Analysis of recombination signal sequences in zebrafish

Recombination signal sequences (RSS) from immunoglobulin and TCRα genes of zebrafish were analyzed in comparison with RSS from human and species-specific features were revealed. In contrast to human RSS, in zebrafish RSS from both VH and TCRα genes the last nonamer position is not conserved. On the contrary, the fourth nonamer position, which is not conserved in human or mouse is conserved in zebrafish. The 12 bp spacers from human and zebrafish RSS contain 9 bp motif resembling nonamer sequence. Spacers in zebrafish 23 bp RSS from both immunoglobulins and TCRα contain 7 bp motif also resembling nonamer sequence while corresponding human sequences do not contain analogous motif. RSS are recognized by RAG1 protein, which also has specific features in teleost suggesting co-evolution of RAG1 with corresponding RSS.