Genomic organization and chromosomal distribution of rat ID elements.

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  • Ono Takao
    Laboratory of Cytogenetics, Division of Bioscience, Graduate School of Environmental Earth Sciences Faculty of Science, Hokkaido University Department of Genetics, Institute for Developmental Research, Aichi Human Service Center
  • Kondoh Yasumitsu
    Aisin Cosmos R & D Co., Ltd. Present address: Advanced Engineering Center, RIKEN
  • Kagiyama Naoto
    Aisin Cosmos R & D Co., Ltd.
  • Sonta Shin-ichi
    Department of Genetics, Institute for Developmental Research, Aichi Human Service Center
  • Yoshida Michihiro C.
    Laboratory of Cytogenetics, Division of Bioscience, Graduate School of Environmental Earth Sciences Faculty of Science, Hokkaido University Chromosome Research Unit, Faculty of Science, Hokkaido University Present address: Hokkaido Information University

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Identifier (ID) elements are members of a family of short interspersed nuclear elements (SINEs) in rodents. We investigated the genomic organization and chromosomal distribution of the ID elements in the rat, mouse and Chinese hamster. Southern blot hybridization analysis revealed that the ID elements are widespread in the rat genome, but concentrated in the mouse and Chinese hamster genomes, and that the copy of ID elements in the rat is about 5 times and 50 times that in the mouse and Chinese hamster, respectively. FISH analysis showed that the ID elements are predominantly distributed in the R-band regions of rat chromosomes. In mouse and Chinese hamster chromosomes, no specific distribution pattern of the ID elements was found. Furthermore, we found a distinct group of derivative ID elements in the rat, which contain partially repeated ID core domains, by PCR amplification using an ID core sequence. Such derivatives were not found in either the mouse or Chinese hamster. These findings suggest that explosive amplification of the ID elements in the rat has been accompanied by the occurrence of derivative ID elements and a predominant localization to the R-band regions. Similar associations found in the Alu family, one of the human SINEs, allow us to speculate that the rat ID elements and the human Alu family have analogous functions in chromosomal organization.

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