title: Distribution of 1000 sequenced T-DNA tags in the Arabidopsis genome.
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.
authors.affiliation: Institute of Plant Biology, Biological Research Center of Hungarian Academy of Sciences, H-6701 Szeged, PO Box 521, Temesvári krt 62, Hungary.
authors.forename: László
authors.initials: L
authors.lastname: Szabados
authors.forename: Izabella
authors.initials: I
authors.lastname: Kovács
authors.forename: Attila
authors.initials: A
authors.lastname: Oberschall
authors.forename: Edit
authors.initials: E
authors.lastname: Abrahám
authors.forename: Irén
authors.initials: I
authors.lastname: Kerekes
authors.forename: Laura
authors.initials: L
authors.lastname: Zsigmond
authors.forename: Réka
authors.initials: R
authors.lastname: Nagy
authors.forename: Martha
authors.initials: M
authors.lastname: Alvarado
authors.forename: Inga
authors.initials: I
authors.lastname: Krasovskaja
authors.forename: Mónika
authors.initials: M
authors.lastname: Gál
authors.forename: Anikó
authors.initials: A
authors.lastname: Berente
authors.forename: George P
authors.initials: GP
authors.lastname: Rédei
authors.forename: Amit Ben
authors.initials: AB
authors.lastname: Haim
authors.forename: Csaba
authors.initials: C
authors.lastname: Koncz
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D018745:Genome, Plant; D008957:Models, Genetic; D016254:Mutagenesis, Insertional; D009154:Mutation; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D016324:Sequence Tagged Sites
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic; D018744:DNA, Plant; C036483:T-DNA