title: Site preferences of insertional mutagenesis agents in Arabidopsis.
abstract: We have performed a comparative analysis of the insertion sites of engineered Arabidopsis (Arabidopsis thaliana) insertional mutagenesis vectors that are based on the maize (Zea mays) transposable elements and Agrobacterium T-DNA. The transposon-based agents show marked preference for high GC content, whereas the T-DNA-based agents show preference for low GC content regions. The transposon-based agents show a bias toward insertions near the translation start codons of genes, while the T-DNAs show a predilection for the putative transcriptional regulatory regions of genes. The transposon-based agents also have higher insertion site densities in exons than do the T-DNA insertions. These observations show that the transposon-based and T-DNA-based mutagenesis techniques could complement one another well, and neither alone is sufficient to achieve the goal of saturation mutagenesis in Arabidopsis. These results also suggest that transposon-based mutagenesis techniques may prove the most effective for obtaining gene disruptions and for generating gene traps, while T-DNA-based agents may be more effective for activation tagging and enhancer trapping. From the patterns of insertion site distributions, we have identified a set of nucleotide sequence motifs that are overrepresented at the transposon insertion sites. These motifs may play a role in the transposon insertion site preferences. These results could help biologists to study the mechanisms of insertions of the insertional mutagenesis agents and to design better strategies for genome-wide insertional mutagenesis.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA. xpan@iastate.edu
authors.forename: Xiaokang
authors.initials: X
authors.lastname: Pan
authors.forename: Yong
authors.initials: Y
authors.lastname: Li
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000502:physiology; D004269:DNA, Bacterial / Q000737:chemistry; D016254:Mutagenesis, Insertional / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; C036483:T-DNA