstract::The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to cu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv543

    authors: Cannone JJ,Sweeney BA,Petrov AI,Gutell RR,Zirbel CL,Leontis N

    更新日期:2015-07-01 00:00:00

  • An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides.

    abstract::DNA polymerases of the A and B families, and reverse transcriptases, share a common mechanism for preventing incorporation of ribonucleotides: a highly conserved active site residue obstructing the position that would be occupied by a 2' hydroxyl group on the incoming nucleotide. In the family Y (lesion bypass) polyme...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg417

    authors: DeLucia AM,Grindley ND,Joyce CM

    更新日期:2003-07-15 00:00:00

  • Regulation of the small regulatory RNA MicA by ribonuclease III: a target-dependent pathway.

    abstract::MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1239

    authors: Viegas SC,Silva IJ,Saramago M,Domingues S,Arraiano CM

    更新日期:2011-04-01 00:00:00

  • Inhibition of gene-specific repair of alkylation damage in cells depleted of poly(ADP-ribose) polymerase.

    abstract::The role of the enzyme poly(adenosine diphosphate-ribose) polymerase (PADPRP) in DNA repair at the level of the gene was investigated with human HeLa cells in which PADPRP antisense transcripts are inducible with dexamethasone. After such induction, the cellular content of PADPRP is reduced by 90%. DNA damage and its ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.22.4620

    authors: Stevnsner T,Ding R,Smulson M,Bohr VA

    更新日期:1994-11-11 00:00:00

  • K-tuple frequency in the human genome and polymerase chain reaction.

    abstract::The frequency occurrences of K-tuple (overlapping sequences of defined length, K) were computed from the known human genome sequences. The significance of these frequencies for the whole human genome was tested by polymerase chain reaction (PCR). A computer programs based on these results was written to choose primers...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.14.3887

    authors: Griffais R,André PM,Thibon M

    更新日期:1991-07-25 00:00:00

  • Domain I of 23S rRNA competes with a paused transcription complex for ribosomal protein L4 of Escherichia coli.

    abstract::Ribosomal protein L4 of Escherichia coli regulates expression of its own eleven gene S10 operon both by inhibiting translation and by stimulating premature termination of transcription. Both regulatory processes presumably involve L4 recognition of the S10 leader RNA. To help define L4's regulatory target, we have inv...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.10.2429

    authors: Zengel JM,Lindahl L

    更新日期:1993-05-25 00:00:00

  • BseSI, a restriction endonuclease from Bacillus stearothermophilus Jo 10-553, which recognizes the novel hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3'.

    abstract::A new restriction endonuclease Bse SI has been isolated from Bacillus stearothermophilus Jo10-553. Bse SI recognizes a degenerate hexanucleotide sequence 5'-G(G/T)GC(A/C)C-3' and cleaves DNA to produce 3[prime]-protruding tetranucleotide ends. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.13.2644

    authors: Steponaviciene D,Maneliene Z,Petrusyte M,Janulaitis A

    更新日期:1999-07-01 00:00:00

  • Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells.

    abstract::RNA sequencing (RNA-Seq) is a powerful tool for analyzing the identity of cellular RNAs but is often limited by the amount of material available for analysis. In spite of extensive efforts employing existing protocols, we observed that it was not possible to obtain useful sequencing libraries from nuclear RNA derived ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv213

    authors: Chu Y,Wang T,Dodd D,Xie Y,Janowski BA,Corey DR

    更新日期:2015-06-23 00:00:00

  • MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences.

    abstract::Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic se...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg561

    authors: Lee BT,Tan TW,Ranganathan S

    更新日期:2003-07-01 00:00:00

  • Nuclear transcriptional activity of the tobacco plastid psbA promoter.

    abstract::The plastid psbA promoter of tobacco was used with the aim to construct plastid specific marker genes. Upon transfer to the tobacco nuclear genome the plastid promoter fragment appeared to specify a messenger RNA. Placed 5' to the bar or nptII coding sequences the level of expression is sufficient to obtain a selectab...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.1.19

    authors: Cornelissen M,Vandewiele M

    更新日期:1989-01-11 00:00:00