Transcriptomics

Dataset Information

3

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


ABSTRACT: 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).

ORGANISM(S): Mus musculus  

SUBMITTER: Hiroshi Ishihara   Yoshiya Shimada  Shizuko Kakinuma  Katsuyoshi Fujikawa  Yoichi Oghiso  Takashi Takabatake  Yasushi Ohmachi  Masako M Nakamura  Tokuhisa Hirouchi  Izumi Tanaka  Kimio Tanaka 

PROVIDER: E-GEOD-9572 | ArrayExpress | 2008-05-03

SECONDARY ACCESSION(S): GSE9572PRJNA103399

REPOSITORIES: GEO, ArrayExpress

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Publications

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

Takabatake Takashi T   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  

Nucleic acids research 20080501 10


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 D  ...[more]

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