A second look at cellular mRNA sequences said to function as internal ribosome entry sites.


:This review takes a second look at a set of mRNAs that purportedly employ an alternative mechanism of initiation when cap-dependent translation is reduced during mitosis or stress conditions. A closer look is necessary because evidence cited in support of the internal initiation hypothesis is often flawed. When putative internal ribosome entry sequences (IRESs) are examined more carefully, they often turn out to harbor cryptic promoters or splice sites. This undermines the dicistronic assay, wherein IRES activity is measured by the ability to support translation of the 3' cistron. Most putative IRESs still have not been checked carefully to determine whether the dicistronic vector produces only the intended dicistronic mRNA. The widespread use of the pRF vector is a major problem because this vector, which has Renilla luciferase as the 5' cistron and firefly luciferase as the 3' cistron, has been found to generate spliced transcripts. RNA transfection assays could theoretically circumvent these problems, but most candidate IRESs score very weakly in that test. The practice of calling even very weak results 'positive' is one of the problems discussed herein. The extremely low efficiency of putative IRESs is inconsistent with their postulated biological roles.'


Nucleic Acids Res


Nucleic acids research


Kozak M





Has Abstract


2005-11-28 00:00:00














  • Effects of pH on the stability of chromatin core particles.

    abstract::Chromatin core particles near physiological ionic strength undergo a reversible transition induced by changes in pH near neutrality. While sedimentation studies indicate no significant effect on size or shape, changes in tyrosine fluorescence anisotropy and in circular dichroism suggest a somewhat looser structure at ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Libertini LJ,Small EW

    更新日期:1984-05-25 00:00:00

  • Expression of C-terminal deleted p53 isoforms in neuroblastoma.

    abstract::The tumor suppressor gene, p53, is rarely mutated in neuroblastomas (NB) at the time of diagnosis, but its dysfunction could result from a nonfunctional conformation or cytoplasmic sequestration of the wild-type p53 protein. However, p53 mutation, when it occurs, is found in NB tumors with drug resistance acquired ove...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Goldschneider D,Horvilleur E,Plassa LF,Guillaud-Bataille M,Million K,Wittmer-Dupret E,Danglot G,de Thé H,Bénard J,May E,Douc-Rasy S

    更新日期:2006-01-01 00:00:00

  • Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13.

    abstract::Cdc13 is an essential protein from Saccharomyces cerevisiae that caps telomeres by protecting the C-rich telomeric DNA strand from degradation and facilitates telomeric DNA replication by telomerase. In vitro, Cdc13 binds TG-rich single-stranded telomeric DNA with high affinity and specificity. A previously identified...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Anderson EM,Halsey WA,Wuttke DS

    更新日期:2002-10-01 00:00:00

  • Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri.

    abstract::Three novel DNA-binding proteins with apparent molecular masses of 7, 10 and 30 kDa have been isolated from the hyperthermophilic methanogen Methanopyrus kandleri. The proteins were identified using a blot overlay assay that was modified to emulate the high ionic strength intracellular environment of M.kandleri protei...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pavlov NA,Cherny DI,Nazimov IV,Slesarev AI,Subramaniam V

    更新日期:2002-02-01 00:00:00

  • Functional characterization of two human MutY homolog (hMYH) missense mutations (R227W and V232F) that lie within the putative hMSH6 binding domain and are associated with hMYH polyposis.

    abstract::The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bai H,Jones S,Guan X,Wilson TM,Sampson JR,Cheadle JP,Lu AL

    更新日期:2005-01-26 00:00:00

  • DNA replication in Physarum polycephalum: characterization of DNA replication products made in vivo in the presence of cycloheximide in strains sensitive and resistant to cycloheximide.

    abstract::Synchronous plasmodia of cycloheximide-sensitive and cycloheximide-resistant strains of Physarum polycephalum were labelled with 3[H]-deoxyadenosine in pulse and pulse-chase experiments in presence and absence of cycloheximide. The replication products were studied with alkaline sucrose gradient sedimentation analysis...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Funderud S,Haugli F

    更新日期:1977-02-01 00:00:00

  • Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm.

    abstract::A phage-display library of random peptides is a combinatorial experimental technique that can be harnessed for studying antibody-antigen interactions. In this technique, a phage peptide library is scanned against an antibody molecule to obtain a set of peptides that are bound by the antibody with high affinity. This s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mayrose I,Shlomi T,Rubinstein ND,Gershoni JM,Ruppin E,Sharan R,Pupko T

    更新日期:2007-01-01 00:00:00

  • Linkage of catalysis and 5' end recognition in ribonuclease RNase J.

    abstract::In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å reso...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Pei XY,Bralley P,Jones GH,Luisi BF

    更新日期:2015-09-18 00:00:00

  • Fast optimal alignment.

    abstract::We show how to speed up sequence alignment algorithms of the type introduced by Needleman and Wunsch (and generalized by Sellers and others). Faster alignment algorithms have been introduced, but always at the cost of possibly getting sub-optimal alignments. Our modification results in the optimal alignment still bein...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fickett JW

    更新日期:1984-01-11 00:00:00

  • VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.

    abstract::With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate the convenient network ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hu Z,Chang YC,Wang Y,Huang CL,Liu Y,Tian F,Granger B,Delisi C

    更新日期:2013-07-01 00:00:00

  • Transcription factor IIA of wheat and human function similarly with plant and animal viral promoters.

    abstract::Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Burke C,Yu XB,Marchitelli L,Davis EA,Ackerman S

    更新日期:1990-06-25 00:00:00

  • Cloning and functional analysis of spliced isoforms of human nuclear factor I-X: interference with transcriptional activation by NFI/CTF in a cell-type specific manner.

    abstract::Previous studies of the epithelial specificity of the human papillomavirus type 16 (HPV-16) enhancer pointed out an important role of nuclear factor I (NFI). In epithelial cells, NFI proteins are derived from the NFI-C gene and referred to as NFI/CTF. In contrast, fibroblasts, where the enhancer is inactive, express h...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Apt D,Liu Y,Bernard HU

    更新日期:1994-09-25 00:00:00

  • Photosnesitization of DNA by gold.

    abstract::Au (III) reacts with DNA at pH 5.6 to form a complex which is sensitive to mid-UV radiation. Cyclobutane pyrimidine dimers are produced at some 15 to 30 times the rate that they are in untreated DNA. The mechanism of photosensitization appears to involve energy absorption by Au-urine and Au-cytosine adducts which can ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wilkins RJ

    更新日期:1978-10-01 00:00:00

  • How 'arm-twisting' by the inducer triggers activation of the MalT transcription factor, a typical signal transduction ATPase with numerous domains (STAND).

    abstract::Signal transduction ATPases with numerous domains (STAND) get activated through inducer-dependent assembly into multimeric platforms. This switch relies on the conversion of their nucleotide-binding oligomerization domain (NOD) from a closed, ADP-bound form to an open, ATP-bound form. The NOD closed form is stabilized...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Danot O

    更新日期:2015-03-31 00:00:00

  • PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

    abstract::The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Urban M,Cuzick A,Rutherford K,Irvine A,Pedro H,Pant R,Sadanadan V,Khamari L,Billal S,Mohanty S,Hammond-Kosack KE

    更新日期:2017-01-04 00:00:00

  • Transcriptional and post-transcriptional regulation of storage protein gene expression in sulfur-deficient pea seeds.

    abstract::We have used in vitro transcription in isolated pea nuclei to determine whether the expression of genes for the seed storage proteins legumin and vicilin is regulated transcriptionally or post-transcriptionally in response to changing sulfur status in the developing seed. During the first 48 h of recovery from S defic...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Beach LR,Spencer D,Randall PJ,Higgins TJ

    更新日期:1985-02-11 00:00:00

  • Engineering of temperature- and light-switchable Cas9 variants.

    abstract::Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function....

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Richter F,Fonfara I,Bouazza B,Schumacher CH,Bratovič M,Charpentier E,Möglich A

    更新日期:2016-11-16 00:00:00

  • Structural organization and differential expression of rice alpha-amylase genes.

    abstract::Rice alpha-amylases are encoded by a multigene family that has previously been classified into 5 hybridization groups. DNA sequence and Southern blot analysis identified three genes (RAmy1A, RAmy1B and RAmy1C) in Group 1 with DNA sequence identity of at least 90%. Hybridization Group 2 is represented by only one gene,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huang N,Koizumi N,Reinl S,Rodriguez RL

    更新日期:1990-12-11 00:00:00

  • The N-terminus of Prp1 (Prp6/U5-102 K) is essential for spliceosome activation in vivo.

    abstract::The spliceosomal protein Prp1 (Prp6/U5-102 K) is necessary for the integrity of pre-catalytic spliceosomal complexes. We have identified a novel regulatory function for Prp1. Expression of mutations in the N-terminus of Prp1 leads to the accumulation of pre-catalytic spliceosomal complexes containing the five snRNAs U...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lützelberger M,Bottner CA,Schwelnus W,Zock-Emmenthal S,Razanau A,Käufer NF

    更新日期:2010-03-01 00:00:00

  • Interaction of N-acetyl-phenylalanyl-tRNAPhe with 70S ribosomes of Escherichia coli.

    abstract::The interaction of N--Acetyl--Phe--tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The entha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Odinzov VB,Kirillov SV

    更新日期:1978-10-01 00:00:00

  • In vivo screening of modified siRNAs for non-specific antiviral effect in a small fish model: number and localization in the strands are important.

    abstract::Small interfering RNAs (siRNAs) are promising new active compounds in gene medicine but the induction of non-specific immune responses following their delivery continues to be a serious problem. With the purpose of avoiding such effects chemically modified siRNAs are tested in screening assay but often only examining ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schyth BD,Bramsen JB,Pakula MM,Larashati S,Kjems J,Wengel J,Lorenzen N

    更新日期:2012-05-01 00:00:00

  • Expression of the thyroid hormone receptor gene, erbAalpha, in B lymphocytes: alternative mRNA processing is independent of differentiation but correlates with antisense RNA levels.

    abstract::The erbAalpha gene encodes two alpha-thyroid hormone receptor isoforms, TRalpha1 and TRalpha2, which arise from alternatively processed mRNAs, erbAalpha1 (alpha1) and erb alpha2 (alpha2). The splicing and alternative polyadenylation patterns of these mRNAs resemble that of mRNAs encoding different forms of immunoglobu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Hastings ML,Milcarek C,Martincic K,Peterson ML,Munroe SH

    更新日期:1997-11-01 00:00:00

  • Characterization of the frameshift signal of Edr, a mammalian example of programmed -1 ribosomal frameshifting.

    abstract::The ribosomal frameshifting signal of the mouse embryonal carcinoma differentiation regulated (Edr) gene represents the sole documented example of programmed -1 frameshifting in mammalian cellular genes [Shigemoto,K., Brennan,J., Walls,E,. Watson,C.J., Stott,D., Rigby,P.W. and Reith,A.D. (2001), Nucleic Acids Res., 29...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Manktelow E,Shigemoto K,Brierley I

    更新日期:2005-03-14 00:00:00

  • The G-rich auxiliary downstream element has distinct sequence and position requirements and mediates efficient 3' end pre-mRNA processing through a trans-acting factor.

    abstract::A downstream G-rich sequence (GRS), GGGGGAGGUGUGGG, has been previously shown to influence the efficiency of 3' end processing of the SV40 late polyadenylation signal. We have now defined several important parameters for GRS-mediated polyadenylation. The ability of the GRS to influence 3' end processing efficiency was...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bagga PS,Ford LP,Chen F,Wilusz J

    更新日期:1995-05-11 00:00:00

  • Asn-tRNA in Lactobacillus bulgaricus is formed by asparaginylation of tRNA and not by transamidation of Asp-tRNA.

    abstract::In many organisms (e.g., gram-positive eubacteria) Gin-tRNA is not formed by direct glutaminylation of tRNAGln but by a specific transamidation of Glu-tRNAGln. We wondered whether a similar transamidation pathway also operates in the formation of Asn-tRNA in these organisms. Therefore we tested in S-100 preparations o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim SI,Nalaskowska M,Germond JE,Pridmore D,Söll D

    更新日期:1996-07-15 00:00:00

  • Alkemio: association of chemicals with biomedical topics by text and data mining.

    abstract:UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have im...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gijón-Correas JA,Andrade-Navarro MA,Fontaine JF

    更新日期:2014-07-01 00:00:00

  • Allotopic expression of mitochondrial-encoded genes in mammals: achieved goal, undemonstrated mechanism or impossible task?

    abstract::Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Perales-Clemente E,Fernández-Silva P,Acín-Pérez R,Pérez-Martos A,Enríquez JA

    更新日期:2011-01-01 00:00:00

  • The complete nucleotide sequence of the RNA coding for the primary translation product of foot and mouth disease virus.

    abstract::The complete nucleotide sequence of the coding region of foot and mouth disease virus RNA (strain A1061) is presented. The sequence extends from the primary initiation site, approximately 1200 nucleotide from the 5' end of the genome, in an open translational reading frame of 6,999 nucleotides to a termination codon 9...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Carroll AR,Rowlands DJ,Clarke BE

    更新日期:1984-03-12 00:00:00

  • Cabeza, a Drosophila gene encoding a novel RNA binding protein, shares homology with EWS and TLS, two genes involved in human sarcoma formation.

    abstract::We have previously described a partial Drosophila cDNA, clone P19, which bears homology to members of the RNA recognition motif (RRM) family of proteins [Haynes et al. (1987) Proc. Natl. Acad. Sci. USA, 84, 1819-1823]. RNA binding as well as involvement in RNA processing has been demonstrated for some RRM proteins. We...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stolow DT,Haynes SR

    更新日期:1995-03-11 00:00:00

  • Complementary addressed modification of yeast tRNA Val 1 with alkylating derivative of d(pC-G)-A. The positions of the alkylated nucleotides and the course of the alkylation in the complex.

    abstract::Yeast tRNA Val 1 alkylation with 2', 3'-O-4-(N-2-chloroethyl-N-methylamino) benzylidene d(pC-G)-A proceeds at 20 degrees - 30 degrees C in the complementary complexes which are formed by d(pC-G)-A greater than RC1 binding to 3 sequences of tRNA Val 1 : psi-C-G58 in the T loop, C-G40 at the 3'-side of the anticodon loo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Grineva NI,Karpova GG,Kuznetsova LM,Venkstern TV,Bayev AA

    更新日期:1977-01-01 00:00:00