Binding of TFIIIA to derivatives of 5S RNA containing sequence substitutions or deletions defines a minimal TFIIIA binding site.

Abstract:

:The repetitive zinc finger domain of transcription factor IIIA binds 5S DNA and 5S RNA with similar affinity. Site directed mutagenesis of the Xenopus borealis somatic 5S RNA gene has been used to produce a series of derivatives of 5S RNA containing local sequence substitutions or sequence deletions. Gel mobility shift analyses of the binding of TFIIIA to these altered 5S RNAs revealed that all three of the helical stems of the 5S RNA secondary structure are required for binding. TFIIIA was observed to bind with normal affinity to RNAs lacking 12 nucleotides at either the loop c or loop e/helix V regions of 5S RNA, as well as to a double mutant containing both deletions. The secondary structure of the resulting 96-nucleotide RNA, studied using structure-specific ribonucleases, was found to resemble the central portion of 5S RNA.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Bogenhagen DF,Sands MS

doi

10.1093/nar/20.11.2639

keywords:

subject

Has Abstract

pub_date

1992-06-11 00:00:00

pages

2639-45

issue

11

eissn

0305-1048

issn

1362-4962

journal_volume

20

pub_type

杂志文章
  • Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases.

    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

    authors: Ryu GM,Song P,Kim KW,Oh KS,Park KJ,Kim JH

    更新日期:2009-03-01 00:00:00

  • JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes.

    abstract::Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn1067

    authors: Cliffe LJ,Kieft R,Southern T,Birkeland SR,Marshall M,Sweeney K,Sabatini R

    更新日期:2009-04-01 00:00:00

  • Single cell epigenetic visualization assay.

    abstract::Characterization of the epigenetic status of individual cells remains a challenge. Current sequencing approaches have limited coverage, and it is difficult to assign an epigenetic status to the transcription state of individual gene alleles in the same cell. To address these limitations, a targeted microscopy-based ep...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkab009

    authors: Kint S,Van Criekinge W,Vandekerckhove L,De Vos WH,Bomsztyk K,Krause DS,Denisenko O

    更新日期:2021-01-28 00:00:00

  • GenBank: update.

    abstract::GenBank is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh045

    authors: Benson DA,Karsch-Mizrachi I,Lipman DJ,Ostell J,Wheeler DL

    更新日期:2004-01-01 00:00:00

  • Fast and global detection of periodic sequence repeats in large genomic resources.

    abstract::Periodically repeating DNA and protein elements are involved in various important biological events including genomic evolution, gene regulation, protein complex formation, and immunity. Notably, the currently used genome editing tools such as ZFNs, TALENs, and CRISPRs are also all associated with periodically repeati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky890

    authors: Mori H,Evans-Yamamoto D,Ishiguro S,Tomita M,Yachie N

    更新日期:2019-01-25 00:00:00

  • Characterization of a DNA binding domain in the C-terminus of HIV-1 integrase by deletion mutagenesis.

    abstract::The integrase (IN) protein of human immunodeficiency virus type 1 (HIV-1) catalyzes site-specific cleavage of 2 bases from the viral long terminal repeat (LTR) sequence yet it binds DNA with little DNA sequence specificity. We have previously demonstrated that the C-terminal half of IN (amino acids 154-288) possesses ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.15.3507

    authors: Woerner AM,Marcus-Sekura CJ

    更新日期:1993-07-25 00:00:00

  • Epigenetics of a tandem DNA repeat: chromatin DNaseI sensitivity and opposite methylation changes in cancers.

    abstract::DNA methylation and chromatin DNaseI sensitivity were analyzed in and adjacent to D4Z4 repeat arrays, which consist of 1 to approximately 100 tandem 3.3-kb units at subtelomeric 4q and 10q. D4Z4 displayed hypomethylation in some cancers and hypermethylation in others relative to normal tissues. Surprisingly, in cancer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn055

    authors: Tsumagari K,Qi L,Jackson K,Shao C,Lacey M,Sowden J,Tawil R,Vedanarayanan V,Ehrlich M

    更新日期:2008-04-01 00:00:00

  • Inherited disorders of cobalamin metabolism disrupt nucleocytoplasmic transport of mRNA through impaired methylation/phosphorylation of ELAVL1/HuR.

    abstract::The molecular mechanisms that underlie the neurological manifestations of patients with inherited diseases of vitamin B12 (cobalamin) metabolism remain to date obscure. We observed transcriptomic changes of genes involved in RNA metabolism and endoplasmic reticulum stress in a neuronal cell model with impaired cobalam...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky634

    authors: Battaglia-Hsu SF,Ghemrawi R,Coelho D,Dreumont N,Mosca P,Hergalant S,Gauchotte G,Sequeira JM,Ndiongue M,Houlgatte R,Alberto JM,Umoret R,Robert A,Paoli J,Jung M,Quadros EV,Guéant JL

    更新日期:2018-09-06 00:00:00

  • Ultraviolet light irradiation of PM2 superhelical DNA.

    abstract::Superhelical PM2 DNA can be photochemically modified by u.v. irradiation. The variation of S20,w with dose shows the following characteristics. There is a linear increase from 28 to 31s produced by a low dose of u.v. irradiation (4,000 ergs/mm2). A plateau in S20,w occurs between 4,000 and 10,000 ergs/mm2. The S20,w t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.5.1243

    authors: Woodworth-Gutai M,Lebowitz J,Kato AC,Denhardt DT

    更新日期:1977-01-01 00:00:00

  • PhiReX: a programmable and red light-regulated protein expression switch for yeast.

    abstract::Highly regulated induction systems enabling dose-dependent and reversible fine-tuning of protein expression output are beneficial for engineering complex biosynthetic pathways. To address this, we developed PhiReX, a novel red/far-red light-regulated protein expression system for use in Saccharomyces cerevisiae. PhiRe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx610

    authors: Hochrein L,Machens F,Messerschmidt K,Mueller-Roeber B

    更新日期:2017-09-06 00:00:00

  • EASI--enrichment of alternatively spliced isoforms.

    abstract::Alternative splicing produces more than one protein from the majority of genes and the rarer forms can have dominant functions. Instability of alternative transcripts can also hinder the study of regulation of gene expression by alternative splicing. To investigate the true extent of alternative splicing we have devel...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl592

    authors: Venables JP,Burn J

    更新日期:2006-01-01 00:00:00

  • Construction of a chromosome-enriched HpaII library from flow-sorted wheat chromosomes.

    abstract::We report here the first successful generation of a chromosome-enriched library from flow sorted plant chromosomes. Chromosomes with a characteristic DNA content (a peak) were sorted from a synchronized cell culture (TaKB1, derived from Triticum aestivum). A HpaII library was constructed from the sorted chromosomes an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.8.1897

    authors: Wang ML,Leitch AR,Schwarzacher T,Heslop-Harrison JS,Moore G

    更新日期:1992-04-25 00:00:00

  • Functional regulation of FEN1 nuclease and its link to cancer.

    abstract::Flap endonuclease-1 (FEN1) is a member of the Rad2 structure-specific nuclease family. FEN1 possesses FEN, 5'-exonuclease and gap-endonuclease activities. The multiple nuclease activities of FEN1 allow it to participate in numerous DNA metabolic pathways, including Okazaki fragment maturation, stalled replication fork...

    journal_title:Nucleic acids research

    pub_type: 杂志文章,评审

    doi:10.1093/nar/gkq884

    authors: Zheng L,Jia J,Finger LD,Guo Z,Zer C,Shen B

    更新日期:2011-02-01 00:00:00

  • A rat brain mRNA encoding a transcriptional activator homologous to the DNA binding domain of retroviral integrases.

    abstract::We have isolated a rat cDNA, named FE65, hybridizing to an mRNA of about 2,300 nucleotides present in rat brain, undetectable in rat liver and very poorly represented in other tissues. An mRNA of the same size is present in human neuroblastoma cells and is absent from other human cell lines. The FE65 cDNA contains an ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.19.5269

    authors: Duilio A,Zambrano N,Mogavero AR,Ammendola R,Cimino F,Russo T

    更新日期:1991-10-11 00:00:00

  • A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage.

    abstract::The infection of Pseudomonas aeruginosa by the giant bacteriophage phiKZ is resistant to host RNA polymerase (RNAP) inhibitor rifampicin. phiKZ encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit RNAPs. Polypeptides of one set are encoded by mid...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1095

    authors: Yakunina M,Artamonova T,Borukhov S,Makarova KS,Severinov K,Minakhin L

    更新日期:2015-12-02 00:00:00

  • Meiosis-specific yeast Hop1 protein promotes synapsis of double-stranded DNA helices via the formation of guanine quartets.

    abstract::In most eukaryotes, genetic exchange between paired homologs occurs in the context of a tripartite proteinaceous structure called the synaptonemal complex (SC). Genetic analyses have revealed that the genes encoding SC proteins are vital for meiotic chromosome pairing and recombination. However, the number, nature and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh559

    authors: Anuradha S,Muniyappa K

    更新日期:2004-04-28 00:00:00

  • The FurA regulon in Anabaena sp. PCC 7120: in silico prediction and experimental validation of novel target genes.

    abstract::In the filamentous cyanobacterium Anabaena sp. PCC 7120, the ferric uptake regulator FurA functions as a global transcriptional regulator. Despite several analyses have focused on elucidating the FurA-regulatory network, the number of target genes described for this essential transcription factor is limited to a handf...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku123

    authors: González A,Angarica VE,Sancho J,Fillat MF

    更新日期:2014-04-01 00:00:00

  • Nucleotide sequence determination of bacteriophage T4 glycine transfer ribonucleic acid.

    abstract::The nucleotide sequence of a T4 tRNA with an anticodon for glycine has been determined using (32)P-labeled material from T4-infected cultures of Escherichiacoli. The sequence is: pGCGGAUAUCGUAUAAUGmGDAUUACCUCAGACUUCCAApsiCUGAUGAUGUGAGTpsiCGAUUCUCAUUAUCCGCUCCA-OH. The 74 nucleotide sequence can be arranged in the class...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/1.10.1287

    authors: Stahl S,Paddock GV,Abelson J

    更新日期:1974-10-01 00:00:00

  • Characterization of RNA helicase A as component of STAT6-dependent enhanceosome.

    abstract::Signal transducer and activator of transcription 6 (STAT6) is a regulator of transcription for interleukin-4 (IL-4)-induced genes. The ability of STAT6 to activate transcription depends on functional interaction with other transcription factors and coactivators. We have characterized the mechanism of STAT6-mediated tr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl539

    authors: Välineva T,Yang J,Silvennoinen O

    更新日期:2006-01-01 00:00:00

  • Transcriptionally competent chromatin assembled with exogenous histones in a yeast whole cell extract.

    abstract::We describe a cell-free chromatin assembly system derived from the yeast Saccharomyces cerevisiae, which efficiently packages DNA into minichromosomes in a reaction dependent on exogenous core histones and an ATP-regenerating system. Both supercoiled and relaxed plasmid DNA serve as templates for nucleosomal loading i...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnh107

    authors: Rodríguez-Campos A,Koop R,Faraudo S,Beato M

    更新日期:2004-07-28 00:00:00

  • Downstream signaling mechanism of the C-terminal activation domain of transcriptional coactivator CoCoA.

    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

    authors: Kim JH,Yang CK,Stallcup MR

    更新日期:2006-05-22 00:00:00

  • Gibbs Recursive Sampler: finding transcription factor binding sites.

    abstract::The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multip...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg608

    authors: Thompson W,Rouchka EC,Lawrence CE

    更新日期:2003-07-01 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

  • Improvements in the phosphoramidite procedure for the synthesis of oligodeoxyribonucleotides.

    abstract::The paper describes an improved method for the synthesis of oligodeoxyribonucleotides using phosphoramidite chemistry. Our procedure relies on novel phosphoramidite intermediates, the deoxyribonucleoside-3'-morpholine-methoxyphosphins. These compounds are extremely stable and can be purified readily. Condensation reac...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.9.2575

    authors: Dörper T,Winnacker EL

    更新日期:1983-05-11 00:00:00

  • Quantitative analysis of specific labelled RNA'S using DNA covalently linked to diazobenzyloxymethyl-paper.

    abstract::Substantial amounts of DNA (at least 25 microgram per cm2) can be stably bound to diazobenzyloxymethyl (DBM)-paper. Complementary RNA will hybridize to the DNA paper almost completely in 24 hours. Using several different conditions of hybridization and washing, the background of RNA bound non-specifically is very low ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.1.195

    authors: Stark GR,Williams JG

    更新日期:1979-01-01 00:00:00

  • SPINE 2: a system for collaborative structural proteomics within a federated database framework.

    abstract::We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laborato...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg397

    authors: Goh CS,Lan N,Echols N,Douglas SM,Milburn D,Bertone P,Xiao R,Ma LC,Zheng D,Wunderlich Z,Acton T,Montelione GT,Gerstein M

    更新日期:2003-06-01 00:00:00

  • Rapid synthesis of oligodeoxyribonucleotides. IV. Improved solid phase synthesis of oligodeoxyribonucleotides through phosphotriester intermediates.

    abstract::A phosphotriester solid phase method on a polyamide support has been used to prepare oligodeoxyribonucleotides up to 12 units long. Compared to solid phase phosphodiester synthesis the new methodology is quicker, more flexible and gives 10-60-fold better overall yields. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.5.1081

    authors: Gait MJ,Singh M,Sheppard RC,Edge MD,Greene AR,Heathcliffe GR,Atkinson TC,Newton CR,Markham AF

    更新日期:1980-03-11 00:00:00

  • Two factor authentication: Asf1 mediates crosstalk between H3 K14 and K56 acetylation.

    abstract::The ability of histone chaperone Anti-silencing factor 1 (Asf1) to direct acetylation of lysine 56 of histone H3 (H3K56ac) represents an important regulatory step in genome replication and DNA repair. In Saccharomyces cerevisiae, Asf1 interacts functionally with a second chaperone, Vps75, and the lysine acetyltransfer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz508

    authors: Cote JM,Kuo YM,Henry RA,Scherman H,Krzizike DD,Andrews AJ

    更新日期:2019-08-22 00:00:00

  • Structural and mechanistic insights into Helicobacter pylori NikR activation.

    abstract::NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1216

    authors: Bahlawane C,Dian C,Muller C,Round A,Fauquant C,Schauer K,de Reuse H,Terradot L,Michaud-Soret I

    更新日期:2010-05-01 00:00:00

  • Oxidative damage to 5-methylcytosine in DNA.

    abstract::Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl gro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.16.3239

    authors: Zuo S,Boorstein RJ,Teebor GW

    更新日期:1995-08-25 00:00:00