E-GEOD-9572 - Microarray-based global mapping of integration sites of retrotransposon, intracisternal A-particle, in mouse genome

Status
Released on 3 May 2008, last updated on 2 May 2014
Organism
Mus musculus
Samples (20)
Arrays (4)
Protocols (11)
Description
Mammalian genomes have evolutionary harbored numerous mobile elements, a part of which are still active and evoke genomic instability. Their movement and positional diversity occasionally result in phenotypic changes and variation by causing altered expression and disruption of neighboring genes in the host genome. Here, we describe a novel microarray-based method by which dispersed genomic locations of a type of retrotransposons in mammalian genome can be identified at a time. By 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-integrating genomic regions. Among 147 putative insertions located nearby the promoter regions, 91 were considered to be present discriminatively in the genome either of C3H/He or C57BL/6J mice, suggesting the existence of considerable strain differences. In addition, by comparing genomic DNAs from a radiation-induced myeloid leukemia and its reference normal tissue, we detected 3 genomic regions around which an IAP element was integrated. These results demonstrate for the first time the successful genome-wide survey of a type of retrotransposon in mammalian genome. Keywords: retrotransposon mapping Genomic DNA fragments containing sequences that flank a mouse retrotransposon are purified and hybridized to the microarray. Experiments are comparisions between signal intensities obtained from Cy3-labeled purified DNA fragments (test) and Cy5-labeled whole genomic DNA fragments (reference).
Experiment type
unknown experiment type 
Contacts
Takashi Takabatake <batake@nirs.go.jp>, Hiroshi Ishihara, Izumi Tanaka, Katsuyoshi Fujikawa, Kimio Tanaka, Masako M Nakamura, Shizuko Kakinuma, Tokuhisa Hirouchi, Yasushi Ohmachi, Yoichi Oghiso, Yoshiya Shimada
Citation
Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome. Takabatake T, Ishihara H, Ohmachi Y, Tanaka I, Nakamura MM, Fujikawa K, Hirouchi T, Kakinuma S, Shimada Y, Oghiso Y, Tanaka K. , Europe PMC 18450814
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