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First published online July 3, 2003; 10.1105/tpc.012559

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The Plant Cell, Vol. 15, 1771-1780, August 2003, Copyright © 2003,
American Society of Plant Biologists

Target Site Specificity of the Tos17 Retrotransposon Shows a Preference for Insertion within Genes and against Insertion in Retrotransposon-Rich Regions of the Genome

Akio Miyaoa, Katsuyuki Tanakab, Kazumasa Muratab, Hiromichi Sawakib, Shin Takedaa, Kiyomi Abea, Yoriko Shinozukab, Katsura Onosatob and Hirohiko Hirochika1,a

a Molecular Genetics Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
b First Research Division, Institute of Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, Tsukuba, Ibaraki 305-0854, Japan

1 To whom correspondence should be addressed. E-mail hirohiko{at}nias.affrc.go.jp; fax 81-(0) 298-38-7020

Because retrotransposons are the major component of plant genomes, analysis of the target site selection of retrotransposons is important for understanding the structure and evolution of plant genomes. Here, we examined the target site specificity of the rice retrotransposon Tos17, which can be activated by tissue culture. We have produced 47,196 Tos17-induced insertion mutants of rice. This mutant population carries ~500,000 insertions. We analyzed >42,000 flanking sequences of newly transposed Tos17 copies from 4316 mutant lines. More than 20,000 unique loci were assigned on the rice genomic sequence. Analysis of these sequences showed that insertion events are three times more frequent in genic regions than in intergenic regions. Consistent with this result, Tos17 was shown to prefer gene-dense regions over centromeric heterochromatin regions. Analysis of insertion target sequences revealed a palindromic consensus sequence, ANGTT-TSD-AACNT, flanking the 5-bp target site duplication. Although insertion targets are distributed throughout the chromosomes, they tend to cluster, and 76% of the clusters are located in genic regions. The mechanisms of target site selection by Tos17, the utility of the mutant lines, and the knockout gene database are discussed.




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