Frequent but biased class switch recombination in the S mu flanking regions

Immunoglobulin (Ig) heavy chain class switch recombination occurs mainly by joining two switch (S) regions, segments of tandemly repeated DNA sequences that lie upstream of heavy chain constant region genes. The products of this recombination event are a chromosomal DNA joint and a 'looped-out' circular DNA joint. Although a previous study showed that 40% of chromosomal joints in the mu gene switch region (S mu) are found in the flanking regions of S mu, which do not contain typical S mu region repeats [1], other studies revealed that almost all recombination sites on looped-out circular DNA are found within S regions [2-4]. To resolve this discrepancy, we have isolated and sequenced 164 DNA fragments containing recombination joints from both chromosomal and looped-out DNA of a single cell line, the murine B lymphoma line CH12F3, which switches from IgM to IgA production with a high frequency upon cytokine stimulation [5]. The recombination sites were distributed almost evenly in the S mu region and its flanking regions, suggesting that the final joining of DNA ends may not necessarily take place in S regions. In contrast, there were few joining sites in the exon located 5' of the switch region (the I mu exon), suggesting that the 3' end of the I mu exon might be the upstream border of the recombination joint.