Abstract：
: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.'
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kozak Mdoi
10.1093/nar/gki958keywords:
subject
Has Abstractpub_date
2005-11-28 00:00:00pages
6593-602issue
20eissn
0305-1048issn
1362-4962pii
33/20/6593journal_volume
33pub_type
杂志文章,评审abstract：:The ability to sense and respond to environmental and physiological signals is critical for the survival of the soil-dwelling Gram-positive bacterium Streptomyces coelicolor. Nutrient deprivation triggers the onset of a complex morphological differentiation process that involves the raising of aerial hyphae and format...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1096
更新日期：2008-02-01 00:00:00
abstract：:The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1188
更新日期：2013-01-01 00:00:00
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
更新日期：2001-04-01 00:00:00
abstract：:Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1195
更新日期：2021-01-11 00:00:00
abstract：:The nucleotide sequence of a region located on the adenovirus type 5 genome between coordinates 59.9 and 62.5 has been determined. This region comprises the 3'-termini of mRNAs coding for the hexon and the DNA binding protein. The sequence reveals the presence of an open reading frame in r-strand transcripts downstrea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.24.6033
更新日期：1980-12-20 00:00:00
abstract：:Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt492
更新日期：2013-08-01 00:00:00
abstract：:The nematode Caenorhabditis elegans contains a small family of vitellogenin genes which is expressed abundantly, but only in the intestine of the adult hermaphrodite worm. In order to identify possible regulatory elements, we have sequenced the DNA surrounding the 5' ends of five of the six genes. Contained within reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.14.5283
更新日期：1985-07-25 00:00:00
abstract：:The mutL and mutS genes of Vibrio cholerae have been identified using interspecific complementation of Escherichia coli mutL and mutS mutants with plasmids containing the gene bank of V. cholerae. The recombinant plasmid pJT470, containing a 4.7 kb fragment of V. cholerae DNA codes for a protein of molecular weight 92...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.15.6241
更新日期：1989-08-11 00:00:00
abstract：:The UCSC Genome Browser (https://genome.ucsc.edu) provides a web interface for exploring annotated genome assemblies. The assemblies and annotation tracks are updated on an ongoing basis-12 assemblies and more than 28 tracks were added in the past year. Two recent additions are a display of CRISPR/Cas9 guide sequences...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1020
更新日期：2018-01-04 00:00:00
abstract：:We have compiled the DNA sequence data for E. coli K12 available from the GENBANK and EMBO databases and over a period of several years independently from the literature. We have introduced all available genetic map data and have arranged the sequences accordingly. As far as possible the overlaps are deleted and a tot...
journal_title：Nucleic acids research
pub_type：
doi：10.1093/nar/17.suppl.r283
更新日期：1989-01-01 00:00:00
abstract：:Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. H...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm322
更新日期：2007-07-01 00:00:00
abstract：:Homologous recombination provides a means for the in vivo construction of recombinant DNA molecules that may be problematic to assemble in vitro. We have investigated the efficiency of recombination within the Caenorhabditis elegans germ line as a function of the length of homology between recombining molecules. Our f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm857
更新日期：2007-01-01 00:00:00
abstract：:Over millions of years the structure and complexity of the transcriptional regulatory network (TRN) in bacteria has changed, reorganized and enabled them to adapt to almost every environmental niche on earth. In order to understand the plasticity of TRNs in bacteria, we studied the conservation of currently known TRNs...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl423
更新日期：2006-07-13 00:00:00
abstract：:The direction of replication of DNA within replicons of Physarum polycephalum was studied by pulse-labelling with 5-bromouracil-deoxyriboside (BrdUrd) and 3H-adenosine deoxyriboside (dAdo), followed by ultraviolet- (UV) -photolysis and analysis of molecular weights of single strand DNA fragments on alkaline sucrose gr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.3.713
更新日期：1978-03-01 00:00:00
abstract：:An updated compilation of 300 E. coli mRNA promoter sequences is presented. For each sequence the most recent relevant paper was checked, to verify the location of the transcriptional start position as identified experimentally. We comment on the reliability of the sequence databanks and analyze the conservation of kn...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.7.1507
更新日期：1993-04-11 00:00:00
abstract：:The chicken erythroid proteins binding to the histone H5 5' promoter and 3' erythroid-specific enhancer regions were identified. In DNase I footprinting and gel mobility shift experiments with immature adult erythrocyte nuclear extracts, we have demonstrated the binding of proteins to the GC-box, a high affinity Sp1 b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.23.6385
更新日期：1992-12-11 00:00:00
abstract：:DNA from healthy Malaysian newborns was studied on gene maps after digestion with different restriction endonucleases. Of 65 newborns, two were found to be carriers of two different variants of triplicated alpha-globin loci. In variant no. 1, found in an Malay, the three alpha-globin genes are in an elongated DNA frag...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.15.3707
更新日期：1981-08-11 00:00:00
abstract：:Camptothecin (CPT), a plant alkaloid with antitumor activity, is a specific inhibitor of eukaryotic DNA topoisomerase I. We have previously isolated and characterized a CPT-resistant topoisomerase I isolated from a CPT-resistant human leukemia cell line, CPT-K5. cDNA clones of topoisomerase I were isolated from the CP...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.1.69
更新日期：1991-01-11 00:00:00
abstract：:Poly A-containing RNA enriched in prolactin-coding sequences was isolated from female rate pituitaries after induction with diethylstilbesterol. Double stranded cDNA was synthesized from this RNA and inserted into plasmid pBR322 at the Pst I site via the poly(dG):polyy(dC) tailing method. E. coli was transformed with ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.3.915
更新日期：1979-03-01 00:00:00
abstract：:Transactivation by the ETS family of transcription factors, whose members share structurally conserved DNA-binding domains, is variably sensitive to methylation of their target genes. The mechanism by which DNA methylation controls ETS proteins remains poorly understood. Uncertainly also pervades the effects of hemi-m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw528
更新日期：2016-10-14 00:00:00
abstract：:Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki480
更新日期：2005-07-01 00:00:00
abstract：:The first step in DNA cleavage at V(D)J recombination signals by RAG1 and RAG2 is creation of a nick at the heptamer/coding flank border. Under proper conditions in vitro the second step, hairpin formation, requires two signals with spacers of 12 and 23 bp, a restriction referred to as the 12/23 rule. Under these cond...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.21.4370
更新日期：1997-11-01 00:00:00
abstract：:LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased af...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh056
更新日期：2004-04-19 00:00:00
abstract：:The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1208
更新日期：2017-03-17 00:00:00
abstract：:A positive cis-acting DNA element in the near 5'-upstream region of the CYP2B1/B2 genes in rat liver was found to play an important role in the transcription of these genes. An oligonucleotide covering -69 to -98 nt mimicked the gel mobility shift pattern given by the fragment -179 to +29 nt, which was earlier found a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.557
更新日期：1992-02-11 00:00:00
abstract：:The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2105
更新日期：1995-06-25 00:00:00
abstract：:Many RNP proteins contain one or more copies of the RNA recognition motif (RRM) and are thought to be involved in cellular RNA metabolism. We have previously characterized in Xenopus a nervous system specific gene, nrp1, that is more similar to the hnRNP A/B proteins than to other known proteins (K. Richter, P. J. Goo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.4.999
更新日期：1993-02-25 00:00:00
abstract：:The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky995
更新日期：2019-01-08 00:00:00
abstract：:FRS1 and FRS2, the structural genes encoding the large (alpha) and small (beta) subunits of yeast phenylalanyl-tRNA synthetase (PheRS) were placed under the control of the lacZ promoter by creating an artificial operon. The FRS2 gene was fused next to the promoter, followed by a 14 base pair intergenic sequence contai...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.8.2087
更新日期：1990-04-25 00:00:00
abstract：:The estrogen receptor (ER) contains two nonacidic transcriptional activation functions, AF-1 and AF-2 (formerly TAF-1 and TAF-2). In this study we show that AF-1 and AF-2 are able to stimulate transcription in vitro in a HeLa cell system when fused to the DNA binding domain of the yeast activator GAL4. We also demonst...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.1.5
更新日期：1993-01-11 00:00:00
