title: Microhomologies between T-DNA ends and target sites often occur in inverted orientation and may be responsible for the high frequency of T-DNA-associated inversions.
abstract: Sequence analysis of left and right border integration sites of independent, single-copy T-DNA inserts in Arabidopsis thaliana revealed three previously unrecognized concomitants of T-DNA integration. First, genomic pre-insertion sites shared sequence similarity not only with the T-DNA left and right border regions, as was previously reported, but also at high frequency with the inverted complement of the T-DNA right border region. Second, palindromic sequences were frequently found to overlap or lie adjacent to genomic target sites, suggesting a high recombinogenic potential for palindromic elements during T-DNA integration and a possible role during the primary contact between the T-DNA and the target DNA. Third, "filler" DNA sequences between genomic pre-insertion site DNA and T-DNA often derive from sequences in the T-DNA left and right border regions that are clustered around palindromic sequences in these T-DNA regions, suggesting that these palindromic elements are "hot spots" for filler DNA formation. The discovery of inverted sequence similarities at the right border suggests a previously unrecognized mode of T-DNA integration that involves heteroduplex formation at both T-DNA borders and with opposite strands of the target DNA. Scanning for sequence similarities in both direct and inverted orientation may increase the probability and/or effectiveness of anchoring the T-DNA to the target DNA. Variations on this scheme may also account for inversion events at the target site of T-DNA integration and inverted T-DNA repeat formation, common sequence organization patterns associated with T-DNA integration.
authors.affiliation: Department of Plant Sciences, University of Arizona, Tucson, AZ 85721-0036, USA. a.mueller@plantbreeding.uni-kiel.de
authors.forename: Andreas E
authors.initials: AE
authors.lastname: Müller
authors.forename: Ross G
authors.initials: RG
authors.lastname: Atkinson
authors.forename: Robert B
authors.initials: RB
authors.lastname: Sandoval
authors.forename: Richard A
authors.initials: RA
authors.lastname: Jorgensen
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D007446:Chromosome Inversion / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D008969:Molecular Sequence Data; D011995:Recombination, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004269:DNA, Bacterial; D018744:DNA, Plant; C036483:T-DNA