THE COMPARATIVE GENOMIC STRUCTURE AND SEQUENCE OF THE SURFEIT GENE HOMOLOGS IN THE PUFFER FISH FUGU RUBRIPES AND THEIR ASSOCIATION WITH CPG-RICH ISLANDS

The puffer fish Fugu rubripes (Fugu) has a compact genome approximatel y one-seventh the size of man, mainly owing to small intron size and t he presence of few dispersed repetitive DNA elements, which greatly fa cilitates the study of its genes at the genomic level. It has been sho wn previously that, whereas the Surfeit genes are tightly clustered at a single locus in mammals and birds, the genes are found at three sep arate loci in the Fugu genome. Here, Fugu gene homologs of all six Sur feit genes (Surf-1 to Surf-6) have been cloned and sequenced, and thei r gene structure has been compared with that of their mammalian and av ian homologs. The predicted protein products of each gene are well con served between vertebrate species, and in most cases their gene struct ures are identical to their mammalian and avian homologs except for th e Fugu Surf-6 gene, which was found to lack an intron present in the m ouse gene. In addition, we have identified conserved regulatory elemen ts at the 5' and 3' ends of the Surf-3/rpL7a gene by comparison with t he mammalian and chicken Surf-3/rpL7a gene homologs, including the pre sence of a polypyrimidine tract at the extreme 5' end of this ribosoma l protein gene. The Fugu Surfeit gene homologs appear to be associated with CpG-rich islands, like the Surfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands cha racteristic of other fish species. Our observations support the use of the Fugu genome to study vertebrate gene structure, to predict the st ructure of mammalian genes, and to identify vertebrate regulatory elem ents.