Itoshi Nikaido ^{1, 2, 3}, Chika Saito ³, Akiko Wakamoto ³, Yasuhiro Tomaru ³, Takahiro Arakawa ³, Yoshihide Hayashizaki ^{1, 3} and Yasushi Okazaki* ^{2, 3}

¹ Division of Genomic Information Resource Exploration, Science of Biological Supramolecular Systems, Yokohama City University, Graduate School of Integrated Science, Yokohama, Kanagawa 230-0045, Japan,
² Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, Saitama Medical School, Saitama 350-1241, Japan and
³ Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Yokohama, Kanagawa 230-0045, Japan

*To whom correspondence should be addressed at Division of Functional Genomics and Systems Medicine, Research Center for Genomic Medicine, 1397-1 Yamane, Hidaka City, Saitama 350-1241, Japan.
Tel: +81 429 85 7319; Fax: +81 429 85 7329; Email: okazaki@saitama-med.ac.jp

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.

INTRODUCTION

Genomic imprinting results in the expression of individual genes from only one of two parental chromosomes and affects growth and behavior after birth in mammals (1). Aberrant imprinting can lead to various diseases due to an effective doubling of gene dosage. Conversely, genetic diseases display complex inheritance patterns, through the male or female line, when the affected gene falls within a maternally or paternally imprinted locus.
Identification of the network of imprinted genes will provide insight into the molecular mechanisms that underlie
imprinting-related phenotypes and diseases. To date 60 imprinted mouse genes have been identified using various methods ( http://www.mgu.har.mrc.ac.uk/imprinting/all_impmaps.html ). Genomic imprinting involves promoter methylation and/or natural antisense transcripts (NATs) of imprinted or neighboring genes (2); however, the details are unclear. Imprinting clearly cannot be predicted from genomic sequencing and annotation alone (1). We have established an efficient method of screening for candidate imprinted transcripts, and target genes by comparing mRNA expression profiles between parthenogenotes and androgenotes using RIKEN cDNA microarrays (3,4). Although our screening method is very efficient, a fraction (32%) of the identified candidate genes proved to be non-imprinted (3). These non-imprinted genes could be regulated by imprinted genes.

To confirm the imprinted status of candidate transcripts, we performed reciprocal crosses with Mus musculus molossinus (MSM), a Japanese wild mouse strain, and analyzed the resulting transcripts for polymorphisms that distinguish paternal from maternal loci. Since MSM is phylogenetically 1 million years apart from common laboratory mouse strains, it exhibits frequent genetic polymorphisms with laboratory mice. To this end, we searched for polymorphisms in the 3'-end of the transcripts between MSM and C57BL/6J mouse lines and the results were assembled into the EICO. In this paper, we report the construction and implementation of the EICO ( http://fantom2.gsc.riken.jp/EICODB/ ), which efficiently stores and retrieves three kinds of data: (i) candidate imprinted transcripts from microarray analysis, (ii) single nucleotide polymorphisms (SNPs) between the 3'-end sequences of the RIKEN full-length cDNAs from C57BL/6J and MSM mice, and (iii) imprinting-related
disease loci extracted from OMIM (5). The relationship between disease loci and novel imprinted mRNAs identifies new candidates that may be involved causally in imprinting-related human genetic diseases.

Table 1. Contents of the EICO.
 

Contents Number SNPs between MSM and C57BL/6J (1) 2850 (1281 genes) Candidate imprinted genes (2) Paternal: 698; maternal: 1403 Genes overlapped between 1 and 2 (3) 243 Candidate imprinted genes on predicted imprinting-related disease loci on human genome (4) 529 genes; 65 diseases; 109 loci Genes overlapped between 3 and 4 114 genes

The EICO has 2850 SNPs, 2101 candidate imprinted genes and 529 candidate imprinted genes within predicted imprinting-related disease loci.

REFERENCES

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1. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, and Jacobsen SE, "Role of the DRM and CMT3 Methyltransferases in RNA-Directed DNA Methylation",  Current Biology, vol 13, no. 24, pp. 2212-2217 (16 December 2003).

2. Report of "RIKEN Mouse Genome Encyclopedia" project: the whole system from mouse house to database.
    Published in Genome Research, vol. 13, no. 6b, pp. 1265-1561 (June2, 2003).

3. Topics in:  Euchromatin,  active DNA, and  RNA  ribo-regulators:

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"Ultrastructural Probes of Active DNA Sites, and the RNA Activators of DNA".
 

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