BCL6 breaks occur preferentially at CpG and WGCW motifs. (A) Distance from BCL6 breakpoint to CpG motif in Ig–BCL6 and non-Ig–BCL6 translocations. The proportions of observed BCL6 breakpoints that occur directly at a CpG site (0 bp) and at distances of 1 to 2 bp, 3 to 4 bp, 5 to 8 bp, and greater than 8 bp from the nearest CpG site are shown in black (non-Ig rearrangements) and in gray (Ig translocations). For comparison, the corresponding proportions for a random distribution of breaks in the 2156-bp BCL6 break window are shown in white. The heights of the white bars reflect the density and spacing of CpG motifs in the break region. For example, 32.6% of the BCL6 breaks in non-Ig rearrangements (P < .003; supplemental Table 2), but only 13.5% of the BCL6 breaks in Ig translocations (P > .15; supplemental Table 1), occur directly at CpG compared with 15.3% for a random distribution of breaks in this region. (B) Timing of chromosomal translocations as a function of B-cell development. Breakpoint motif analysis suggests that most lymphoma translocations occur either in germinal center B-cells, when AID and BCL6 are highly expressed, or in pro-B/pre-B cells, when the RAG complex is highly expressed and AID is expressed at very low levels. The Ig breaks in most Ig-MYC and Ig-BCL6 translocations are in S_H regions, which contain hundreds of WGCW repeats, and the MYC and BCL6 breaks occur near WGCW and related motifs scattered throughout these partner loci (red text in figure). The Ig breaks in most pro-B/pre-B cell translocations are generated at J_H and D_H segments by the RAG complex as part of the V(D)J recombination process (blue text). Most CpG breaks occur at Ig partner loci in pro-B/pre-B cell translocations, but also in a subset of non-Ig–BCL6 rearrangements that probably occur in germinal center B-cells (orange text).