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Nucleic Acids Research Advance Access published online on May 1, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn235
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods online

Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome

Takashi Takabatake1,*, Hiroshi Ishihara2, Yasushi Ohmachi3, Izumi Tanaka2, Masako M. Nakamura4, Katsuyoshi Fujikawa1, Tokuhisa Hirouchi1, Shizuko Kakinuma3, Yoshiya Shimada3, Yoichi Oghiso1 and Kimio Tanaka1

1Department of Radiobiology, Institute for Environmental Sciences, 2-121, Hacchazawa, Takahoko, Rokkasho, Aomori 039-3213, Japan, 2Research Center for Radiation Emergency Medicine, 3Research Center for Radiation Protection, National Institute of Radiological Sciences, 4-9-1, Anagawa, Inage-ku, Chiba 263-8555 and 4Genetic Biochemistry Division, Tohoku Environmental Sciences Services Corporation, 1-19-22, Kogawamachi, Mutsu, Aomori 035-0071, Japan

*To whom correspondence should be addressed. Tel: +81 43 206 3160; Fax: +81 43 206 4138; Email: batake{at}nirs.go.jp Present address: Takashi Takabatake, Experimental Radiobiology for Children's Health Research Group, National Institute of Radiological Sciences, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan

Received November 28, 2007. Revised April 14, 2008. Accepted April 14, 2008.

Mammalian genomes contain numerous evolutionary harbored mobile elements, a part of which are still active and may cause genomic instability. Their movement and positional diversity occasionally result in phenotypic changes and variation by causing altered expression or disruption of neighboring host genes. Here, we describe a novel microarray-based method by which dispersed genomic locations of a type of retrotransposon in a mammalian genome can be identified. Using this method, we mapped the DNA elements for a mouse retrotransposon, intracisternal A-particle (IAP), within genomes of C3H/He and C57BL/6J inbred mouse strains; consequently we detected hundreds of probable IAP cDNA–integrated genomic regions, in which a considerable number of strain-specific putative insertions were included. In addition, by comparing genomic DNAs from radiation-induced myeloid leukemia cells and its reference normal tissue, we detected three genomic regions around which an IAP element was integrated. These results demonstrate the first successful genome-wide mapping of a retrotransposon type in a mammalian genome.


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