Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome.
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.
Takabatake
Takashi
T
Department of Radiobiology, Institute for Environmental Sciences, 2-121, Hacchazawa, Takahoko, Rokkasho, Aomori 039-3213, Japan. batake@nirs.go.jp
Ishihara
Hiroshi
H
Ohmachi
Yasushi
Y
Tanaka
Izumi
I
Nakamura
Masako M
MM
Fujikawa
Katsuyoshi
K
Hirouchi
Tokuhisa
T
Kakinuma
Shizuko
S
Shimada
Yoshiya
Y
Oghiso
Yoichi
Y
Tanaka
Kimio
K
D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D005260:Female; D007426:Genes, Intracisternal A-Particle; D023281:Genomics / Q000379:methods*; D007953:Leukemia, Radiation-Induced / Q000235:genetics; D051379:Mice; D008809:Mice, Inbred C3H; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020079:Terminal Repeat Sequences