Transcriptional activation of the human prostatic acid phosphatase gene by NF-kappaB via a novel hexanucleotide-binding site.

Abstract:

:Human prostatic acid phosphatase (PAcP) is a prostate epithelium-specific differentiation antigen. Cellular PAcP functions as a neutral protein tyrosine phosphatase and is involved in regulating androgen-promoted prostate cancer cell proliferation. Despite the fact that the promoter of the PAcP gene has been cloned, the transcriptional factors that regulate PAcP expression remain unidentified. This article describes our analyses of the promoter of the PAcP gene. Deletion analyses of the promoter sequence up to -4893 (-4893/+87) revealed that a 577 bp fragment (-1356/-779) represents the unique positive cis-active element in human prostate cancer cells but not in HeLa cervix carcinoma cells. Interestingly, the 577 bp fragment contains a non-consensus nuclear factor kappaB (NF-kappaB)-binding site that is required for NF-kappaB up-regulation in prostate cancer cells, while NF-kappaB failed to have the same effect in HeLa cells. Conversely, inhibition of the NF-kappaB pathway stopped p65 NF-kappaB activation of the p1356 promoter activity. Gel shift and mutation analyses determined that AGGTGT (-1254/-1249) is the core sequence for NF-kappaB-binding and activation. Biologically, tumor necrosis factor-alpha (TNF-alpha) activated endogenous PAcP expression in LNCaP human prostate cancer cells. The data collectively indicate that NF-kappaB up-regulates PAcP promoter activity via its binding to the AGGTGT motif, a novel binding sequence located inside the cis-active enhancer element in human prostate cancer cells.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Zelivianski S,Glowacki R,Lin MF

doi

10.1093/nar/gkh677

keywords:

subject

Has Abstract

pub_date

2004-07-07 00:00:00

pages

3566-80

issue

12

eissn

0305-1048

issn

1362-4962

pii

32/12/3566

journal_volume

32

pub_type

杂志文章
  • The European Nucleotide Archive in 2020.

    abstract::The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scie...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1028

    authors: Harrison PW,Ahamed A,Aslam R,Alako BTF,Burgin J,Buso N,Courtot M,Fan J,Gupta D,Haseeb M,Holt S,Ibrahim T,Ivanov E,Jayathilaka S,Balavenkataraman Kadhirvelu V,Kumar M,Lopez R,Kay S,Leinonen R,Liu X,O'Cathail C,Pa

    更新日期:2021-01-08 00:00:00

  • CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA.

    abstract::Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw475

    authors: Zhou J,Wu R,Xue X,Qin Z

    更新日期:2016-08-19 00:00:00

  • Optimizing DNA assembly based on statistical language modelling.

    abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx859

    authors: Fang G,Zhang S,Dong Y

    更新日期:2017-12-15 00:00:00

  • Database on the structure of large ribosomal subunit RNA.

    abstract::Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.1.92

    authors: De Rijk P,Van de Peer Y,De Wachter R

    更新日期:1996-01-01 00:00:00

  • Capping of vesicular stomatitis virus pre-mRNA is required for accurate selection of transcription stop-start sites and virus propagation.

    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

    authors: Ogino T

    更新日期:2014-10-29 00:00:00

  • Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning.

    abstract::Nucleosomes are the most abundant protein-DNA complexes in eukaryotes that provide compaction of genomic DNA and are implicated in regulation of transcription, DNA replication and repair. The details of DNA positioning on the nucleosome and the DNA conformation can provide key regulatory signals. Hydroxyl-radical foot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx616

    authors: Shaytan AK,Xiao H,Armeev GA,Wu C,Landsman D,Panchenko AR

    更新日期:2017-09-19 00:00:00

  • DNA repair of pyrimidine dimers and 6-4 photoproducts in the ribosomal DNA.

    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

    authors: Balajee AS,May A,Bohr VA

    更新日期:1999-06-15 00:00:00

  • The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.

    abstract::The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introd...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky467

    authors: Rodriguez-R LM,Gunturu S,Harvey WT,Rosselló-Mora R,Tiedje JM,Cole JR,Konstantinidis KT

    更新日期:2018-07-02 00:00:00

  • Comparative whole genome transcriptome analysis of three Plasmodium falciparum strains.

    abstract::Gene expression patterns have been demonstrated to be highly variable between similar cell types, for example lab strains and wild strains of Saccharomyces cerevisiae cultured under identical growth conditions exhibit a wide range of expression differences. We have used a genome-wide approach to characterize transcrip...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj517

    authors: Llinás M,Bozdech Z,Wong ED,Adai AT,DeRisi JL

    更新日期:2006-02-21 00:00:00

  • Skeletal muscle actin mRNA. Characterization of the 3' untranslated region.

    abstract::Plasmids p749, p106, and p150 contain cDNA inserts complementary to rat skeletal muscle actin mRNA. Nucleotide sequence analysis indicates the following sequence relationships: p749 specifies codons 171 to 360; p150 specifies codons 357 to 374 together with 120 nucleotides of the 3'-non-translated region; p106 specifi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.3.579

    authors: Shani M,Nudel U,Zevin-Sonkin D,Zakut R,Givol D,Katcoff D,Carmon Y,Reiter J,Frischauf AM,Yaffe D

    更新日期:1981-02-11 00:00:00

  • Extraction of transcription regulatory signals from genome-wide DNA-protein interaction data.

    abstract::Deciphering gene regulatory network architecture amounts to the identification of the regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind, expression profiles they dictate and more complex relationships between alternative regulatory partnerships and alternative regulatory motifs...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki166

    authors: Garten Y,Kaplan S,Pilpel Y

    更新日期:2005-01-31 00:00:00

  • Coordinated regulation of mitochondrial topoisomerase IB with mitochondrial nuclear encoded genes and MYC.

    abstract::Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr208

    authors: Zoppoli G,Douarre C,Dalla Rosa I,Liu H,Reinhold W,Pommier Y

    更新日期:2011-08-01 00:00:00

  • Direct cross-linking of snRNP proteins F and 70K to snRNAs by ultra-violet radiation in situ.

    abstract::Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.23.10985

    authors: Woppmann A,Rinke J,Lührmann R

    更新日期:1988-12-09 00:00:00

  • 3D-Image analysis platform monitoring relocation of pluripotency genes during reprogramming.

    abstract::Nuclear organization of chromatin is an important level of genome regulation with positional changes of genes occurring during reprogramming. Inherent variability of biological specimens, wide variety of sample preparation and imaging conditions, though pose significant challenges to data analysis and comparison. Here...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr486

    authors: Jost KL,Haase S,Smeets D,Schrode N,Schmiedel JM,Bertulat B,Herzel H,Cremer M,Cardoso MC

    更新日期:2011-09-01 00:00:00

  • The regulatory region of phage fr replicase cistron. III. Initiation activity of specific fr RNA fragments.

    abstract::RNA fragments from phage fr covering the complete or part of the replicase cistron initiation region have been used as templates in the formation of a ribosomal initiation complex in vitro. The results so obtained together with our earlier findings in a similar approach applied to fragments of the structurally related...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.23.7763

    authors: Berzin V,Cielens I,Jansone I,Gren EJ

    更新日期:1982-12-11 00:00:00

  • GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

    abstract::Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.12.2607

    authors: Besemer J,Lomsadze A,Borodovsky M

    更新日期:2001-06-15 00:00:00

  • The Mediator subunit MED1/TRAP220 is required for optimal glucocorticoid receptor-mediated transcription activation.

    abstract::The MED1/TRAP220 subunit of the Mediator plays a key role in facilitating ligand-dependent interactions of this multisubunit coactivator complex with nuclear receptors through their ligand binding domains. The isolated MED1/TRAP220 protein previously was shown to interact with glucocorticoid receptor (GR) in a ligand-...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm661

    authors: Chen W,Roeder RG

    更新日期:2007-01-01 00:00:00

  • Fractionation and characterization of satellite DNAs of the kangaroo rat (Dipodomys ordii).

    abstract::Nuclear DNA from liver cells of the kangaroo rat species Dipodomysordii was fractionated and characterized with the aid of buoyant density gradients in neutral and alkaline CsCl and in Ag(+)-Cs(2)SO(4). More than one-half of the DNA was present in three density satellites, a greater proportion than in any other specie...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/1.4.559

    authors: Hatch FT,Mazrimas JA

    更新日期:1974-04-01 00:00:00

  • PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION.

    abstract::Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1286

    authors: Elati M,Nicolle R,Junier I,Fernández D,Fekih R,Font J,Képès F

    更新日期:2013-02-01 00:00:00

  • Data mining for proteins characteristic of clades.

    abstract::A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl440

    authors: Bern M,Goldberg D,Lyashenko E

    更新日期:2006-01-01 00:00:00

  • Nucleotide sequence and corresponding amino acid sequence of the gene for the major antigen of foot and mouth disease virus.

    abstract::A segment of 1160 nucleotides of the FMDV genome has been sequenced using three overlapping fragments of cloned cDNA from FMDV strain O1K. This sequence contains the coding sequence for the viral capsid protein VP1 as shown by its homology to known and newly determined amino acid sequences from this man antigenic poly...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.8.1919

    authors: Kurz C,Forss S,Küpper H,Strohmaier K,Schaller H

    更新日期:1981-04-24 00:00:00

  • Controlled loading of oligodeoxyribonucleotide monolayers onto unoxidized crystalline silicon; fluorescence-based determination of the surface coverage and of the hybridization efficiency; parallel imaging of the process by Atomic Force Microscopy.

    abstract::Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the inciden...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnj034

    authors: Cattaruzza F,Cricenti A,Flamini A,Girasole M,Longo G,Prosperi T,Andreano G,Cellai L,Chirivino E

    更新日期:2006-02-28 00:00:00

  • OMA 2011: orthology inference among 1000 complete genomes.

    abstract::OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1238

    authors: Altenhoff AM,Schneider A,Gonnet GH,Dessimoz C

    更新日期:2011-01-01 00:00:00

  • SV40 deletion mutants lacking the 21-bp repeated sequences are viable, but have noncomplementable deficiencies.

    abstract::We have constructed deletion mutants of simian virus 40 (SV40) lacking the two tandemly repeated copies or all three copies of the 21-bp repeated sequence located in the origin region. The mutants were viable, but had lower infectivities compared to the wild type. The mutant lacking two copies of the 21-bp repeat grew...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.5.1601

    authors: Hartzell SW,Yamaguchi J,Subramanian KN

    更新日期:1983-03-11 00:00:00

  • Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility.

    abstract::Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. We developed a new single-molecule method to probe non-specific DNA interactions for two HMGB homologs: the human HMGB2 box A domain and yeast Nhp6Ap, along with chimeric mutants replacin...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1031

    authors: McCauley MJ,Rueter EM,Rouzina I,Maher LJ 3rd,Williams MC

    更新日期:2013-01-07 00:00:00

  • Antibodies to N6-(delta2-isopentenyl) adenosine and its nucleotide: interaction with purified tRNAs and with bases, nucleosides and nucleotides of the isopentenyladenosine family.

    abstract::The interaction of antibodies directed toward N6-(delta2-isopentenyl)adenosine, i6Ado, or its nucleotide with related bases, nucleosides, nucleotides and purified tRNAs is described. The selectivity of the antibody preparation was tested in inhibition experiments utilizing a sensitive radioimmunoassay to quantitate th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.9.3439

    authors: Milstone DS,Vold BS,Glitz DG,Shutt N

    更新日期:1978-09-01 00:00:00

  • The kinetic properties of cruciform extrusion are determined by DNA base-sequence.

    abstract::The extrusion kinetics of two cruciforms derived from unrelated DNA sequences differ markedly. Kinetic barriers exist for both reactions, necessitating elevated temperatures before extrusion proceeds at measureable speeds, but the dependence upon temperature and ionic strength is quite different for the two sequences....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.5.1443

    authors: Lilley DM

    更新日期:1985-03-11 00:00:00

  • Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks.

    abstract::Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompan...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw679

    authors: Xu Y,Guo M,Liu X,Wang C,Liu Y,Liu G

    更新日期:2016-11-16 00:00:00

  • GenBank.

    abstract::GenBank(®) (http://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 300 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing proj...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1216

    authors: Benson DA,Clark K,Karsch-Mizrachi I,Lipman DJ,Ostell J,Sayers EW

    更新日期:2015-01-01 00:00:00

  • Molecular characteristics of reiterative DNA unwinding by the Caenorhabditis elegans RecQ helicase.

    abstract::The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz708

    authors: Choi S,Lee SW,Kim H,Ahn B

    更新日期:2019-10-10 00:00:00