Abstract:
:The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is unable to activate the hb-CAT reporter in Drosophila cells, to analyze the role of co-factors in regulating Bcd function. We show that increased concentrations of the co-activator dCBP in cells can switch this protein from its inactive state to an active state on the hb-CAT reporter. The C-terminal portion of Bcd(A57-61) is required to mediate such activity-rescuing function of dCBP. Although capable of binding to DNA in vitro, Bcd(A57-61) is unable to access the hb enhancer element in cells, suggesting that its DNA binding defect is only manifested in a cellular context. Increased concentrations of dCBP restore not only the ability of Bcd(A57-61) to access the hb enhancer element in cells but also the occupancy of the general transcription factors TBP and TFIIB at the reporter promoter. These and other results suggest that an activator can undergo switches between its active and inactive states through sensing the opposing actions of positive and negative co-factors.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Fu D,Ma Jdoi
10.1093/nar/gki691keywords:
subject
Has Abstractpub_date
2005-07-19 00:00:00pages
3985-93issue
13eissn
0305-1048issn
1362-4962pii
33/13/3985journal_volume
33pub_type
杂志文章abstract::Modified bases, such as O6-methylguanines, are produced in cells exposed to alkylating agents and cause apoptosis. In human cells treated with N-methyl-N-nitrosourea, we detected a protein complex composed of MutSalpha, MutLalpha and PCNA on damaged DNA by immunoprecipitation method using chromatin extracts, in which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki878
更新日期:2005-10-04 00:00:00
abstract::We have studied a novel class of DNA sequences that cause DNA polymerases to pause. These sequences have the central consensus Py-G-C and are not necessarily adjacent to hairpins in the DNA template. Since most consensus sequences do not cause pauses under standard conditions, additional template features must exist t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.14.2774
更新日期:1996-07-15 00:00:00
abstract::We have developed an improved method for photofootprinting in vivo which utilizes the thermostable DNA polymerase from T. aquaticus (Taq) in a primer extension assay. UV light is used to introduce photoproducts into the genomic DNA of intact yeast cells. The photoproducts are then detected and mapped at the nucleotide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.1.171
更新日期:1989-01-11 00:00:00
abstract::Friedreich ataxia (FRDA) is caused by hyperexpansion of GAA*TTC repeats located in the first intron of the FXN gene, which inhibits transcription leading to the deficiency of frataxin. The FXN gene is an excellent target for therapeutic intervention since (i) 98% of patients carry the same type of mutation, (ii) the m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn604
更新日期:2008-11-01 00:00:00
abstract::Identification of MHC-binding peptides is a prerequisite in rational design of T-cell based peptide vaccines. During the past decade a number of computational approaches have been introduced for the prediction of MHC-binding peptides, efficiently reducing the number of candidate binders that need to be experimentally ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl284
更新日期:2006-07-01 00:00:00
abstract::We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp479
更新日期:2009-07-01 00:00:00
abstract::Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3'-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3' splice site] were typically e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh604
更新日期:2004-05-20 00:00:00
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
doi:10.1093/nar/gkw930
更新日期:2016-11-16 00:00:00
abstract::The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.10.2313
更新日期:1998-05-15 00:00:00
abstract::The class II genes of the major histocompatibility complex (MHC) encode a family of cell surface glycoproteins that present processed antigen to the T cell receptor. Class II genes are regulated coordinately, responding to both immunologic and developmental signals. Conserved sequence elements 5' to class II genes hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.6.1243
更新日期:1991-03-25 00:00:00
abstract::SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.14.e71
更新日期:2001-07-15 00:00:00
abstract::MiRNAs post-transcriptionally regulate gene expression by recruiting the miRNA-induced silencing complex (miRISC) to target mRNAs. However, the mechanisms by which miRISC components are maintained at appropriate levels for proper function are largely unknown. Here, we demonstrate that Caenorhabditis elegans TEG-1 regu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw836
更新日期:2017-02-17 00:00:00
abstract::Conformations of 8-bromo-2'-[unk]-triisopropylbenzenesulfonyladenosine ([unk]) and its 3'-[unk]-isomer ([unk]) in solution have been determined by the use of intramolecular nuclear Overhauser effects in (1)H NMR spectroscopy. Compound [unk] has been proved to have a conformation in which the adenosine and benzene ring...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.6.823
更新日期:1974-06-01 00:00:00
abstract::Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn358
更新日期:2008-08-01 00:00:00
abstract::Sas2p is a histone acetyltransferase implicated in the regulation of transcriptional silencing, and ORC is the six-subunit origin recognition complex involved in the initiation of DNA replication and the establishment of transcriptionally silent chromatin by silencers in yeast. We show here that SAS2 deletion (sas2Del...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn465
更新日期:2008-09-01 00:00:00
abstract::Influenza A viruses are hosted by numerous avian and mammalian species, which have shaped their evolution into distinct lineages worldwide. The viral genome consists of eight RNA segments that are frequently exchanged between different viruses via a process known as genetic reassortment. A complete genotype nomenclatu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm365
更新日期:2007-07-01 00:00:00
abstract::One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the characterization of regulatory motifs playing key roles in the regulation of gene expression at transcriptional and post-tran...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh465
更新日期:2004-07-01 00:00:00
abstract::We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions. Therefore, a comparison of phosphovariants between individuals or be...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1008
更新日期:2009-03-01 00:00:00
abstract::DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1500
更新日期:2002-04-01 00:00:00
abstract::In many viruses and transposons, expression of some genes requires alternative reading of the genetic code, also called recoding. Such events depend on specific mRNA sequences and can lead to read through of an in-frame stop codon or to +1 or -1 frameshifting. Here, we addressed the issue of conservation of recoding r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.9.1557
更新日期:1995-05-11 00:00:00
abstract::The human beta-actin promoter, including its 5' flanking region and 5' untranslated region, is ubiquitously active in mammalian cells in culture. In this report we investigated the transcriptional activity of, and the protein-DNA interactions that occur within, the proximal region of the human beta-actin promoter. Eff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.24.6913
更新日期:1991-12-25 00:00:00
abstract::We developed an integrated method to identify aptamers with only 10 fixed nucleotides through ligation and removal of primer binding sites within the systematic evolution of ligands by exponential enrichment (SELEX) process. This Tailored-SELEX approach was validated by identifying a Spiegelmer ('mirror-image aptamer'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng130
更新日期:2003-11-01 00:00:00
abstract::KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh991
更新日期:2004-12-15 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::We have examined the replication patterns of ribosomal DNA plasmids in vivo and in vitro using Xenopus eggs. Plasmids carrying different parts of the Xenopus ribosomal DNA sequence were allowed to replicate either in vitro in an egg extract or in vivo after microinjection into unfertilized eggs. The replication interm...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1463
更新日期:1992-04-11 00:00:00
abstract::Signals setting the level of transcription of the tRNA-tufB operon have been studied by deletion mapping. TufB transcription was measured in vivo with plasmid-borne tRNA-tufB:galk operon fusions. Removal of the sequences from -133 to -58 with respect to the transcription start point, results in a 90% decrease of tufB ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9515
更新日期:1987-11-25 00:00:00
abstract::The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2576
更新日期:1994-07-11 00:00:00
abstract::An efficient procedure for the synthesis of unnatural alpha-anomeric oligodeoxyribonucleotides is described. This solid-phase procedure is based on the use of alpha-nucleoside phosphoramidites and alpha-nucleoside derivatized solid supports corresponding to the four natural bases and allow rapid synthesis of oligonucl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.3.833
更新日期:1988-02-11 00:00:00
abstract::Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3'UTR of selenoprotein mRNAs, and trans-acting factors. Among these, the SECIS Binding Protein 2 (SBP2) is central to the mechanism...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp078
更新日期:2009-04-01 00:00:00
abstract::The multifunctional RNA-dependent RNA polymerase L protein of vesicular stomatitis virus catalyzes unconventional pre-mRNA capping via the covalent enzyme-pRNA intermediate formation, which requires the histidine-arginine (HR) motif in the polyribonucleotidyltransferase domain. Here, the effects of cap-defective mutat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku901
更新日期:2014-10-29 00:00:00