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  Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome

Szabados, L., Kovacs, I., Oberschall, A., Abraham, E., Kerekes, I., Zsigmond, L., et al. (2002). Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome. Plant Journal, 32(2), 233-242.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3D67-F Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-3D68-D
Genre: Journal Article

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 Creators:
Szabados, L., Author
Kovacs, I., Author
Oberschall, A.1, Author              
Abraham, E., Author
Kerekes, I., Author
Zsigmond, L., Author
Nagy, R., Author
Alvarado, M. C., Author
Krasovskaja, I., Author
Gal, M., Author
Berente, A., Author
Redei, G. P., Author
Ben Haim, A., Author
Koncz, C.2, Author              
Affiliations:
1Dept. of Genetic Principles of Plant Breeding (Jozef Schell), MPI for Plant Breeding Research, Max Planck Society, ou_1113567              
2Dept. of Plant Developmental Biology (George Coupland), MPI for Plant Breeding Research, Max Planck Society, ou_1113571              

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Free keywords: T-DNA; insertion mutagenesis; Arabidopsis; sequenced tags; functional genomics
 Abstract: Induction of knockout mutations by T-DNA insertion mutagenesis is widely used in studies of plant gene functions. To assess the efficiency of this genetic approach, we have sequenced PCR amplified junctions of 1000 T-DNA insertions and analysed their distribution in the Arabidopsis genome. Map positions of 973 tags could be determined unequivocally, indicating that the majority of T-DNA insertions landed in chromosomal domains of high gene density. Only 4.7% of insertions were found in interspersed, centromeric, telomeric and rDNA repeats, whereas 0.6% of sequenced tags identified chromosomally integrated segments of organellar DNAs. 35.4% of T-DNAs were localized in intervals flanked by ATG and stop codons of predicted genes, showing a distribution of 62.2% in exons and 37.8% in introns. The frequency of T-DNA tags in coding and intergenic regions showed a good correlation with the predicted size distribution of these sequences in the genome. However, the frequency of T- DNA insertions in 3'- and 5'-regulatory regions of genes, corresponding to 300 bp intervals 3' downstream of stop and 5' upstream of ATG codons, was 1.7-2.3-fold higher than in any similar interval elsewhere in the genome. The additive frequency of insertions in 5'-regulatory regions and coding domains provided an estimate for the mutation rate, suggesting that 47.8% of mapped T-DNA tags induced knockout mutations in Arabidopsis .

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Language(s): eng - English
 Dates: 2002-10
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: eDoc: 28776
ISI: 000178605000009
 Degree: -

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Title: Plant Journal
  Alternative Title : Plant J.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 32 (2) Sequence Number: - Start / End Page: 233 - 242 Identifier: ISSN: 0960-7412