GENOMIC ORGANIZATION OF THE TCR BETA-CHAIN DIVERSITY (D-BETA) AND JOINING (J-BETA) SEGMENTS IN THE RAINBOW-TROUT - PRESENCE OF MANY REPEATED SEQUENCES

This work describes a 5.5kb genomic sequence of the rainbow trout T-ce ll receptor beta-chain locus. It includes, from 5' to 3', a D beta gen e, 10 J beta genes and the 5'-end of the first C beta exon. The trout D beta-J beta-C beta locus is about the same size as the mouse, rat an d human homologous loci, but it is less compact and contains 10 J beta segments instead of the 6-7 found in mammals. The trout D beta coding sequence is identical to those of the mouse, rat and human D beta, an d the D beta recombination signal sequences (RSS) are also very well c onserved. Each trout J beta segment is flanked in 5' by a 7-mer RSS, w hich matches with the canonical conserved 7-mer sequences of all RSS. However, 6 of the 10 J beta segments have no characteristic 9-mer RSS, although at least some of them are well expressed (J beta 1 and J bet a 2). The J beta region of the trout TcR beta locus contains numerous micro/minisatellite repeated DNA sequences; some of these repeats cont ain heptamer RSS-like sequences that could interfere with J beta expre ssion. Knowledge of the germline boundaries of the trout D beta and J beta ends makes it possible to evaluate precisely the exonuclease acti vity and N-nucleotide addition at the D beta-J beta junctions of the r earranged TcR beta chain genes. Many (40%) of the D beta-J beta juncti ons in the adult trout have no N-nucleotides, compared to 26.4% in adu lt mice, and 37% of the adult trout TcR beta transcripts are out of fr ame. Thus, there may be major differences in the T-cell developmental kinetics and selection in fish and mammals. (C) 1997 Elsevier Science Ltd.