Home LiteratureArticle Details
PMID: 12897251 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome.

The Plant cell ·Vol. 15 ·No. 8 ·2003-08-00 ·Pages 1771-80

Miyao A, Tanaka K, Murata K, Sawaki H, Takeda S, Abe K, Shinozuka Y, Onosato K, Hirochika H

Abstract

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 approximately 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. --The nucleotide sequence data were uploaded to the DDBJ, EMBL, and GenBank nucleotide sequence databases under accession numbers AG020727 to AG025611 and AG205093 to AG215049.

MeSH Terms
Base Composition Base Sequence Binding Sites/genetics DNA, Plant/chemistry,genetics Genes, Plant Genome, Plant Molecular Sequence Data Mutagenesis, Insertional Oryza/genetics Retroelements/genetics
Chemicals
DNA, Plant Retroelements
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Miyao Akio
Molecular Genetics Department, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
Tanaka Katsuyuki
Murata Kazumasa
Sawaki Hiromichi
Takeda Shin
Abe Kiyomi
Shinozuka Yoriko
Onosato Katsura
Hirochika Hirohiko
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.012559
Published
2003-08-00
Pages
1771-80
Language
English
Region
England
NLM ID
9208688
PMCID
PMC167168
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1105/tpc.012559 PMC Full Text View journal details
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