Site preferences of insertional mutagenesis agents in Arabidopsis

Pan, X., Li, Y., Stein, L. D. (2005) Site preferences of insertional mutagenesis agents in Arabidopsis. Plant Physiol, 137 (1). pp. 168-75. ISSN 0032-0889 (Print)

URL: http://www.plantphysiol.org/cgi/content/abstract/1...
DOI: 10.1104/pp.104.053215

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.

Item Type: Paper
Uncontrolled Keywords: Arabidopsis genetics Base Sequence DNA Transposable Elements physiology tDNA DNA, Bacterial chemistry Mutagenesis Insertional genetics
Subjects: organism description > plant > Arabidopsis
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: CSHL Librarian
Date Deposited: 09 Jan 2012 14:16
Last Modified: 09 Jan 2012 14:16
URI: http://repository.cshl.edu/id/eprint/22671

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