SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRbeta enhancer (Ebeta).

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 hypersensitivity assays, we show here that overexpression of the MAR binding proteins SMAR1 and Cux/CDP modulate the chromatin structure at MARbeta. We further demonstrate that the silencer function of MARbeta is mediated independently by SMAR1 and Cux/CDP as judged by their ability to repress Ebeta-dependent reporter gene expression. Moreover, the repressor activity of SMAR1 is strongly enhanced in the presence of Cux/CDP. These two proteins physically interact with each other and colocalize within the perinuclear region through a SMAR1 domain required for repression. The repression domain of SMAR1 is separate from the MARbeta binding domain and contains a nuclear localization signal and an arginine-serine (RS)-rich domain, characteristic of pre-mRNA splicing regulators. Our data suggest that at the double positive stage of T cell development, cis-acting MARbeta elements recruit the strong negative regulators Cux and SMAR1 to control Ebeta-mediated recombination and transcription.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Kaul-Ghanekar R,Jalota A,Pavithra L,Tucker P,Chattopadhyay S

doi

10.1093/nar/gkh807

keywords:

subject

Has Abstract

pub_date

2004-09-15 00:00:00

pages

4862-75

issue

16

eissn

0305-1048

issn

1362-4962

pii

32/16/4862

journal_volume

32

pub_type

杂志文章
  • CORUM: the comprehensive resource of mammalian protein complexes.

    abstract::Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scient...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm936

    authors: Ruepp A,Brauner B,Dunger-Kaltenbach I,Frishman G,Montrone C,Stransky M,Waegele B,Schmidt T,Doudieu ON,Stümpflen V,Mewes HW

    更新日期:2008-01-01 00:00:00

  • IS3 can function as a mobile promoter in E. coli.

    abstract::We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.19.5935

    authors: Charlier D,Piette J,Glansdorff N

    更新日期:1982-10-11 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

    doi:10.1093/nar/gkm1062

    authors: Venditti V,Niccolai N,Butcher SE

    更新日期:2008-03-01 00:00:00

  • Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.

    abstract::Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz725

    authors: Yerlici VT,Lu MW,Hoge CR,Miller RV,Neme R,Khurana JS,Bracht JR,Landweber LF

    更新日期:2019-10-10 00:00:00

  • Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.

    abstract::Loss-of-function (LOF) methods such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing provide unparalleled power for studying the biological function of genes of interest. However, a major concern is non-specific targeting, which involves depletion of transcripts other than those in...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky437

    authors: Stojic L,Lun ATL,Mangei J,Mascalchi P,Quarantotti V,Barr AR,Bakal C,Marioni JC,Gergely F,Odom DT

    更新日期:2018-07-06 00:00:00

  • Characterization of a human cDNA encoding a widely expressed and highly conserved cysteine-rich protein with an unusual zinc-finger motif.

    abstract::A human term placental cDNA library was screened at low stringency with a human prolactin cDNA probe. One of the cDNAs isolated hybridizes to a 1.8 kb mRNA present in all four tissues of the placenta as well as to every nucleated tissue and cell line tested. The sequence of the full-length cDNA was determined. An exte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.13.3871

    authors: Liebhaber SA,Emery JG,Urbanek M,Wang XK,Cooke NE

    更新日期:1990-07-11 00:00:00

  • The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region.

    abstract::The C/D box scaRNA2 is predicted to guide specific 2'-O-methylation of U2 snRNA. In contrast to other SCARNA genes, SCARNA2 appears to be independently transcribed. By transient expression of SCARNA2-reporter gene constructs, we have demonstrated that this gene is transcribed by RNA polymerase II and that the promoter...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp988

    authors: Gérard MA,Myslinski E,Chylak N,Baudrey S,Krol A,Carbon P

    更新日期:2010-01-01 00:00:00

  • 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, t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh677

    authors: Zelivianski S,Glowacki R,Lin MF

    更新日期:2004-07-07 00:00:00

  • The malaria parasite Plasmodium falciparum encodes members of the Puf RNA-binding protein family with conserved RNA binding activity.

    abstract::A novel class of RNA-binding proteins, Puf, regulates translation and RNA stability by binding to specific sequences in the 3'-untranslated region of target mRNAs. Members of this protein family share a conserved Puf domain consisting of eight 36 amino acid imperfect repeats. Here we report two Puf family member genes...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf600

    authors: Cui L,Fan Q,Li J

    更新日期:2002-11-01 00:00:00

  • Hemicatenanes form upon inhibition of DNA replication.

    abstract::Plasmid DNA incubated in interphase Xenopus egg extracts is normally assembled into chromatin and then into synthetic nuclei which undergo one round of regulated replication. During a study of restriction endonuclease cut plasmid replication intermediates (RIs) by the Brewer-Fangman 2D gel electrophoresis technique, w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.10.2187

    authors: Lucas I,Hyrien O

    更新日期:2000-05-15 00:00:00

  • AUGUSTUS: a web server for gene finding in eukaryotes.

    abstract::We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh379

    authors: Stanke M,Steinkamp R,Waack S,Morgenstern B

    更新日期:2004-07-01 00:00:00

  • A processed chicken pseudogene (CPS1) related to the ras oncogene superfamily.

    abstract::We describe the first polyA-containing processed pseudogene reported in the chicken. It includes a 0.52 kb open reading frame which could encode a 175 amino acid protein. The putative protein shows extensive homology to the ras oncogene superfamily, being most closely related to the yeast protein YP2. It is one of the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.5.2123

    authors: Alsip GR,Konkel DA

    更新日期:1986-03-11 00:00:00

  • Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus.

    abstract::Homing endonucleases recognize long target DNA sequences generating an accurate double-strand break that promotes gene targeting through homologous recombination. We have modified the homodimeric I-CreI endonuclease through protein engineering to target a specific DNA sequence within the human RAG1 gene. Mutations in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq801

    authors: Muñoz IG,Prieto J,Subramanian S,Coloma J,Redondo P,Villate M,Merino N,Marenchino M,D'Abramo M,Gervasio FL,Grizot S,Daboussi F,Smith J,Chion-Sotinel I,Pâques F,Duchateau P,Alibés A,Stricher F,Serrano L,Blanco FJ,Mo

    更新日期:2011-01-01 00:00:00

  • Evaluation of 2'-hydroxyl protection in RNA-synthesis using the H-phosphonate approach.

    abstract::A number of different protecting groups were compared with respect to their usefulness for protection of 2'-hydroxyl functions during synthesis of oligoribonucleotides using the H-phosphonate approach. The comparison was between the t-butyldimethylsilyl (t-BDMSi), the o-chlorobenzoyl (o-CIBz), the tetrahydropyranyl (T...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.1.94

    authors: Rozners E,Westman E,Strömberg R

    更新日期:1994-01-11 00:00:00

  • Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs.

    abstract::The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal effi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq616

    authors: Berger SM,Pesold B,Reber S,Schönig K,Berger AJ,Weidenfeld I,Miao J,Berger MR,Gruss OJ,Bartsch D

    更新日期:2010-09-01 00:00:00

  • Detection of labelled RNA species by contact hybridization.

    abstract::An improved contact hybridization technique for the analysis of labelled RNA species is presented. The method combines high sensitivity of detection with the high resolution of polyacrylamide gel electrophoresis and should be especially useful for the characterization of transient RNA precursor molecules. Its applicat...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.9.2963

    authors: Burckhardt J,Telford J,Birnstiel ML

    更新日期:1979-07-11 00:00:00

  • Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid.

    abstract::Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.8.3427

    authors: Sano T,Uyeda I,Shikata E,Ohno T,Okada Y

    更新日期:1984-04-25 00:00:00

  • Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA.

    abstract::The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv870

    authors: Hashimoto H,Pais JE,Dai N,Corrêa IR Jr,Zhang X,Zheng Y,Cheng X

    更新日期:2015-12-15 00:00:00

  • Biological activity of the intact and cleaved DNA of the simian adenovirus 7.

    abstract::Only the deproteinized DNA preparations of the simian adenovirus of the type 7 (SA 7) exhibited transforming and tumorigenic activity. The complex of the SA7 DNA with terminal protein (TP) did not exhibit either transforming or tumorigenic activity in cell cultures. In contrast to the transforming potential the infect...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.9.3119

    authors: Ponomareva TI,Grodnitskaya NA,Goldberg EE,Chaplygina NM,Naroditsky BS,Tikchonenko TI

    更新日期:1979-07-11 00:00:00

  • Global landscape of mouse and human cytokine transcriptional regulation.

    abstract::Cytokines are cell-to-cell signaling proteins that play a central role in immune development, pathogen responses, and diseases. Cytokines are highly regulated at the transcriptional level by combinations of transcription factors (TFs) that recruit cofactors and the transcriptional machinery. Here, we mined through thr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky787

    authors: Carrasco Pro S,Dafonte Imedio A,Santoso CS,Gan KA,Sewell JA,Martinez M,Sereda R,Mehta S,Fuxman Bass JI

    更新日期:2018-10-12 00:00:00

  • Counterion distribution around DNA: variation with conformation and sequence.

    abstract::The three-dimensional Poisson-Boltzmann equation for the distribution of counterion charge density around double helical DNA has been solved by an iterative procedure. These computations have been performed for 0.01M monovalent salt solutions. A systematic study of the ten possible sequences found among adjacent nucle...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.3.1479

    authors: Pack GR,Wong L,Prasad CV

    更新日期:1986-02-11 00:00:00

  • Multiple defects in translation associated with altered ribosomal protein L4.

    abstract::The ribosomal proteins L4 and L22 form part of the peptide exit tunnel in the large ribosomal subunit. In Escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. The structures of the 30S as well as the 50S subunits from each antibiotic resistant mutan...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh913

    authors: O'Connor M,Gregory ST,Dahlberg AE

    更新日期:2004-10-27 00:00:00

  • The life sciences Global Image Database (GID).

    abstract::Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solutio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.1.336

    authors: Gonzalez-Couto E,Hayes B,Danckaert A

    更新日期:2001-01-01 00:00:00

  • Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants.

    abstract::The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.18.3666

    authors: Kim JW,Kim HC,Kim GM,Yang JM,Boeke JD,Nam K

    更新日期:2000-09-15 00:00:00

  • Fission yeast with DNA polymerase delta temperature-sensitive alleles exhibits cell division cycle phenotype.

    abstract::DNA polymerases alpha and delta are essential enzymes believed to play critical roles in initiation and replication of chromosome DNA. In this study, we show that the genes for Schizosaccharomyces pombe (S.pombe) DNA polymerase alpha and delta (pol alpha+ and pol delta+) are essential for cell viability. Disruption of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/21.16.3821

    authors: Francesconi S,Park H,Wang TS

    更新日期:1993-08-11 00:00:00

  • Cellular gene induction during herpes simplex virus infection can occur without viral protein synthesis.

    abstract::Infection of cultured cells with herpes simplex virus (HSV) results in the transcriptional induction of a small number of cellular genes. Although the majority of such genes are dependent upon viral protein synthesis for their induction, a small minority are not. These genes are induced by events occurring prior to th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.23.9261

    authors: Kemp LM,Preston CM,Preston VG,Latchman DS

    更新日期:1986-12-09 00:00:00

  • Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.

    abstract::Codon usage data has been compiled for 110 yeast genes. Cluster analysis on relative synonymous codon usage revealed two distinct groups of genes. One group corresponds to highly expressed genes, and has much more extreme synonymous codon preference. The pattern of codon usage observed is consistent with that expected...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.13.5125

    authors: Sharp PM,Tuohy TM,Mosurski KR

    更新日期:1986-07-11 00:00:00

  • Nucleotide sequence and expression of a Pseudomonas savastanoi cytokinin biosynthetic gene: homology with Agrobacterium tumefaciens tmr and tzs loci.

    abstract::The nucleotide sequence of a Pseudomonas trans-zeatin producing gene (ptz) from the pCK1 plasmid of Pseudomonas syringae pv. savastanoi strain 1006 has been determined. This gene confers upon E. coli the ability to synthesize and secrete several cytokinins including trans-zeatin, iso-pentenyladenine and their respecti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.6.2555

    authors: Powell GK,Morris RO

    更新日期:1986-03-25 00:00:00

  • Repair of DNA strand gaps and nicks containing 3'-phosphate and 5'-hydroxyl termini by purified mammalian enzymes.

    abstract::A putative role for mammalian polynucleotide kinases that possess both 5'-phosphotransferase and 3'-phosphatase activity is the restoration of DNA strand breaks with 5'-hydroxyl termini or 3'-phosphate termini, or both, to a form that supports the subsequent action of DNA repair polymerases and DNA ligases, i.e. 5'-ph...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.19.4395

    authors: Karimi-Busheri F,Lee J,Tomkinson AE,Weinfeld M

    更新日期:1998-10-01 00:00:00

  • Biotin-tagged cDNA expression libraries displayed on lambda phage: a new tool for the selection of natural protein ligands.

    abstract::cDNA expression libraries displayed on lambda phage have been successfully employed to identify partners involved in antibody-antigen, protein- protein and DNA-protein interactions and represent a novel approach to functional genomics. However, as in all other cDNA expression libraries based on fusion to a carrier pol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnf077

    authors: Ansuini H,Cicchini C,Nicosia A,Tripodi M,Cortese R,Luzzago A

    更新日期:2002-08-01 00:00:00