Genomic organization of the TcR beta-chain diversity (Dbeta) and joining (Jbeta) segments in the rainbow trout: presence of many repeated sequences.

This work describes a 5.5 kb genomic sequence of the rainbow trout T-cell receptor beta-chain locus. It includes, from 5' to 3', a Dbeta gene, 10 Jbeta genes and the 5'-end of the first Cbeta exon. The trout Dbeta-Jbeta-Cbeta locus is about the same size as the mouse, rat and human homologous loci, but it is less compact and contains 10 Jbeta segments instead of the 6-7 found in mammals. The trout Dbeta coding sequence is identical to those of the mouse, rat and human Dbeta, and the Dbeta recombination signal sequences (RSS) are also very well conserved. Each trout Jbeta segment is flanked in 5' by a 7-mer RSS, which matches with the canonical conserved 7-mer sequences of all RSS. However, 6 of the 10 Jbeta segments have no characteristic 9-mer RSS, although at least some of them are well expressed (Jbeta1 and Jbeta2). The Jbeta region of the trout TcRbeta locus contains numerous micro/minisatellite repeated DNA sequences; some of these repeats contain heptamer RSS-like sequences that could interfere with Jbeta expression. Knowledge of the germline boundaries of the trout Dbeta and Jbeta ends makes it possible to evaluate precisely the exonuclease activity and N-nucleotide addition at the Dbeta-Jbeta junctions of the rearranged TcRbeta chain genes. Many (40%) of the Dbeta-Jbeta junctions in the adult trout have no N-nucleotides, compared to 26.4% in adult mice, and 37% of the adult trout TcRbeta transcripts are out of frame. Thus, there may be major differences in the T-cell developmental kinetics and selection in fish and mammals.