Characterization and mapping of the double-stranded regions involved in activation of PKR within a cellular RNA from 3T3-F442A cells.

Abstract:

:PKR is a doubled-stranded RNA-dependent protein kinase which is implicated in the regulation of several cellular processes, including cell proliferation. PKR undergoes phosphorylation and activation in mouse embryonic 3T3-F442A cells in response to endogenous RNA(s). Activation of PKR is related to growth and differentiation of these cells. A cellular regulatory RNA (R-RNA) which activates PKR has been isolated from these cells and its cDNA partially sequenced. Here we have characterized the R-RNA transcript with respect to nuclease sensitivity and the extent of double-stranded structure involved in activation of PKR. The location of the activating sequence was mapped to a contiguous 226/252 nt region of the R-RNA transcript by hybridization to its cDNA fragments. Hybridization with a panel of short oligodeoxynucleotides complementary to the R-RNA, coupled with protein kinase analysis, was used to probe the 252 nt region for critical sequences. Three short non-contiguous sequences which appear most important for activation of PKR were identified within the 252 nt region. Thus, these studies have identified specific sequences most important for activation of PKR. Furthermore, since the above antisense oligodeoxynucleotides inhibit enzyme activation, our results exemplify an unusual mode of action of antisense sequences on the activation of PKR by disruption of RNA secondary structure.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Petryshyn RA,Ferrenz AG,Li J

doi

10.1093/nar/25.13.2672

subject

Has Abstract

pub_date

1997-07-01 00:00:00

pages

2672-8

issue

13

eissn

0305-1048

issn

1362-4962

pii

gka426

journal_volume

25

pub_type

杂志文章
  • Aspects of specific protein-DNA interaction; multi-mode binding of the oligopeptide antibiotic netropsin to (A.T)-rich DNA segments.

    abstract::By means of titration viscometry a number of distinct modes could be resolved for the interaction between the antibiotic netropsin and DNA species of 50, 58, and 69 mole + (A+T) below r = 0.04 netropsin molecules bound per DNA phosphate group. The number of corresponding binding sites increases with a high power of th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/7.5.1375

    authors: Reinert KE,Stutter E,Schweiss H

    更新日期:1979-11-10 00:00:00

  • A minor class of 5S rRNA genes in Saccharomyces cerevisiae X2180-1B, one member of which lies adjacent to a Ty transposable element.

    abstract::In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.10.4083

    authors: Piper PW,Lockheart A,Patel N

    更新日期:1984-05-25 00:00:00

  • VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data.

    abstract::Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether individual genes are significantly activated or repressed by a particular stimulus. We have previously presented two Ba...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki443

    authors: Hsiao A,Ideker T,Olefsky JM,Subramaniam S

    更新日期:2005-07-01 00:00:00

  • Comparative genomic analysis of equilibrative nucleoside transporters suggests conserved protein structure despite limited sequence identity.

    abstract::Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf564

    authors: Sankar N,Machado J,Abdulla P,Hilliker AJ,Coe IR

    更新日期:2002-10-15 00:00:00

  • MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

    abstract::MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and va...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm216

    authors: Davis IW,Leaver-Fay A,Chen VB,Block JN,Kapral GJ,Wang X,Murray LW,Arendall WB 3rd,Snoeyink J,Richardson JS,Richardson DC

    更新日期:2007-07-01 00:00:00

  • Precursors to 16S and 23S ribosomal RNA from a ribonuclear III-strain of Escherichia coli contain intact RNase III processing sites.

    abstract::Escherichia coli cells lacking the ribosomal RNA processing enzyme RNase III do no excise the normal RNA precursors p16a (17S) and p23a from nascent rRNA transcripts. These cells produce, instead, slightly larger p16b and p23b precursors. Digestion of p16b or p23b rRNA with RNases A plus T1 yields double-stranded frag...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.8.1873

    authors: Gegenheimer P,Apirion D

    更新日期:1980-04-25 00:00:00

  • Ribosomal RNA metabolism in cucumber leaf mesophyll protoplasts.

    abstract::Aspects of the metabolism of RNA have been studied in enzymatically isolated protoplasts from cotyledon and first leaf mesophyll tissue of two cultivars of cucumber. The first leaf mesophyll protoplasts incorporated (3H)-uridine into ribosomal RNA at a constant rate for up to 25 hr in a simple salts medium and for up ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.7.1111

    authors: Coutts RH,Barnett A,Wood KR

    更新日期:1975-07-01 00:00:00

  • Codon usage in Pseudomonas aeruginosa.

    abstract::We have generated a codon usage table for Pseudomonas aeruginosa. Codon usage in P. aeruginosa is extremely biased. In contrast to E. coli and yeast, P. aeruginosa preferentially uses those codons within a synonymous codon group with the strongest predicted codon-anticodon interaction. We were unable to correlate a pa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.19.9323

    authors: West SE,Iglewski BH

    更新日期:1988-10-11 00:00:00

  • Nucleotide sequence of the narL gene that is involved in global regulation of nitrate controlled respiratory genes of Escherichia coli.

    abstract::The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.5.1965

    authors: Gunsalus RP,Kalman LV,Stewart RR

    更新日期:1989-03-11 00:00:00

  • Pyrophosphate-condensing activity linked to nucleic acid synthesis.

    abstract::In some preparations of DNA dependent RNA polymerase a new enzymatic activity has been found which catalyzes the condensation of two pyrophosphate molecules, liberated in the process of RNA synthesis, to one molecule of orthophosphate and one molecule of Mg (or Mn) - chelate complex with trimetaphosphate. This activit...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.4.1521

    authors: Volloch VZ,Rits S,Tumerman L

    更新日期:1979-04-01 00:00:00

  • Massively parallel characterization of restriction endonucleases.

    abstract::Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specifi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt257

    authors: Kamps-Hughes N,Quimby A,Zhu Z,Johnson EA

    更新日期:2013-06-01 00:00:00

  • The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry.

    abstract::The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodies...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz574

    authors: Fuchs E,Falschlunger C,Micura R,Breuker K

    更新日期:2019-08-22 00:00:00

  • Does the HIV-1 primer activation signal interact with tRNA3(Lys) during the initiation of reverse transcription?

    abstract::Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer ac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg187

    authors: Goldschmidt V,Ehresmann C,Ehresmann B,Marquet R

    更新日期:2003-02-01 00:00:00

  • The genes for yeast ribosomal proteins S24 and L46 are adjacent and divergently transcribed.

    abstract::Unlike most yeast ribosomal protein genes studied so far the genes coding for S24 and L46 are adjacent on the genome. Sequence analysis showed that the two genes are transcribed divergently, their initiation codons being 630 bp apart. Taking the respective ATG translation start sites as reference points, the 5'- end o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.3.701

    authors: Leer RJ,van Raamsdonk-Duin MM,Kraakman P,Mager WH,Planta RJ

    更新日期:1985-02-11 00:00:00

  • Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.

    abstract::The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh531

    authors: Su TJ,Connolly BA,Darlington C,Mallin R,Dryden DT

    更新日期:2004-04-23 00:00:00

  • Improved nucleotide selectivity and termination of 3'-OH unblocked reversible terminators by molecular tuning of 2-nitrobenzyl alkylated HOMedU triphosphates.

    abstract::We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1293

    authors: Litosh VA,Wu W,Stupi BP,Wang J,Morris SE,Hersh MN,Metzker ML

    更新日期:2011-03-01 00:00:00

  • Saccharomyces genome database informs human biology.

    abstract::The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1112

    authors: Skrzypek MS,Nash RS,Wong ED,MacPherson KA,Hellerstedt ST,Engel SR,Karra K,Weng S,Sheppard TK,Binkley G,Simison M,Miyasato SR,Cherry JM

    更新日期:2018-01-04 00:00:00

  • Dual transcriptional-translational cascade permits cellular level tuneable expression control.

    abstract::The ability to induce gene expression in a small molecule dependent manner has led to many applications in target discovery, functional elucidation and bio-production. To date these applications have relied on a limited set of protein-based control mechanisms operating at the level of transcription initiation. The dis...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv912

    authors: Morra R,Shankar J,Robinson CJ,Halliwell S,Butler L,Upton M,Hay S,Micklefield J,Dixon N

    更新日期:2016-02-18 00:00:00

  • Efficient extension of a misaligned tRNA-primer during replication of the HIV-1 retrovirus.

    abstract::The human immunodeficiency virus (HIV) and other retroviruses show extensive genomic variation, which is primarily due to error-prone replication by the viral reverse transcriptase (RT) enzymes. RT errors include misincorporation with subsequent extension of the mismatched terminal base, and extension of realigned pri...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.8.1319

    authors: Das AT,Berkhout B

    更新日期:1995-04-25 00:00:00

  • Tumour suppressor ING1b maintains genomic stability upon replication stress.

    abstract::The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is important for preventing genomic instability and cancer development. Previously, it was shown that cells deficient in tum...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1337

    authors: Wong RP,Lin H,Khosravi S,Piche B,Jafarnejad SM,Chen DW,Li G

    更新日期:2011-05-01 00:00:00

  • Replacement and insertion of nucleotides at the anticodon loop of E. coli tRNAMetf by ligation of chemically synthesized ribooligonucleotides.

    abstract::Insertion of the four major nucleotides at the 5'-side of the anticodon triplet of E. coli tRNAMetf was performed by joining of the half molecules obtained by limited digestion with RNase A and the chemically synthesized tetranucleotide pN-C-A-U using RNA ligase. Insertion of U-U at the 5'-side or A and A-A at the 3'-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.10.3685

    authors: Doi T,Yamane A,Matsugi J,Ohtsuka E,Ikehara M

    更新日期:1985-05-24 00:00:00

  • In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II.

    abstract::Hammerhead ribozymes were transcribed from a dsDNA template containing four random nucleotides between stems II and III, which replace the naturally occurring GAA nucleotides. In vitro selection was used to select hammerhead ribozymes capable of in cis cleavage using denaturing polyacrylamide gels for the isolation of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.22.4401

    authors: Thomson JB,Sigurdsson ST,Zeuch A,Eckstein F

    更新日期:1996-11-15 00:00:00

  • The Genome Database for Rosaceae (GDR): year 10 update.

    abstract::The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1012

    authors: Jung S,Ficklin SP,Lee T,Cheng CH,Blenda A,Zheng P,Yu J,Bombarely A,Cho I,Ru S,Evans K,Peace C,Abbott AG,Mueller LA,Olmstead MA,Main D

    更新日期:2014-01-01 00:00:00

  • miROrtho: computational survey of microRNA genes.

    abstract::MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn707

    authors: Gerlach D,Kriventseva EV,Rahman N,Vejnar CE,Zdobnov EM

    更新日期:2009-01-01 00:00:00

  • All Tcf HMG box transcription factors interact with Groucho-related co-repressors.

    abstract::Tcf/Lef family transcription factors are the downstream effectors of the Wingless/Wnt signal transduction pathway. Upon Wingless/Wnt signalling, beta-catenin translocates to the nucleus, interacts with Tcf (1-3) and thus activates transcription of target genes (4,5). Tcf factors also interact with members of the Grouc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.7.1410

    authors: Brantjes H,Roose J,van De Wetering M,Clevers H

    更新日期:2001-04-01 00:00:00

  • The role of acetylation in rDNA transcription.

    abstract::Treatment of NIH 3T3 cells with trichostatin A (TSA), an inhibitor of histone deacetylase (HDAC), resulted in a dose-dependent increase in transcription from a rDNA reporter and from endogenous rRNA genes. Chromatin immunoprecipitation using anti-acetyl-histone H4 antibodies demonstrated a direct effect of TSA on the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.20.4114

    authors: Hirschler-Laszkiewicz I,Cavanaugh A,Hu Q,Catania J,Avantaggiati ML,Rothblum LI

    更新日期:2001-10-15 00:00:00

  • Genotypic analysis of multiple loci in somatic cells by whole genome amplification.

    abstract::To screen multiple loci in small purified samples of diploid and aneuploid cells a PCR-based technique of whole genome amplification was adapted to the study of somatic lesions. DNA samples from different numbers of flow-sorted diploid and aneuploid cells from biopsies were amplified with a degenerate 15mer primer. Al...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.17.3488

    authors: Barrett MT,Reid BJ,Joslyn G

    更新日期:1995-09-11 00:00:00

  • Local potentiation of stress-responsive genes by upstream noncoding transcription.

    abstract::It has been postulated that a myriad of long noncoding RNAs (lncRNAs) contribute to gene regulation. In fission yeast, glucose starvation triggers lncRNA transcription across promoter regions of stress-responsive genes including fbp1 (fructose-1,6-bisphosphatase1). At the fbp1 promoter, this transcription promotes chr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw142

    authors: Takemata N,Oda A,Yamada T,Galipon J,Miyoshi T,Suzuki Y,Sugano S,Hoffman CS,Hirota K,Ohta K

    更新日期:2016-06-20 00:00:00

  • Halogenation of tubercidin by N-halosuccinimides. A direct route to 5-bromotubercidin, a reversible inhibitor of RNA synthesis in eukaryotic cells.

    abstract::Tubercidin may be directly brominated by reaction with N-bromosuccinimide in DMF to give 5-bromotubercidin, a reversible inhibitor of RNA synthesis. When buffered with potassium acetate the major product is 6-bromotubercidin. 5,6-Dibromotubercidin is formed in minor amounts under both conditions. N-Chlorosuccinimide a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.24.6213

    authors: Bergstrom DE,Brattesani AJ

    更新日期:1980-12-20 00:00:00

  • Microbial species delineation using whole genome sequences.

    abstract::Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv657

    authors: Varghese NJ,Mukherjee S,Ivanova N,Konstantinidis KT,Mavrommatis K,Kyrpides NC,Pati A

    更新日期:2015-08-18 00:00:00