THE COMPOSITION OF CODING JOINTS FORMED IN V(D)J RECOMBINATION IS STRONGLY AFFECTED BY THE NUCLEOTIDE-SEQUENCE OF THE CODING ENDS AND THEIRRELATIONSHIP TO THE RECOMBINATION SIGNAL SEQUENCES

V(D)J recombination proceeds in two stages, Precise cleavage at the bo rder of the conserved recombination signal sequences (RSSs) and the co ding ends results in flush double-stranded signal ends and coding ends terminating in hairpins, In the second stage, the signal and coding e nds are processed into signal and coding joints, Coding ends containin g certain nucleotide homopolymers affect the efficiency of V(D)J recom bination, In this study, we have tested the effect of small changes in coding-end nucleotide composition on the frequency of coding- and sig nal joint formation, Furthermore, we have determined the sequences of coding joints resulting from recombination of coding ends with differe nt compositions, We found that the presence of two T nucleotides 5' of both RSSs, but not a single T, reduces the frequency of signal joint formation, i.e., interferes with the cleavage stage of V(D)J recombina tion, However, coding-joint processing is sensitive even to a single T . Both the sequence of the coding ends and the particular RSS (12-mer or 23-mer) with which the coding end is associated affect the final co mposition of the coding joints. Thus, the presence of P nucleotides, t he conservation of one undeleted coding end, the formation of joints w ithout any deletions, and the template-dependent insertion of nucleoti des are strongly influenced by the coding-end nucleotide composition a nd/or RSS association, The implications of these results with respect to the processing of coding ends are discussed.