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

BMC Genomics. 2003 Jul 23;4(1):30. doi: 10.1186/1471-2164-4-30.

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Chromosome Mapping
  • Chromosomes, Human, Pair 12 / genetics*
  • Conserved Sequence / genetics
  • DNA / chemistry
  • DNA / genetics
  • DNA-Binding Proteins / genetics
  • Gene Order
  • Humans
  • Molecular Sequence Data
  • Proto-Oncogene Proteins c-ets
  • Repressor Proteins / genetics
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Synteny / genetics*
  • Takifugu / genetics*

Substances

  • DNA-Binding Proteins
  • ETS translocation variant 6 protein
  • Proto-Oncogene Proteins c-ets
  • Repressor Proteins
  • DNA

Associated data

  • GENBANK/AY339212
  • GENBANK/AY339213