Site preferences of insertional mutagenesis agents in Arabidopsis

Pan X, Li Y, Stein L (2005)
Plant Physiology 137(1): 168-175.

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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.
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Pan X, Li Y, Stein L. Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology. 2005;137(1):168-175.
Pan, X., Li, Y., & Stein, L. (2005). Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology, 137(1), 168-175.
Pan, X., Li, Y., and Stein, L. (2005). Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology 137, 168-175.
Pan, X., Li, Y., & Stein, L., 2005. Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology, 137(1), p 168-175.
X. Pan, Y. Li, and L. Stein, “Site preferences of insertional mutagenesis agents in Arabidopsis”, Plant Physiology, vol. 137, 2005, pp. 168-175.
Pan, X., Li, Y., Stein, L.: Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiology. 137, 168-175 (2005).
Pan, X., Li, Yong, and Stein, L. “Site preferences of insertional mutagenesis agents in Arabidopsis”. Plant Physiology 137.1 (2005): 168-175.
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