The role of recombination signal sequences in the preferential joining by deletion in D(H)-J(H) recombination and in the ordered rearrangement of the IgH locus

The bias favoring deletion over inversion in D(H)-J(H) rearrangement has been known for years, but the underlying mechanism has yet to be fully defined. It has been suggested that the ratio of deletion/inversion is determined by the combined effect of two factors: (i) the relative strengths of 5' and 3' recombination signal sequences (RSS) of a D(H) segment, and (ii) the efficiency with which the deletional product (one joint) forms relative to the inversional product (two joints). In this study, we analyzed for the first time the effect of factor 1 alone on the biased 3' RSS utilization in D(H)-J(H) joining by using deletional plasmids in an extrachromosomal substrate V(D)J recombination assay. It was found that the 3' RSS and associated coding end (12 bp) mediate recombination more efficiently than the 5' RSS/coding end on D(H)-J(H) plasmids. These results demonstrate that the effect of the RSS/coding end alone can account, at least partially, for the predominant deletion in D(H)-J(H) recombination. The potential effect of the relative strength of RSS and associated coding end on the ordered rearrangement of D(H)-J(H) followed by V(H) to D(H)-J(H) was also assessed. When recombination frequencies of D → J (3' D(H) to J3) were compared with frequencies of V → D (V(H)PJ14 to 3' D(H) or V(H)OX2 to 3' D(H)), it was found that V → D joining was, if anything, more efficient than D → J joining. Therefore, if all three segments were accessible, RSS/coding end effects would not contribute to the ordered rearrangement of the IgH locus.