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 hos...
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| Veröffentlicht in: | Nucleic acids research 2008-06, Vol.36 (10), p.e59-e59 |
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| creator | Takabatake, Takashi Ishihara, Hiroshi Ohmachi, Yasushi Tanaka, Izumi Nakamura, Masako M Fujikawa, Katsuyoshi Hirouchi, Tokuhisa Kakinuma, Shizuko Shimada, Yoshiya Oghiso, Yoichi Tanaka, Kimio |
| description | 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. |
| doi_str_mv | 10.1093/nar/gkn235 |
| format | Article |
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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. 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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.</description><subject>Animals</subject><subject>Chromosome Mapping - methods</subject><subject>Female</subject><subject>Genes, Intracisternal A-Particle</subject><subject>Genomics - methods</subject><subject>Leukemia, Radiation-Induced - genetics</subject><subject>Methods Online</subject><subject>Mice</subject><subject>Mice, Inbred C3H</subject><subject>Mice, Inbred C57BL</subject><subject>Oligonucleotide Array Sequence Analysis - methods</subject><subject>Terminal Repeat Sequences</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNqN0U1v1DAQBuAIgehSuPADIEKCAyLU448kviCVClhQEQcooF6sSXaSuk3sYGcRlfjxJGRVPg6Ikw_z-NXYb5LcBfYUmBYHDsNBe-G4UNeSFYicZ1Ln_HqyYoKpDJgs95JbMZ4zBhKUvJnsQSkVK0Guku9vbR08hoCXWYWRNmnb-Qq7tMdhsK5NfZNaN1IbcLTepdGOFNPGh3Q8ozTQGPwY0MXBR--ezDRgbeNIwU0hh9mAYbR1R_Po55XebyOlLTnf0-3kRoNdpDu7cz85efniw9E6O3736vXR4XFW51yMWaNzVCVKgZqwpErpRm0Aak01a1hZkag01AUwJlWlEDZABKrQFQGwitdiP3m25A7bqqdNTfOWnRmC7TFcGo_W_Dlx9sy0_qvhkitZwBTwaBcQ_JctxdH0NtbUdehoeo8BXWitQf8HzAtRlGKCD_6C5347_1k0nLF86gdm9HhBU0UxBmquVgZm5urNVL1Zqp_wvd8f-Yvuup7AwwX47fDvoGxxc43friSGCzMvr8z686l5s37OTj-Whfk0-fuLb9AbbION5uQ9ZyAY00xwzsUPTTfS9Q</recordid><startdate>20080601</startdate><enddate>20080601</enddate><creator>Takabatake, Takashi</creator><creator>Ishihara, Hiroshi</creator><creator>Ohmachi, Yasushi</creator><creator>Tanaka, Izumi</creator><creator>Nakamura, Masako M</creator><creator>Fujikawa, Katsuyoshi</creator><creator>Hirouchi, Tokuhisa</creator><creator>Kakinuma, Shizuko</creator><creator>Shimada, Yoshiya</creator><creator>Oghiso, Yoichi</creator><creator>Tanaka, Kimio</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>FBQ</scope><scope>BSCLL</scope><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>5PM</scope></search><sort><creationdate>20080601</creationdate><title>Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome</title><author>Takabatake, Takashi ; 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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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>18450814</pmid><doi>10.1093/nar/gkn235</doi><oa>free_for_read</oa></addata></record> |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Chromosome Mapping - methods Female Genes, Intracisternal A-Particle Genomics - methods Leukemia, Radiation-Induced - genetics Methods Online Mice Mice, Inbred C3H Mice, Inbred C57BL Oligonucleotide Array Sequence Analysis - methods Terminal Repeat Sequences |
| title | Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome |
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