HEAVY-CHAIN JOINING REGION SEGMENTS OF THE CHANNEL CATFISH - GENOMIC ORGANIZATION AND PHYLOGENETIC IMPLICATIONS

The JH locus of the channel catfish has been characterized to determin e the organization and structural diversity of JH segments. These anal yses indicate that there are a total of nine JH segments tightly clust ered within a region spanning about 2.2 kb. The JH locus is closely li nked to the CH1 domain of the expressed catfish H chain; the distance between the CH proximal JH segment (JH9) and the CH1 domain is about 1 .8 kb. Each JH segment has an upstream recombination sequence, which i ncludes a T-rich nonamer, a 22- to 24-bp spacer, and a phylogeneticall y conserved heptamer. Each JH segment also has an open reading frame t hat encodes the conserved framework region 4 tryptophan (Trp-103) and terminates with a RNA donor splice site. The catfish JH locus contains an internal repetitive sequence region characterized by a short (183- 188 bp) repeat that occurs sequentially five times. Strong sequence ho mology as well as the unified length of the repeated sequences indicat e that JH segments JH3-JH7 probably arose as the result of a series of homologous but unequal crossover events. Sequence alignments of the d uplicated JH segments indicates that there is diversity within the 5-1 1 nucleotides located immediately downstream from the heptamer, an obs ervation which indicates that closely related JH segments can serve to enhance CDR3 diversity in the expressed H chain. Comparisons of the g enomic JH sequences with different cDNA clones indicate that each JH s egment is probably functional and that junctional diversity serves an important role in the generation of CDR3 diversity. In addition, singl e base differences observed in comparisons of JH-encoded regions indic ate that there is probably somatic mutation or allelic variation of ge nomic JH segments. These studies suggest that the characteristic struc ture and organizational pattern of JH segments in higher vertebrates m ay have evolved early in vertebrate phylogeny at the level of the bony fish.