A New Resource of Locally Transposed Dissociation Elements for Screening Gene-Knockout Lines in Silico on the Arabidopsis Genome

We transposed Dissociation (Ds) elements from three start loci on chromosome 5 in Arabidopsis (Nossen ecotype) by using a local transposition system. We determined partial genomic sequences flanking the Ds elements and mapped the elements' insertion sites in 1,173 transposed lines by comparison...

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Veröffentlicht in:Plant physiology (Bethesda) 2002-08, Vol.129 (4), p.1695-1699
Hauptverfasser: Ito, Takuya, Motohashi, Reiko, Kuromori, Takashi, Saho Mizukado, Sakurai, Tetsuya, Hiroko Kanahara, Seki, Motoaki, Shinozaki, Kazuo
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container_issue 4
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container_title Plant physiology (Bethesda)
container_volume 129
creator Ito, Takuya
Motohashi, Reiko
Kuromori, Takashi
Saho Mizukado
Sakurai, Tetsuya
Hiroko Kanahara
Seki, Motoaki
Shinozaki, Kazuo
description We transposed Dissociation (Ds) elements from three start loci on chromosome 5 in Arabidopsis (Nossen ecotype) by using a local transposition system. We determined partial genomic sequences flanking the Ds elements and mapped the elements' insertion sites in 1,173 transposed lines by comparison with the published genomic sequence. Most of the lines contained a single copy of the Ds element. One-half of the lines contained Ds on chromosome 5; in particular, insertion "hot spots" near the three start loci were clearly observed. In the other lines, the Ds elements were transposed across chromosomes. We found other insertion hot spots at the tops of chromosomes 2 and 4, near nucleolus organizer regions 2 and 4, respectively. Another characteristic feature was that the Ds elements tended to transpose near the chromosome ends and rarely transposed near centromeres. The distribution patterns differed among the three start loci, even though they possessed the same Ds construct. More than one-half of the Ds elements were inserted irregularly into the genome; that is, they did not retain the perfect inverted repeat sequence of Ds nor leave perfect target site duplications. This precise analysis of distribution patterns will contribute to a comprehensive understanding of the transposing mechanism. From these Ds insertion sites, we have constructed a database for screening gene-knockout mutants in silico. In 583 of the 1,173 lines, the Ds elements were inserted into protein-coding genes, which suggests that these lines are gene-knockout mutants. The database and individual lines will be available freely for academic use from the RIKEN Bio-Resource Center (http://www.brc.riken.go.jp/Eng/index.html).
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More than one-half of the Ds elements were inserted irregularly into the genome; that is, they did not retain the perfect inverted repeat sequence of Ds nor leave perfect target site duplications. This precise analysis of distribution patterns will contribute to a comprehensive understanding of the transposing mechanism. From these Ds insertion sites, we have constructed a database for screening gene-knockout mutants in silico. In 583 of the 1,173 lines, the Ds elements were inserted into protein-coding genes, which suggests that these lines are gene-knockout mutants. 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More than one-half of the Ds elements were inserted irregularly into the genome; that is, they did not retain the perfect inverted repeat sequence of Ds nor leave perfect target site duplications. This precise analysis of distribution patterns will contribute to a comprehensive understanding of the transposing mechanism. From these Ds insertion sites, we have constructed a database for screening gene-knockout mutants in silico. In 583 of the 1,173 lines, the Ds elements were inserted into protein-coding genes, which suggests that these lines are gene-knockout mutants. 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We determined partial genomic sequences flanking the Ds elements and mapped the elements' insertion sites in 1,173 transposed lines by comparison with the published genomic sequence. Most of the lines contained a single copy of the Ds element. One-half of the lines contained Ds on chromosome 5; in particular, insertion "hot spots" near the three start loci were clearly observed. In the other lines, the Ds elements were transposed across chromosomes. We found other insertion hot spots at the tops of chromosomes 2 and 4, near nucleolus organizer regions 2 and 4, respectively. Another characteristic feature was that the Ds elements tended to transpose near the chromosome ends and rarely transposed near centromeres. The distribution patterns differed among the three start loci, even though they possessed the same Ds construct. 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subjects Arabidopsis - genetics
Base Sequence
Biological and medical sciences
Chromosome Mapping
Chromosomes
Data lines
Databases, Factual
DNA
DNA Transposable Elements - genetics
DNA, Plant - genetics
Fundamental and applied biological sciences. Psychology
Genetic loci
Genetic transposition
Genetics, Genomics, and Molecular Evolution
Genic rearrangement. Recombination. Transposable element
Genome, Plant
Genomes
Genomics
Internet
Molecular and cellular biology
Molecular genetics
Molecular Sequence Data
Mutagenesis, Insertional - methods
Mutation
Plants
Polymerase Chain Reaction
Transposons
title A New Resource of Locally Transposed Dissociation Elements for Screening Gene-Knockout Lines in Silico on the Arabidopsis Genome
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