Site preferences of insertional mutagenesis agents in Arabidopsis

Pan, X., Li, Y., Stein, L. D. (January 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: January 2005
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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