NUCLEOTIDE DELETION AND P-ADDITION IN V(D)J RECOMBINATION - A DETERMINANT ROLE OF THE CODING-END SEQUENCE

During V(D)J recombination, the coding ends to be joined are extensive ly modified. Those modifications, termed coding-end processing, consis t of removal and addition of various numbers of nucleotides, We previo usly showed in vivo that coding-end processing is specific far each co ding end, suggesting that specific motifs in a coding-end sequence inf luence nucleotide deletion and P-region formation. Ln this study, me c reated a panel of recombination substrates containing actual immunoglo bulin and T-cell receptor coding-end sequences and dissected the role of each motif hv comparing its processing pattern with those of varian ts containing minimal nucleotide changes from the original sequence. O ur results demonstrate the determinant role of specific sequence motif s on coding-end processing and also the importance of the contort in w hich they are found. We show that minimal nucleotide changes in keg po sitions of a coding-end sequence can result in dramatic changes in the processing pattern. We propose that each coding-end sequence dictates a unique hairpin structure, the result of a particular energy conform ation between nucleotides organizing the loop and the stem, and that t he interplay between this structure and specific sequence motifs influ ences the frequency and location of nicks which open the coding-end ha irpin, These findings indicate that the sequences of the coding ends d etermine their own processing and have a profound impact on the develo pment of the primary B- and T-cell repertoires.