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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

Site Preferences of Insertional Mutagenesis Agents in Arabidopsis

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 (X.P., L.S.); and Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany (Y.L.)

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.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.104.053215.

^* Corresponding author; e-mail xpan{at}iastate.edu; fax 515–294–6755.

Received September 9, 2004; returned for revision November 13, 2004; accepted November 15, 2004.

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