Discovery of Imprinted Transcripts in the Mouse Transcriptome Using Large-Scale Expression Profiling

  1. Itoshi Nikaido1,2,
  2. Chika Saito1,
  3. Yosuke Mizuno1,
  4. Makiko Meguro3,
  5. Hidemasa Bono1,
  6. Moritoshi Kadomura1,
  7. Tomohiro Kono4,
  8. Gerard A. Morris5,
  9. Paul A. Lyons5,
  10. Mitsuo Oshimura3,
  11. RIKEN GER Group1,
  12. GSL Members 6,7,
  13. Yoshihide Hayashizaki1,6, and
  14. Yasushi Okazaki1,8
  1. 1Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku Yokohama, Kanagawa 230-0045, Japan
  2. 2Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Yokohama, Kanagawa 230-0045, Japan
  3. 3Department of Molecular and Cell Genetics, School of Life Sciences, Faculty of Medicine, Tottori University, Yonago, Tottori 683-8503, Japan
  4. 4Department of BioScience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
  5. 5JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 2XY, UK
  6. 6Genome Science Laboratory, RIKEN, Hirosawa, Wako, Saitama 351-0198, Japan

Abstract

Candidate imprinted transcriptional units in the mouse genome were identified systematically from 27,663 FANTOM2 full-length mouse cDNA clones by expression profiling. Large-scale cDNA microarrays were used to detect differential expression dependent upon chromosomal parent of origin by comparing the mRNA levels in the total tissue of 9.5 dpc parthenogenote and androgenote mouse embryos. Of the FANTOM2 transcripts, 2114 were identified as candidates on the basis of the array data. Of these, 39 mapped to known imprinted regions of the mouse genome, 56 were considered as nonprotein-coding RNAs, and 159 were natural antisense transcripts. The imprinted expression of two transcripts located in the mouse chromosomal region syntenic to the human Prader-Willi syndrome region was confirmed experimentally. We further mapped all candidate imprinted transcripts to the mouse and human genome and were shown in correlation with the imprinting disease loci. These data provide a major resource for understanding the role of imprinting in mammalian inherited traits.

Footnotes

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1055303.

  • ↵7 Shinji Kondo, Takahiro Arakawa, Piero Carninci, and Jun Kawai.

  • ↵8 Corresponding author. E-MAIL rgscerg{at}gsc.riken.go.jp; FAX 81-45-503-9216.

    • Accepted February 19, 2003.
    • Received December 5, 2002.
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  1. doi: 10.1101/gr.1055303 Genome Res. 13: 1402-1409 Cold Spring Harbor Laboratory Press

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