The role of recombination signal sequences in the preferential joining by deletion in DH-JH recombination and in the ordered rearrangement of the IgH locus

The bias favoring deletion over inversion in DH-JH rearrangement has beenknown for years, but the underlying mechanism has yet to be fully defined.It has been suggested that the ratio of deletion/inversion is determined bythe combined effect of two factors: (i) the relative strengths of 5' and 3'recombination signal sequences (RSS) of a DH segment, and (ii) theefficiency with which the deletional product (one joint) forms relative tothe inversional product (two joints). In this study, we analyzed for thefirst time the effect of factor 1 alone on the biased 3' RSS utilization inDH-JH joining by using deletional plasmids in an extrachromosomal substrateV(D)J recombination assay. It was found that the 3' RSS and associatedcoding end (12 bp) mediate recombination more efficiently than the 5'RSS/coding end DH-JH plasmids. These results demonstrate that the effect ofthe RSS/coding end alone can account, at least partially, for thepredominant deletion in DH-JH recombination. The potential effect of therelative strength of RSS and associated coding end on the orderedrearrangement of DH-JH followed by VH to DH-JH was also assessed. Whenrecombination frequencies of D-->J (3' DH to J3) were compared withfrequencies of V-- >D (VHPJ14 to 3' DH or VHOX2 to 3' DH), it was foundthat V-->D joining was, if anything, more efficient than D-->Jjoining. Therefore, if all three segments were accessible, RSS/coding endeffects would not contribute to the ordered rearrangement of the IgH locus.