Amplification of genomic sequences flanking transposable elements in host and heterologous plants: a tool for transposon tagging and genome characterization.

Abstract:

:The isolation of sequences flanking integrated transposable elements is an important step in gene tagging strategies. We have demonstrated that sequences flanking transposons integrated into complex genomes can be simply and rapidly obtained using the polymerase chain reaction. Amplification of such sequences was established in a model system, a transgenic tobacco plant carrying a single Ac element, and successfully applied to the cloning of a specific Spm element from a maize line carrying multiple Spm hybridizing sequences. The described utilization of methylation sensitive restriction enzymes (including those with degenerate recognition sequences) in the generation of templates for amplification will simplify the cloning and mapping of genomic sequences adjacent to transposable elements.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Earp DJ,Lowe B,Baker B

doi

10.1093/nar/18.11.3271

subject

Has Abstract

pub_date

1990-06-11 00:00:00

pages

3271-9

issue

11

eissn

0305-1048

issn

1362-4962

journal_volume

18

pub_type

杂志文章
  • Ribosomal DNA genes of Bombyx mori: a minor fraction of the repeating units contain insertions.

    abstract::We have analyzed multiple recombinant DNA clones containing ribosomal RNA repeat units of the silkmoth, Bombyx mori. In combination with genomic DNA blots, analysis of these clones indicated that the rDNA repeat of B. mori is 10.8 kilobase pair in length and tandemly repeated in the genome, as reported by Manning et a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.11.4703

    authors: Lecanidou R,Eickbush TH,Kafatos FC

    更新日期:1984-06-11 00:00:00

  • Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes.

    abstract::The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding speci...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp464

    authors: Zambelli F,Pesole G,Pavesi G

    更新日期:2009-07-01 00:00:00

  • Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.

    abstract::Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA-RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a bio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx115

    authors: Vazquez-Anderson J,Mihailovic MK,Baldridge KC,Reyes KG,Haning K,Cho SH,Amador P,Powell WB,Contreras LM

    更新日期:2017-05-19 00:00:00

  • Intramolecular DNA melting between stable helical segments: melting theory and metastable states.

    abstract::Melting of DNA in a segment bounded at both ends by regions of greater stability during electrophoresis in denaturing gradient gels show complex properties, not accommodated with standard melting theory. Compact bands of some DNA molecules become anomalously broadened at the retardation level in a denaturing gradient,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.14.2775

    authors: Abrams ES,Murdaugh SE,Lerman LS

    更新日期:1995-07-25 00:00:00

  • Elements at the 5' end of Xist harbor SPEN-independent transcriptional antiterminator activity.

    abstract::The Xist lncRNA requires Repeat A, a conserved RNA element located in its 5' end, to induce gene silencing during X-chromosome inactivation. Intriguingly, Repeat A is also required for production of Xist. While silencing by Repeat A requires the protein SPEN, how Repeat A promotes Xist production remains unclear. We r...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa789

    authors: Trotman JB,Lee DM,Cherney RE,Kim SO,Inoue K,Schertzer MD,Bischoff SR,Cowley DO,Calabrese JM

    更新日期:2020-10-09 00:00:00

  • The hnRNP F protein: unique primary structure, nucleic acid-binding properties, and subcellular localization.

    abstract::More than 20 different heterogeneous nuclear ribonucleoproteins (hnRNPs) are associated with pre-mRNAs in the nucleus of mammalian cells and these proteins appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. The arrangement of hnRNP proteins on pre-mRNAs is likely to be unique f...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/22.6.1059

    authors: Matunis MJ,Xing J,Dreyfuss G

    更新日期:1994-03-25 00:00:00

  • Junctions of the large single copy region and the inverted repeats in Spinacia oleracea and Nicotiana debneyi chloroplast DNA: sequence of the genes for tRNAHis and the ribosomal proteins S19 and L2.

    abstract::This work describes the organization, at the nucleotide sequence level, of genes flanking the junctions of the large single copy regions and the inverted repeats of Spinacia oleracea (spinach) and Nicotiana debneyi chloroplast DNAs. In both genomes, trnH1, the gene for tRNA-His(GUG) is located at the extremity of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.16.6547

    authors: Zurawski G,Bottomley W,Whitfeld PR

    更新日期:1984-08-24 00:00:00

  • A periodic pattern of mRNA secondary structure created by the genetic code.

    abstract::Single-stranded mRNA molecules form secondary structures through complementary self-interactions. Several hypotheses have been proposed on the relationship between the nucleotide sequence, encoded amino acid sequence and mRNA secondary structure. We performed the first transcriptome-wide in silico analysis of the huma...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl287

    authors: Shabalina SA,Ogurtsov AY,Spiridonov NA

    更新日期:2006-05-08 00:00:00

  • Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.

    abstract::The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1316

    authors: Patra A,Harp J,Pallan PS,Zhao L,Abramov M,Herdewijn P,Egli M

    更新日期:2013-02-01 00:00:00

  • Groove-binding unsymmetrical cyanine dyes for staining of DNA: syntheses and characterization of the DNA-binding.

    abstract::Two new crescent-shaped unsymmetrical cyanine dyes have been synthesised and their interactions with DNA have been investigated by different spectroscopic methods. These dyes are analogues to a minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known interc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg821

    authors: Karlsson HJ,Eriksson M,Perzon E,Akerman B,Lincoln P,Westman G

    更新日期:2003-11-01 00:00:00

  • Specific ribosomal RNA recognition by a fragment of E. coli ribosomal protein S4 missing the C-terminal 36 amino acid residues.

    abstract::We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.17.6343

    authors: Changchien LM,Craven GR

    更新日期:1985-09-11 00:00:00

  • Synthesis, thermal stability and resistance to enzymatic hydrolysis of the oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridines.

    abstract::The synthesis of oligonucleotides (ODNs) containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine (D) is described, and thermal stability and resistance to enzymatic hydrolysis of the ODNs are compared with ODNs containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine (H). The ODNs containing D and the complementary RNA de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg374

    authors: Ito T,Ueno Y,Komatsu Y,Matsuda A

    更新日期:2003-05-15 00:00:00

  • The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.

    abstract::The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public data...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkj145

    authors: Liolios K,Tavernarakis N,Hugenholtz P,Kyrpides NC

    更新日期:2006-01-01 00:00:00

  • Solution structure and functional importance of a conserved RNA hairpin of eel LINE UnaL2.

    abstract::The eel long interspersed element (LINE) UnaL2 and its partner short interspersed element (SINE) share a conserved 3' tail that is critical for their retrotransposition. The predicted secondary structure of the conserved 3' tail of UnaL2 RNA contains a stem region with a putative internal loop. Deletion of the putativ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl664

    authors: Nomura Y,Kajikawa M,Baba S,Nakazato S,Imai T,Sakamoto T,Okada N,Kawai G

    更新日期:2006-01-01 00:00:00

  • ComplexContact: a web server for inter-protein contact prediction using deep learning.

    abstract::ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky420

    authors: Zeng H,Wang S,Zhou T,Zhao F,Li X,Wu Q,Xu J

    更新日期:2018-07-02 00:00:00

  • PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.

    abstract::We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify th...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl170

    authors: Moretti S,Reinier F,Poirot O,Armougom F,Audic S,Keduas V,Notredame C

    更新日期:2006-07-01 00:00:00

  • Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy.

    abstract::The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1013

    authors: Wacker A,Weigand JE,Akabayov SR,Altincekic N,Bains JK,Banijamali E,Binas O,Castillo-Martinez J,Cetiner E,Ceylan B,Chiu LY,Davila-Calderon J,Dhamotharan K,Duchardt-Ferner E,Ferner J,Frydman L,Fürtig B,Gallego J,Grün JT

    更新日期:2020-12-16 00:00:00

  • AlleleHMM: a data-driven method to identify allele specific differences in distributed functional genomic marks.

    abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz176

    authors: Chou SP,Danko CG

    更新日期:2019-06-20 00:00:00

  • Engineering a high-affinity methyl-CpG-binding protein.

    abstract::Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By multimerizing the MDB domain of Mbd1, we engineered a poly-MBD protein that displays methyl-CpG-specific binding in vitro with a dissoci...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl527

    authors: Jørgensen HF,Adie K,Chaubert P,Bird AP

    更新日期:2006-08-07 00:00:00

  • Self-assembly of DNA-streptavidin nanostructures and their use as reagents in immuno-PCR.

    abstract::The self-assembly of bis-biotinylated double-stranded DNA and the tetravalent biotin-binding protein streptavidin (STV) have been studied by non-denaturing gel electrophoresis and atomic force microscopy (AFM). The rapid self-assembly reproducibly generated populations of individual oligomeric complexes. Most striking...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.23.4553

    authors: Niemeyer CM,Adler M,Pignataro B,Lenhert S,Gao S,Chi L,Fuchs H,Blohm D

    更新日期:1999-12-01 00:00:00

  • Diels-Alder cycloadditions in water for the straightforward preparation of peptide-oligonucleotide conjugates.

    abstract::The Diels-Alder reaction between diene-modified oligonucleotides and maleimide-derivatized peptides afforded peptide-oligonucleotide conjugates with high purity and yield. Synthesis of the reagents was easily accomplished by on-column derivatization of the corresponding peptides and oligonucleotides. The cycloaddition...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gnj020

    authors: Marchán V,Ortega S,Pulido D,Pedroso E,Grandas A

    更新日期:2006-02-14 00:00:00

  • SETDB1, HP1 and SUV39 promote repositioning of 53BP1 to extend resection during homologous recombination in G2 cells.

    abstract::Recent studies have shown that homologous recombination (HR) requires chromatin repression as well as relaxation at DNA double strand breaks (DSBs). HP1 and SUV39H1/2 are repressive factors essential for HR. Here, we identify SETDB1 as an additional compacting factor promoting HR. Depletion of HP1, SUV39, SETDB1 or BR...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv722

    authors: Alagoz M,Katsuki Y,Ogiwara H,Ogi T,Shibata A,Kakarougkas A,Jeggo P

    更新日期:2015-09-18 00:00:00

  • The sequence of the gene for cytochrome c oxidase subunit I, a frameshift containing gene for cytochrome c oxidase subunit II and seven unassigned reading frames in Trypanosoma brucei mitochondrial maxi-circle DNA.

    abstract::A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.19.7327

    authors: Hensgens LA,Brakenhoff J,De Vries BF,Sloof P,Tromp MC,Van Boom JH,Benne R

    更新日期:1984-10-11 00:00:00

  • Curved DNA fragments display retarded elution upon anion exchange HPLC.

    abstract::Restriction fragments containing established curved regions, such as the pBR322 tn3 region, the phage lambda attP region and the SV40 T-antigen and terminus of replication regions, exhibit systematically retarded elution upon anion exchange based HPLC. Using this method, we were able to detect readily other SV40 curve...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.15.4181

    authors: Fack F,Sarantoglou V

    更新日期:1991-08-11 00:00:00

  • Regulatory factor-X binding to mutant HLA-DRA promoter sequences.

    abstract::The class II genes of the major histocompatibility complex (MHC) encode a family of cell surface glycoproteins that present processed antigen to the T cell receptor. Class II genes are regulated coordinately, responding to both immunologic and developmental signals. Conserved sequence elements 5' to class II genes hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.6.1243

    authors: Hasegawa SL,Sloan JH,Reith W,Mach B,Boss JM

    更新日期:1991-03-25 00:00:00

  • The Genome Database for Rosaceae (GDR): year 10 update.

    abstract::The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1012

    authors: Jung S,Ficklin SP,Lee T,Cheng CH,Blenda A,Zheng P,Yu J,Bombarely A,Cho I,Ru S,Evans K,Peace C,Abbott AG,Mueller LA,Olmstead MA,Main D

    更新日期:2014-01-01 00:00:00

  • Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria.

    abstract::The evolution of regulatory networks in Bacteria has largely been explained at macroevolutionary scales through lateral gene transfer and gene duplication. Transcription factors (TF) have been found to be less conserved across species than their target genes (TG). This would be expected if TFs accumulate mutations fas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa162

    authors: Ali F,Seshasayee ASN

    更新日期:2020-05-07 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

  • Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro.

    abstract::The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa479

    authors: Zhang X,Zhang Y,Zhang W

    更新日期:2020-07-09 00:00:00

  • Automated Gene Ontology annotation for anonymous sequence data.

    abstract::Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg582

    authors: Hennig S,Groth D,Lehrach H

    更新日期:2003-07-01 00:00:00