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Open Access Research article

Analysis of the conservation of synteny between Fugu and human chromosome 12

Alexandre Montpetit12, Michael D Wilson4, Mario Chevrette5, Ben F Koop4 and Daniel Sinnett123*

Author Affiliations

1 Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, Sainte-Justine Hospital, 3175 Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada

2 Department of Biochemistry, University of Montreal, Montreal, QC, Canada

3 Department of Pediatrics, University of Montreal, Montreal, QC, Canada

4 Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada

5 The Research Institute of the McGill University Health Centre and Department of Surgery, McGill University, Montreal, QC, H3G 1A4, Canada

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BMC Genomics 2003, 4:30  doi:10.1186/1471-2164-4-30

Published: 23 July 2003

Abstract

Background

The pufferfish Fugu rubripes (Fugu) with its compact genome is increasingly recognized as an important vertebrate model for comparative genomic studies. In particular, large regions of conserved synteny between human and Fugu genomes indicate its utility to identify disease-causing genes. The human chromosome 12p12 is frequently deleted in various hematological malignancies and solid tumors, but the actual tumor suppressor gene remains unidentified.

Results

We investigated approximately 200 kb of the genomic region surrounding the ETV6 locus in Fugu (fETV6) in order to find conserved functional features, such as genes or regulatory regions, that could give insight into the nature of the genes targeted by deletions in human cancer cells. Seven genes were identified near the fETV6 locus. We found that the synteny with human chromosome 12 was conserved, but extensive genomic rearrangements occurred between the Fugu and human ETV6 loci.

Conclusion

This comparative analysis led to the identification of previously uncharacterized genes in the human genome and some potentially important regulatory sequences as well. This is a good indication that the analysis of the compact Fugu genome will be valuable to identify functional features that have been conserved throughout the evolution of vertebrates.