INFLUENCE OF CODING-END SEQUENCE ON CODING-END PROCESSING IN V(D)J RECOMBINATION

The large diversity of the Ig and TCR repertoires is accounted for by combinatorial assembly of the germ-line-encoded V, D, and J gene segme nts, as well as extensive modification at the junctions during the rec ombination process. Those modifications, termed coding-end processing, consist of removal and addition of an apparently random number of nuc leotides. To obtain further insights into the mechanism of the coding- end processing, we constructed a large data base of several Ig and TCR coding ends obtained in vivo, using conditions that avoid potential b ias by cellular selection events. We show that the processing patterns are not random, but rather specific for each coding end, suggesting t hat specific motifs in the coding-end sequence influence the processin g. We found a good correlation between the presence of internal stretc hes of at least three A.T nucleotides, absence of stretches of G.C nuc leotides, and high average nucleotide deletion. Based on a detailed an alysis of the processing patterns, we propose that nicks of the hairpi n intermediate take place preferentially in potential open structures formed by weaker pairings of A.T stretches. Together, these findings i ndicate that the sequence of the coding end plays an important role in nonrandom aspects of the recombination mechanism. This suggests that coding-end sequences might have been selected throughout evolution to participate in an early control of the development of the primary repe rtoire.