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.
We have developed an integrated database that is specialized for the study of imprinted disease genes. The database contains novel candidate imprinted genes identified by the RIKEN full-length mouse cDNA microarray study, information on validated single nucleotide polymorphisms (SNPs) to confirm imprinting using reciprocal mouse crosses and the predicted physical position of imprinting-related disease loci in the mouse and human genomes. It has two user-friendly search interfaces: the SNP-central view (MuSCAT: MoUse SNP CATalog) and the candidate gene-central view (CITE: Candidate Imprinted Transcripts by Expression). The database, EICO (Expression-based Imprint Candidate Organizer), can be accessed via the World Wide Web (http://fantom2.gsc.riken.jp/EICODB/) and the DAS client software. These data and interfaces facilitate understanding of the mechanism of imprinting in mammalian inherited traits.
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