Abstract:
:Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional complex formation could be mimicked by pre-assembling activator and certain general transcription factors on the promoter and then adding nuclear extract. The minimal activated complex with this characteristic contained general factors TFIID and TFIIA. The ability of the TFIID:TFIIA complex to complete assembly rapidly was reduced by the same TATA box mutation that reduced reinitiation rate. Band shift experiments also showed that this same mutation lowered the stability of the TBP:TFIIA complex on the DNA. The results suggest that TATA-dependent variations in retention of the TFIID:TFIIA complex after release of the polymerase could be a primary determinant of reinitiation rate, allowing diversity in promoter strength to be related to diversity in TATA element sequences.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yean D,Gralla JDdoi
10.1093/nar/27.3.831subject
Has Abstractpub_date
1999-02-01 00:00:00pages
831-8issue
3eissn
0305-1048issn
1362-4962pii
gkc158journal_volume
27pub_type
杂志文章abstract::The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2523
更新日期:1986-03-25 00:00:00
abstract::We report the use of an engineered ribozyme to produce a circular human exon in vitro. Specifically, we have designed a derivative of a yeast self-splicing group II intron that is able to catalyze the formation of a circular exon encoding the first kringle domain (K1) of the human tissue plasminogen activator protein....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.24.5085
更新日期:1997-12-15 00:00:00
abstract::Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1253
更新日期:2014-12-16 00:00:00
abstract::Mature tRNAPhe from Escherichia coli and the transcript of its gene lacking modified nucleotides were compared by a variety of physical techniques. Melting experiments revealed that at a low Mg2+level the transcript was partially denatured, while the mature tRNA possessed intact tertiary interactions. Mg2+binding to b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2723
更新日期:1998-06-01 00:00:00
abstract::Adaptation of the P1 phage-derived Cre /loxP site- specific recombination system to the gene targeting technique allows for the conditional deletion of genes in mice. To selectively modify genes in B lymphocytes, we have generated mice (designated CD19-Cre) which express cre under the transcriptional control of the B ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.6.1317
更新日期:1997-03-15 00:00:00
abstract::The abundance and cell cycle dependent expression of the mRNA for human nonhistone protein HMG-17 were studied in synchronized HeLa cells. Slot blot analysis indicates that the HMG-17 mRNA is a very abundant message, significantly more so than histone or actin mRNA. RNA prepared from tissue culture cells contains high...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.8.3549
更新日期:1987-04-24 00:00:00
abstract::Some human cancers maintain their telomeres using the alternative lengthening of telomeres (ALT) mechanism; a process thought to involve recombination. Different types of recombinational telomere elongation pathways have been identified in yeasts. In senescing yeast telomerase deletion (ter1-Delta) mutants with very s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp814
更新日期:2010-01-01 00:00:00
abstract::At either end of the nopaline Ti-plasmid T-region resides a copy of a 25 bp repeated element. The normal T-DNA endpoint is 1 bp internal of the right copy, with the transcription initiation site of the nopaline synthase (nos) gene being approximately 300 bp away in the same direction. Here we describe results which de...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.15.6031
更新日期:1984-08-10 00:00:00
abstract::Exonic splicing enhancer (ESE) sequences are bound by serine & arginine-rich (SR) proteins, which in turn enhance the recruitment of splicing factors. It was inferred from measurements of splicing around twenty years ago that Drosophila doublesex ESEs are bound stably by SR proteins, and that the bound proteins intera...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky056
更新日期:2018-03-16 00:00:00
abstract::The nucleolus is a unique structural component of interphase nuclei where the ribosomal genes, trans-cribed by RNA polymerase I (RNA pol I), are organized. In the present study, the repair of UV-induced photolesions was investigated in the ribosomal DNA (rDNA) in relation to RNA pol I transcription. We used hamster ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.12.2511
更新日期:1999-06-15 00:00:00
abstract::RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured non-coding RNAs, with a focus on structural similarities. The classification is hierarchical and similar to the system used in the SCOP and CATH databases of protein structures. Its central leve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx966
更新日期:2018-01-04 00:00:00
abstract::Human somatic cells have essentially no telomerase activity. Telomerase is linked to tumor genesis and is a valuable marker for malignant growth. Extreme paucity of the enzyme neccessitated development of a PCR-based assay, 'telomeric repeat amplification protocol' (TRAP). Unfortunately, this method is not without dif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.4.919
更新日期:1997-02-15 00:00:00
abstract::A very mild and efficient procedure has been developed for the preparation of C-5 substituted deoxyuridines. The substituent carries a masked primary aliphatic amino group. These compounds are readily converted into their phosphoramidites and can be used to prepare oligonucleotides carrying one or more aliphatic amino...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4857
更新日期:1987-06-25 00:00:00
abstract::DNA polymerase lambda (pol lambda) is a member of the X family DNA polymerases and is endowed with multiple enzymatic activities. In this work we investigated the in vitro miscoding properties of full-length, human pol lambda either in the absence or in the presence of the human auxiliary proteins proliferating cell n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl032
更新日期:2006-03-06 00:00:00
abstract::Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based integrated database on cell cycle regulation in mammals in normal and pathological states (Cyclonet database). It integrates...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl912
更新日期:2007-01-01 00:00:00
abstract::Post-translational modifications (such as ubiquitination) of clock proteins are critical in maintaining the precision and robustness of the evolutionarily conserved circadian clock. Ubiquitination of the core clock transcription factor BMAL1 (brain and muscle Arnt-like 1) has recently been reported. However, it remain...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku225
更新日期:2014-05-01 00:00:00
abstract::Microsatellites, such as (TG)n found at random throughout the genome, or as 3' extensions of Alu sequences are being increasingly used as genetic markers because of their pluriallelic character. The search for polymorphic microsatellites is time consuming, however, as it is necessary to sequence clones containing the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.6.1333
更新日期:1992-03-25 00:00:00
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
更新日期:2015-07-27 00:00:00
abstract::A molecular rotor thioflavin T (ThT) is usually used as a fluorescent ligand specific for G-quadruplexes. Here, we demonstrate that ThT can tightly bind non-G-quadruplex DNAs with several GA motifs and dimerize them in a parallel double-stranded mode, accompanied by over 100-fold enhancement in the fluorescence emissi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx942
更新日期:2017-12-01 00:00:00
abstract::A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku306
更新日期:2014-07-01 00:00:00
abstract::Analysis of 41 histone homologous clones from an isogenic gene library of Drosophila melanogaster showed that non-histone fragments interrupt the histone repetitive clusters at several sites. Long (L) and short (S) forms of the repeating units are distinguished by the insertion of 240 bp into the spacer between H1 and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.1.225
更新日期:1989-01-11 00:00:00
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
更新日期:1996-11-15 00:00:00
abstract::Interactions between subunits in the Saccharomyces cerevisiae ribosome are mediated by universal and eukaryote-specific intersubunit bridges. Universal bridges are positioned close to the ribosomal functional centers, while eukaryote-specific bridges are mainly located on the periphery of the ribosome. Two bridges, eB...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1083
更新日期:2019-01-10 00:00:00
abstract::The transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas9) utlilize distinct molecular mechanisms in targeting site recognition. The two proteins can be modified to carry additional functional domains to regulate exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku836
更新日期:2014-11-10 00:00:00
abstract::Evidence will be presented to show that the reagents 3a-c (X = O) obtained by the reaction of 2-chlorophenylphosphorodichloridate with 1-hydroxybenzotriazole or 1-hydroxy-6-trifluoromethyl (6-nitro) benzotriazoles, respectively, do not give, under normal coupling conditions, phosphorylation of the lactam functions in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.14.5885
更新日期:1986-07-25 00:00:00
abstract::Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentially, the resulting challenges must be met with rapid infrastructure dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1084
更新日期:2019-01-08 00:00:00
abstract::Replication of the promiscuous plasmid pMV158 requires expression of the initiator repB gene, which is controlled by the repressor CopG. Genes repB and copG are co-transcribed from promoter P(cr). We have studied the interactions between RNA polymerase, CopG and the promoter to elucidate the mechanism of repression by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp503
更新日期:2009-08-01 00:00:00
abstract::The 5'- and 3'-untranslated regions (5'- and 3'-UTRs) of eukaryotic mRNAs are known to play a crucial role in post-transcriptional regulation of gene expression modulating nucleo-cytoplasmic mRNA transport, translation efficiency, subcellular localization and stability. UTRdb is a specialized database of 5' and 3' unt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.335
更新日期:2002-01-01 00:00:00
abstract::The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp936
更新日期:2010-01-01 00:00:00
abstract::The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1503
更新日期:2016-04-20 00:00:00