High-level transgene expression by homologous recombination-mediated gene transfer.

Abstract:

:Gene transfer and expression in eukaryotes is often limited by a number of stably maintained gene copies and by epigenetic silencing effects. Silencing may be limited by the use of epigenetic regulatory sequences such as matrix attachment regions (MAR). Here, we show that successive transfections of MAR-containing vectors allow a synergistic increase of transgene expression. This finding is partly explained by an increased entry into the cell nuclei and genomic integration of the DNA, an effect that requires both the MAR element and iterative transfections. Fluorescence in situ hybridization analysis often showed single integration events, indicating that DNAs introduced in successive transfections could recombine. High expression was also linked to the cell division cycle, so that nuclear transport of the DNA occurs when homologous recombination is most active. Use of cells deficient in either non-homologous end-joining or homologous recombination suggested that efficient integration and expression may require homologous recombination-based genomic integration of MAR-containing plasmids and the lack of epigenetic silencing events associated with tandem gene copies. We conclude that MAR elements may promote homologous recombination, and that cells and vectors can be engineered to take advantage of this property to mediate highly efficient gene transfer and expression.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Grandjean M,Girod PA,Calabrese D,Kostyrko K,Wicht M,Yerly F,Mazza C,Beckmann JS,Martinet D,Mermod N

doi

10.1093/nar/gkr436

subject

Has Abstract

pub_date

2011-08-01 00:00:00

pages

e104

issue

15

eissn

0305-1048

issn

1362-4962

pii

gkr436

journal_volume

39

pub_type

杂志文章
  • The H19/let-7 double-negative feedback loop contributes to glucose metabolism in muscle cells.

    abstract::The H19 lncRNA has been implicated in development and growth control and is associated with human genetic disorders and cancer. Acting as a molecular sponge, H19 inhibits microRNA (miRNA) let-7. Here we report that H19 is significantly decreased in muscle of human subjects with type-2 diabetes and insulin resistant ro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1160

    authors: Gao Y,Wu F,Zhou J,Yan L,Jurczak MJ,Lee HY,Yang L,Mueller M,Zhou XB,Dandolo L,Szendroedi J,Roden M,Flannery C,Taylor H,Carmichael GG,Shulman GI,Huang Y

    更新日期:2014-12-16 00:00:00

  • Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity.

    abstract::PUF proteins, named for Drosophila Pumilio (PUM) and Caenorhabditis elegans fem-3-binding factor (FBF), recognize specific sequences in the mRNAs they bind and control. RNA binding by classical PUF proteins is mediated by a characteristic PUM homology domain (PUM-HD). The Puf1 and Puf2 proteins possess a distinct arch...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz583

    authors: Qiu C,Dutcher RC,Porter DF,Arava Y,Wickens M,Hall TMT

    更新日期:2019-09-19 00:00:00

  • A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

    abstract::Tumor formation is partially driven by DNA copy number changes, which are typically measured using array comparative genomic hybridization, SNP arrays and DNA sequencing platforms. Many techniques are available for detecting recurring aberrations across multiple tumor samples, including CMAR, STAC, GISTIC and KC-SMART...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt155

    authors: van Dyk E,Reinders MJ,Wessels LF

    更新日期:2013-05-01 00:00:00

  • The imprinted gene and parent-of-origin effect database.

    abstract::The database of imprinted genes and parent-of-origin effects in animals (http://www.otago.ac.nz/IGC ) is a collation of genes and phenotypes for which parent-of-origin effects have been reported. The database currently includes over 220 entries, which describe over 40 imprinted genes in human, mouse and other animals....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.1.275

    authors: Morison IM,Paton CJ,Cleverley SD

    更新日期:2001-01-01 00:00:00

  • BSD: the Biodegradative Strain Database.

    abstract::The Biodegradative Strain Database (BSD) is a freely-accessible, web-based database providing detailed information on degradative bacteria and the hazardous substances that they degrade, including corresponding literature citations, relevant patents and links to additional web-based biological and chemical data. The B...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg032

    authors: Urbance JW,Cole J,Saxman P,Tiedje JM

    更新日期:2003-01-01 00:00:00

  • The U2 RNA analogue of Trypanosoma brucei gambiense: implications for a splicing mechanism in trypanosomes.

    abstract::We have isolated the gene coding for the U2 analogue in trypanosomes. The 148 nucleotide long U2 RNA is capped and transcribed from a single copy gene. The 5' half of the molecule is highly homologous to mammalian U2 RNA, while the 3' half does not show any significant sequence homology with the mammalian counterpart....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.22.8893

    authors: Tschudi C,Richards FF,Ullu E

    更新日期:1986-11-25 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

  • Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.

    abstract::Phospho3D is a database of three-dimensional (3D) structures of phosphorylation sites (P-sites) derived from the Phospho.ELM database, which also collects information on the residues surrounding the P-site in space (3D zones). The database also provides the results of a large-scale structural comparison of the 3D zone...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq936

    authors: Zanzoni A,Carbajo D,Diella F,Gherardini PF,Tramontano A,Helmer-Citterich M,Via A

    更新日期:2011-01-01 00:00:00

  • Inhibition of self-splicing group I intron RNA: high-throughput screening assays.

    abstract::High-throughput screening assays have been developed to rapidly identify small molecule inhibitors targeting catalytic group I introns. Biochemical reactions catalyzed by a self-splicing group I intron derived from Pneumocystis carinii or from bacteriophage T4 have been investigated. In vitro biochemical assays amenab...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.24.5051

    authors: Mei HY,Cui M,Sutton ST,Truong HN,Chung FZ,Czarnik AW

    更新日期:1996-12-15 00:00:00

  • Recognition sequences of type II restriction systems are constrained by the G + C content of host genomes.

    abstract::I show that the recognition sequences of Type II restriction systems are correlated with the G + C content of the host bacterial DNA. Almost all restriction systems with G + C rich tetranucleotide recognition sequences are found in species with A + T rich genomes, whereas G + C rich hexanucleotide and octanucleotide r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.5.2283

    authors: McClelland M

    更新日期:1988-03-25 00:00:00

  • Quantifying deleterious effects of regulatory variants.

    abstract::The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed C...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1263

    authors: Li S,Alvarez RV,Sharan R,Landsman D,Ovcharenko I

    更新日期:2017-03-17 00:00:00

  • GenBank.

    abstract::GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 260 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the web-based BankIt or st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm929

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

    更新日期:2008-01-01 00:00:00

  • A new minor groove binding asymmetric cyanine reporter dye for real-time PCR.

    abstract::The minor groove binding asymmetric cyanine dye 4-[(3-methyl-6-(benzothiazol-2-yl)-2,3-dihydro- (benzo-1,3-thiazole)-2-methylidene)]-1-methyl-pyridin ium iodide (BEBO) is tested as sequence non- specific label in real-time PCR. The fluorescence intensity of BEBO increases upon binding to double-stranded DNA allowing e...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gng045

    authors: Bengtsson M,Karlsson HJ,Westman G,Kubista M

    更新日期:2003-04-15 00:00:00

  • Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues.

    abstract::While most of the recent improvements in multiple sequence alignment accuracy are due to better use of vertical information, which include the incorporation of consistency-based pairwise alignments and the use of profile alignments, we observe that it is possible to further improve accuracy by taking into account alig...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn945

    authors: Lu Y,Sze SH

    更新日期:2009-02-01 00:00:00

  • GWIDD: Genome-wide protein docking database.

    abstract::Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp944

    authors: Kundrotas PJ,Zhu Z,Vakser IA

    更新日期:2010-01-01 00:00:00

  • Isolation of mouse reticulocyte globin messenger ribonucleoprotein by affinity chromatography using oligo(T)-cellulose.

    abstract::Mouse globin messenger ribonucleoprotein (mRNP) has been isolated from reticulocyte polysomes by affinity chromatography to oligo(T)-cellulose, using a procedure modified from that of Lindberg and Sundquist. The messenger RNA and protein moieties fo the mRNP are indistinguishable from those isolated by less rapid tech...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/2.12.2251

    authors: Burns AT,Williamson R

    更新日期:1975-12-01 00:00:00

  • Distinct promoter elements mediate the co-operative effect of Brn-3a and p53 on the p21 promoter and their antagonism on the Bax promoter.

    abstract::Although the promoters of both the Bax and p21 genes are activated by p53, they differ in the effect on this activation of the POU family transcription factor Brn-3a. Thus, Brn-3a inhibits activation of the Bax promoter by p53 but enhances the ability of p53 to activate the p21 promoter. We demonstrate that repression...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf610

    authors: Perez-Sanchez C,Budhram-Mahadeo VS,Latchman DS

    更新日期:2002-11-15 00:00:00

  • Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.

    abstract::Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt713

    authors: El Omari K,Meier C,Kainov D,Sutton G,Grimes JM,Poranen MM,Bamford DH,Tuma R,Stuart DI,Mancini EJ

    更新日期:2013-11-01 00:00:00

  • Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1.

    abstract::Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt547

    authors: Guja KE,Venkataraman K,Yakubovskaya E,Shi H,Mejia E,Hambardjieva E,Karzai AW,Garcia-Diaz M

    更新日期:2013-09-01 00:00:00

  • Intron mobility in phage T4 is dependent upon a distinctive class of endonucleases and independent of DNA sequences encoding the intron core: mechanistic and evolutionary implications.

    abstract::Although mobility of the phylogenetically widespread group I introns appears to be mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of the td and sunY introns are different from their eukaryotic counterparts. Most notably, they cleave at a distance from the intron insertion site...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.13.3763

    authors: Bell-Pedersen D,Quirk S,Clyman J,Belfort M

    更新日期:1990-07-11 00:00:00

  • Analysis of the 3' flanking region of the human c-myc gene in lymphomas with the t(8;22) and t(2;8) chromosomal translocations.

    abstract::We have cloned and mapped the sequences extending 38 kb 3' of the c-myc gene. This region is found to be highly repetitive in nature and hybridizes extensively with a BLUR 8 Alu probe. Unique sequence probes derived from this region were used to map the chromosomal breakpoints of a number of lymphoma cell lines with t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.10.4037

    authors: Sun LK,Showe LC,Croce CM

    更新日期:1986-05-27 00:00:00

  • Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex.

    abstract::Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, w...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1296

    authors: Liu H,Cai C,Haruehanroengra P,Yao Q,Chen Y,Yang C,Luo Q,Wu B,Li J,Ma J,Sheng J,Gan J

    更新日期:2017-03-17 00:00:00

  • Point mutations in the Rpb9-homologous domain of Rpc11 that impair transcription termination by RNA polymerase III.

    abstract::RNA polymerase III recognizes and pauses at its terminator, an oligo(dT) tract in non-template DNA, terminates 3' oligo(rU) synthesis within this sequence, and releases the RNA. The pol III subunit Rpc11p (C11) mediates RNA 3'-5' cleavage in the catalytic center of pol III during pausing. The amino and carboxyl region...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr182

    authors: Iben JR,Mazeika JK,Hasson S,Rijal K,Arimbasseri AG,Russo AN,Maraia RJ

    更新日期:2011-08-01 00:00:00

  • Putative subunits of the maize origin of replication recognition complex ZmORC1-ZmORC5.

    abstract::The finding in animal species of complexes homologous to the products of six Saccharomyces cerevisiae genes, origin of replication recognition complex (ORC), has suggested that ORC-related mechanisms have been conserved in all eukaryotes. In plants, however, the only cloned putative homologs of ORC subunits are the Ar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg138

    authors: Witmer X,Alvarez-Venegas R,San-Miguel P,Danilevskaya O,Avramova Z

    更新日期:2003-01-15 00:00:00

  • Highly recurring sequence elements identified in eukaryotic DNAs by computer analysis are often homologous to regulatory sequences or protein binding sites.

    abstract::We have used computer assisted dot matrix and oligonucleotide frequency analyses to identify highly recurring sequence elements of 7-11 base pairs in eukaryotic genes and viral DNAs. Such elements are found much more frequently than expected, often with an average spacing of a few hundred base pairs. Furthermore, the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.4.1835

    authors: Bodnar JW,Ward DC

    更新日期:1987-02-25 00:00:00

  • General method of rapid Smith/Birnstiel mapping adds for gap closure in shotgun microbial genome sequencing projects: application to Pseudomonas putida KT2440.

    abstract::A physical mapping strategy has been developed to verify and accelerate the assembly and gap closure phase of a microbial genome shotgun-sequencing project. The protocol was worked out during the ongoing Pseudomonas putida KT2440 genome project. A macro-restriction map was constructed by linking probe hybridisation of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.22.e110

    authors: Weinel C,Tümmler B,Hilbert H,Nelson KE,Kiewitz C

    更新日期:2001-11-15 00:00:00

  • Endoplasmic reticulum stress increases AT1R mRNA expression via TIA-1-dependent mechanism.

    abstract::As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1368

    authors: Backlund M,Paukku K,Kontula KK,Lehtonen JY

    更新日期:2016-04-20 00:00:00

  • A comprehensive list of cloned human DNA sequences.

    abstract::A list of DNA sequences cloned from the human genome is presented. Intended as a guide to clone availability, this list includes published reports of cDNA, genomic and synthetic clones comprising gene and pseudogene sequences, uncharacterised DNA segments and repetitive DNA elements. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.suppl.r403

    authors: Schmidtke J,Cooper DN

    更新日期:1988-01-01 00:00:00

  • Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods.

    abstract::RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks289

    authors: Bizarro CV,Alemany A,Ritort F

    更新日期:2012-08-01 00:00:00

  • Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis.

    abstract::The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks755

    authors: Rochat T,Nicolas P,Delumeau O,Rabatinová A,Korelusová J,Leduc A,Bessières P,Dervyn E,Krásny L,Noirot P

    更新日期:2012-10-01 00:00:00