Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA.


:We have purified to near homogeneity a novel nuclear protein from HeLa cells, that specifically binds to scaffold or matrix attachment region DNA elements (S/MAR DNA). The protein, designated SAF-B for scaffold attachment factor B, is an abundant component of chromatin, but not of the nuclear matrix and is expressed in all human tissues investigated. Antibodies against the purified protein were raised in rabbit and used to isolate the complete cDNA encoding SAF-B by immunoscreening. As predicted from the cDNA sequence, SAF-B contains 849 amino acids (96 696 Da), without significant homology to any known protein. SAF-B is rich in charged residues, leading to an aberrant migration on SDS gels, and has two putative bipartite nuclear localisation signals.


Nucleic Acids Res


Nucleic acids research


Renz A,Fackelmayer FO




Has Abstract


1996-03-01 00:00:00














  • ASD: a comprehensive database of allosteric proteins and modulators.

    abstract::Allostery is the most direct, rapid and efficient way of regulating protein function, ranging from the control of metabolic mechanisms to signal-transduction pathways. However, an enormous amount of unsystematic allostery information has deterred scientists who could benefit from this field. Here, we present the AlloS...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Huang Z,Zhu L,Cao Y,Wu G,Liu X,Chen Y,Wang Q,Shi T,Zhao Y,Wang Y,Li W,Li Y,Chen H,Chen G,Zhang J

    更新日期:2011-01-01 00:00:00

  • Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL.

    abstract::The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Venditti V,Niccolai N,Butcher SE

    更新日期:2008-03-01 00:00:00

  • Impact of probe annotation on the integration of miRNA-mRNA expression profiles for miRNA target detection.

    abstract::MicroRNAs (miRNAs) are small non-coding RNAs that mediate gene expression at the post-transcriptional and translational levels by an imperfect binding to target mRNA 3'UTR regions. While the ab-initio computational prediction of miRNA-mRNA interactions still poses significant challenges, it is possible to overcome som...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sales G,Coppe A,Bicciato S,Bortoluzzi S,Romualdi C

    更新日期:2010-04-01 00:00:00

  • Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.

    abstract::Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Gelfand MS,Koonin EV,Mironov AA

    更新日期:2000-02-01 00:00:00

  • A new method for predicting signal sequence cleavage sites.

    abstract::A new method for identifying secretory signal sequences and for predicting the site of cleavage between a signal sequence and the mature exported protein is described. The predictive accuracy is estimated to be around 75-80% for both prokaryotic and eukaryotic proteins. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: von Heijne G

    更新日期:1986-06-11 00:00:00

  • Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization.

    abstract::The photostability and narrow emission spectra of non-organic quantum dot fluorophores (QDs) make them desirable candidates for fluorescent in situ hybridization (FISH) to study the expression of specific mRNA transcripts. We developed a novel method for direct QD labeling of modified oligonucleotide probes through st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chan P,Yuen T,Ruf F,Gonzalez-Maeso J,Sealfon SC

    更新日期:2005-10-13 00:00:00

  • Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis.

    abstract::Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Trilling M,Bellora N,Rutkowski AJ,de Graaf M,Dickinson P,Robertson K,Prazeres da Costa O,Ghazal P,Friedel CC,Albà MM,Dölken L

    更新日期:2013-09-01 00:00:00

  • Specific binding of MobA, a plasmid-encoded protein involved in the initiation and termination of conjugal DNA transfer, to single-stranded oriT DNA.

    abstract::MobA protein, encoded by the broad host-range plasmid R1162, is required for conjugal mobilization of this plasmid. The protein is an essential part of the relaxosome, and is also necessary for the termination of strand transfer. In vitro, MobA is a nuclease specific for one of the two DNA strands of the origin of tra...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bhattacharjee MK,Meyer RJ

    更新日期:1993-09-25 00:00:00

  • Structure of recombinant rat UBF by electron image analysis and homology modelling.

    abstract::We have studied the structure of recombinant rat UBF (rrUBF), an RNA polymerase I transcription factor, by electron microscopy and image analysis of single particles contrasted with methylamine tungstate. Recombinant rat UBF appeared to be a flat, U-shaped protein with a central region of low density. In the dominant ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Neil KJ,Ridsdale RA,Rutherford B,Taylor L,Larson DE,Glibetic M,Rothblum LI,Harauz G

    更新日期:1996-04-15 00:00:00

  • Effects of base substituents on the hydration of B- and Z-DNA: correlations to the B- to Z-DNA transition.

    abstract::We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kagawa TF,Howell ML,Tseng K,Ho PS

    更新日期:1993-12-25 00:00:00

  • Efficient reamplification of differential display products by transient ligation and thermal asymmetric PCR.

    abstract::A new method for specific reamplification of DDRT-PCR products is presented. After transient ligation of the primary DDRT-PCR fragments into a T-vector, the cDNAs of interest were reamplified by hemi-nested PCR and thermally asymmetric cycles. In contrast to the originally described protocol, this method of reamplific...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bonnet S,Prévot G,Bourgouin C

    更新日期:1998-02-15 00:00:00

  • Stabilization of XIAP mRNA through the RNA binding protein HuR regulated by cellular polyamines.

    abstract::The X chromosome-linked inhibitor of apoptosis protein (XIAP) is the most potent intrinsic caspase inhibitor and plays an important role in the maintenance of intestinal epithelial integrity. The RNA binding protein, HuR, regulates the stability and translation of many target transcripts. Here, we report that HuR asso...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang X,Zou T,Rao JN,Liu L,Xiao L,Wang PY,Cui YH,Gorospe M,Wang JY

    更新日期:2009-12-01 00:00:00

  • A self-initiating eukaryotic transient gene expression system based on contransfection of bacteriophage T7 RNA polymerase and DNA vectors containing a T7 autogene.

    abstract::A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chen X,Li Y,Xiong K,Wagner TE

    更新日期:1994-06-11 00:00:00

  • ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.

    abstract::Biological pathways can provide key information on the organization of biological systems. ArrayXPath (http://www.snubi.org/software/ArrayXPath/) is a web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chung HJ,Kim M,Park CH,Kim J,Kim JH

    更新日期:2004-07-01 00:00:00

  • Covalent attachment of synthetic DNA to self-assembled monolayer films.

    abstract::The covalent attachment of thiol-modified DNA oligomers; to self-assembled monolayer silane films on fused silica and oxidized silicon substrates is described. A heterobifunctional crosslinking molecule bearing both thiol- and amino-reactive moieties was used to tether a DNA oligomer (modified at its terminus with a t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Chrisey LA,Lee GU,O'Ferrall CE

    更新日期:1996-08-01 00:00:00

  • Altered expression and editing of miRNA-100 regulates iTreg differentiation.

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    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Negi V,Paul D,Das S,Bajpai P,Singh S,Mukhopadhyay A,Agrawal A,Ghosh B

    更新日期:2015-09-18 00:00:00

  • Purification and characterization of the MspI DNA methyltransferase cloned and overexpressed in E. coli.

    abstract::The MspI restriction-modification system, which recognizes the sequence 5'-CCGG-3', has been previously cloned and sequenced (1). We subcloned the methyltransferase gene (M.MspI) downstream of the ptac promoter in the multicopy vector pUC119 and overexpressed it in E. coli. Upon induction with IPTG, M.MspI constitutes...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Dubey AK,Mollet B,Roberts RJ

    更新日期:1992-04-11 00:00:00

  • Genome-scale design of PCR primers and long oligomers for DNA microarrays.

    abstract::During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Haas SA,Hild M,Wright AP,Hain T,Talibi D,Vingron M

    更新日期:2003-10-01 00:00:00

  • fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.

    abstract::Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across tax...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhu C,Mahlich Y,Miller M,Bromberg Y

    更新日期:2018-01-04 00:00:00

  • Struct2Net: a web service to predict protein-protein interactions using a structure-based approach.

    abstract::Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein-protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Singh R,Park D,Xu J,Hosur R,Berger B

    更新日期:2010-07-01 00:00:00

  • Epigenetic features of human telomeres.

    abstract::Although subtelomeric regions in humans are heterochromatic, the epigenetic nature of human telomeres remains controversial. This controversy might have been influenced by the confounding effect of subtelomeric regions and interstitial telomeric sequences (ITSs) on telomeric chromatin structure analyses. In addition, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Cubiles MD,Barroso S,Vaquero-Sedas MI,Enguix A,Aguilera A,Vega-Palas MA

    更新日期:2018-03-16 00:00:00

  • Combined SSCP/duplex analysis by capillary electrophoresis for more efficient mutation detection.

    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


    authors: Kozlowski P,Krzyzosiak WJ

    更新日期:2001-07-15 00:00:00

  • Transition-state destabilization reveals how human DNA polymerase β proceeds across the chemically unstable lesion N7-methylguanine.

    abstract::N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilz...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Koag MC,Kou Y,Ouzon-Shubeita H,Lee S

    更新日期:2014-07-01 00:00:00

  • The initiator element of the Drosophila beta2 tubulin gene core promoter contributes to gene expression in vivo but is not required for male germ-cell specific expression.

    abstract::The tissue-specific expression of the Drosophila beta 2 tubulin gene ( B2t ) is accomplished by the action of a 14-bp activator element (beta2UE1) in combination with certain regulatory elements of the TATA-less, Inr-containing B2t core promoter. We performed an in vivo analysis of the Inr element function in the B2t ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Santel A,Kaufmann J,Hyland R,Renkawitz-Pohl R

    更新日期:2000-03-15 00:00:00

  • rDNA in Locusta migratoria is very variable: two introns and extensive restriction site polymorphisms in the spacer.

    abstract::Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Schäfer M,Kunz W

    更新日期:1985-02-25 00:00:00

  • Selective isolation and detailed analysis of intra-RNA cross-links induced in the large ribosomal subunit of E. coli: a model for the tertiary structure of the tRNA binding domain in 23S RNA.

    abstract::Intramolecular RNA cross-links were induced within the large ribosomal subunit of E. coli by mild ultraviolet irradiation. Regions of the 23S RNA previously implicated in interactions with ribosomal-bound tRNA were then specifically excised by addressed cleavage using ribonuclease H, in conjunction with synthetic comp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Mitchell P,Osswald M,Schueler D,Brimacombe R

    更新日期:1990-08-11 00:00:00

  • Effects of double-strand break repair proteins on vertebrate telomere structure.

    abstract::Although telomeres are not recognized as double-strand breaks (DSBs), some DSB repair proteins are present at telomeres and are required for telomere maintenance. To learn more about the telomeric function of proteins from the homologous recombination (HR) and non-homologous end joining pathways (NHEJ), we have screen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Wei C,Skopp R,Takata M,Takeda S,Price CM

    更新日期:2002-07-01 00:00:00

  • Solid-phase synthesis of polynucleotides. IV. Usage of polystyrene resins for the synthesis of polydeoxyribonucleotides by the phosphostriester method.

    abstract::Contrary to the expectation, the Merrifield polystyrene resin, 2% cross-linked by divinylbenzene, is as efficient as the polyacrylmorpholide resin for the synthesis of polydeoxyribonucleotides using a phosphotriester method. On the Merrifield resin, the tetradecamer, dTpCpGpTpCpApApCpTpGpGpCpTpT, and the hexadecamer, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Miyoshi K,Arentzen R,Huang T,Itakura K

    更新日期:1980-11-25 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


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

    更新日期:1996-01-01 00:00:00

  • A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals.

    abstract::Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing an...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Turakhia Y,Chen HI,Marcovitz A,Bejerano G

    更新日期:2020-09-18 00:00:00