Abstract:
:Hexokinase 2 is an essential factor for signalling repression through the Saccharomyces cerevisiae high-glucose sensing pathway. The main regulatory mechanism that controls the HXK2 gene expression in yeast is mediated by the Rgt1 and Med8 transcription factors, which repress HXK2 expression in low-glucose containing media. In this study, we show that the repression activity of Rgt1 is regulated by Snf1 and Tpk3 protein kinases. Binding of Rgt1 to the HXK2 promoter requires Rgt1 phosphorylation by Snf1 or by an Snf1-dependent protein kinase. Conversely, Rgt1 hyperphosphorylation by the Tpk3 or by a Tpk3-dependent protein kinase dissociates Rgt1 from the repressor complex. Two-hybrid and chromatin immunoprecipitation experiments indicate that an Snf1-dependent interaction between Rgt1 and Med8 in the repressor complex is also essential for Rgt1 repression. The repression of HXK2 transcription by Rgt1 likely occurs through the formation of a DNA loop in the HXK2 locus, spanning the promoter and coding regions. These results suggest that a novel silent-chromatin loop is responsible for Rgt1-dependent transcriptional regulation of the HXK2 gene.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Palomino A,Herrero P,Moreno Fdoi
10.1093/nar/gkl028keywords:
subject
Has Abstractpub_date
2006-03-09 00:00:00pages
1427-38issue
5eissn
0305-1048issn
1362-4962pii
34/5/1427journal_volume
34pub_type
杂志文章abstract::The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.5.667
更新日期:1975-05-01 00:00:00
abstract::The Kruppel-like factor 5 (KLF5/IKLF) belongs to the Kruppel family of genes which bind GC-rich DNA elements and activate or repress their target genes in a promoter context and/or cellular environment-dependent manner. In the present study, we used the Gal4 fusion assay system to characterize the mechanism of transac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg310
更新日期:2003-04-15 00:00:00
abstract::Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn207
更新日期:2008-06-01 00:00:00
abstract::G-quadruplex (G4) DNA structures are linked to key biological processes and human diseases. Small molecules that target specific G4 DNA structures and signal their presence would therefore be of great value as chemical research tools with potential to further advance towards diagnostic and therapeutic developments. Ho...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1205
更新日期:2020-02-20 00:00:00
abstract::EpoDB is a database of genes expressed in vertebrate red blood cells. It is also a prototype for the creation of cell and tissue-specific databases from multiple external sources. The information in EpoDB obtained from GenBank, SWISS-PROT, Transfac, TRRD and GERD is curated to provide high quality data for sequence an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.200
更新日期:1999-01-01 00:00:00
abstract::The rolling circle DNA replication structures generated by the in vitro phage T4 replication system were analyzed using two-dimensional agarose gels. Replication structures were generated in the presence or absence of T4 primase (gp61), permitting the analysis of replication forks with either duplex or single-stranded...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.11.2166
更新日期:1996-06-01 00:00:00
abstract::Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1319
更新日期:2019-04-08 00:00:00
abstract::Recognizing the methylation status of specific DNA sequences is central to the function of many systems in eukaryotes and prokaryotes. Restriction-modification systems have to distinguish between 'self' and 'non-self' DNA and depend on the inability of restriction endonucleases to cleave their DNA substrates when the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.16.3143
更新日期:2000-08-15 00:00:00
abstract::GeneAlign is a coding exon prediction tool for predicting protein coding genes by measuring the homologies between a sequence of a genome and related sequences, which have been annotated, of other genomes. Identifying protein coding genes is one of most important tasks in newly sequenced genomes. With increasing numbe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl307
更新日期:2006-07-01 00:00:00
abstract::iSARST is a web server for efficient protein structural similarity searches. It is a multi-processor, batch-processing and integrated implementation of several structural comparison tools and two database searching methods: SARST for common structural homologs and CPSARST for homologs with circular permutations. iSARS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp291
更新日期:2009-07-01 00:00:00
abstract::We describe a versatile genetic system for rapid analysis of mammalian gene function. In this, loss of reporter activity in a novel embryonic stem (ES) cell line enables rapid identification of targeting to the ubiquitously expressed Rosa26 locus. Subsequent regulation of gene activity is governed by a dual regulatory...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni146
更新日期:2005-10-12 00:00:00
abstract::We present the preparation of an ion exchange paper which can be used as a solid carrier in the transfer of RNA from gels. In addition to detection by blot hybridization to specific probes, transferred RNA can be characterized by cell-free translation in situ. Preparation of the paper is simple, inexpensive and reprod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.16.4831
更新日期:1982-08-25 00:00:00
abstract::The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh236
更新日期:2004-02-11 00:00:00
abstract::Redefinition of UAG, UAA and UGA to specify a standard amino acid occurs in response to recoding signals present in a minority of mRNAs. This 'read-through' is in competition with termination and is utilized for gene expression. One of the recoding signals known to stimulate read-through is a hexanucleotide sequence o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.9.2011
更新日期:2002-05-01 00:00:00
abstract::Mono- and polyclonal antibodies directed against different domains of the potato leafroll luteovirus (PLRV) P1 (ORF1) protein were applied to the analysis of P1 expression during PLRV replication in planta. Western analyses detected P1 and a protein of approximately 25 kDa (P1-C25) that accumulated to readily detectab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.421
更新日期:1999-01-15 00:00:00
abstract::Human telomerase RNA (hTR) contains several guanine tracts at its 5'-end that can form a G4-quadruplex structure. Previous evidence suggests that a G4-quadruplex within this region disrupts the formation of an important structure within hTR known as the P1 helix, a critical element in defining the template boundary fo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1306
更新日期:2012-05-01 00:00:00
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
doi:10.1093/nar/18.23.7007
更新日期:1990-12-11 00:00:00
abstract::7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique Pol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku711
更新日期:2014-09-01 00:00:00
abstract::A solution of benzenesulphonic acid (3%, w/v) in a dimethylformamide and dichloromethane mixture (9:1, v/v) is shown to be a very effective reagent for the detritylation of deoxyoligonucleotides attached to a solid support. The levels of depurination with this reagent were lower than those observed with other reagents...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.18.5605
更新日期:1982-09-25 00:00:00
abstract::Microsatellites are widely used as genetic markers because they are co-dominant, multiallelic, easily scored and highly polymorphic. A major drawback of microsatellite markers is the time and cost required to characterise them. We have developed a novel technique to reduce this cost by producing a microsatellite-rich ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.21.4369
更新日期:1996-11-01 00:00:00
abstract::We describe PReMod, a new database of genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. The prediction algorithm, described previously in Blanchette et al. (2006) Genome Res., 16, 656-668, exploits the fact that many known CRMs are made of clusters of phylogenetically conser...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl879
更新日期:2007-01-01 00:00:00
abstract::The genomic distribution of 23 nuclear genes from three dicotyledons (pea, sunflower, tobacco) and five monocotyledons of the Gramineae family (barley, maize, rice, oat, wheat) was studied by localizing these genes in DNA fractions obtained by preparative centrifugation in Cs2SO4/BAMD density gradients. Each one of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.7.1859
更新日期:1990-04-11 00:00:00
abstract::Chromatin modulation at various cis-acting elements is critical for V(D)J recombination during T and B cell development. MARbeta, a matrix-associated region (MAR) located upstream of the T cell receptor beta (TCRbeta) enhancer (Ebeta), serves a crucial role in silencing Ebeta-mediated TCR activation. By DNaseI hyperse...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh807
更新日期:2004-09-15 00:00:00
abstract::DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no single method can identify the location, direction and speed of replication forks with high resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa517
更新日期:2020-09-04 00:00:00
abstract::chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression profiling. The server implements a probe selection algorithm that takes as an input, in addition to the target sequences...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq517
更新日期:2010-07-01 00:00:00
abstract::In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNP...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl475
更新日期:2006-01-01 00:00:00
abstract::To elucidate the general constraints imposed on the structure of the D- and T-loops in functional tRNAs, active suppressor tRNAs were selected in vivo from a combinatorial tRNA gene library in which several nucleotide positions of these loops were randomized. Analysis of the nucleotide sequences of the selected clones...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg448
更新日期:2003-07-15 00:00:00
abstract::Methylation of the 2'-hydroxyl-group of ribonucleotides is found in all major classes of RNA in eukaryotes and is one of the most abundant posttranscriptional modifications of stable RNAs. In spite of intense studies, the multiple functions of RNA 2'-O-methylation are still not understood. One major obstacle in the fi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw200
更新日期:2016-05-05 00:00:00
abstract::The coiled-coil coactivator (CoCoA) is a transcriptional coactivator for nuclear receptors and enhances nuclear receptor function by the interaction with the bHLH-PAS domain (AD3) of p160 coactivators. The C-terminal activation domain (AD) of CoCoA possesses strong transactivation activity and is required for the coac...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl361
更新日期:2006-05-22 00:00:00
abstract::We have analyzed the ATPase activity exhibited by the UvrABC DNA repair complex. The UvrA protein is an ATPase whose lack of DNA dependence may be related to the ATP induced monomer-dimer transitions. ATP induced dimerization may be responsible for the enhanced DNA binding activity observed in the presence of ATP. Alt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.11.4145
更新日期:1989-06-12 00:00:00