Increased microhomologies and mutation frequencies at Sμ-Sγ3 junctions in Mlh1^GR/GR switching B cells. (A) Distribution of breakpoints (open triangles) within Sμ and Sγ3 SRs from 27 and 22 successful recombination events in six WT and seven Mlh1^GR/GR mice, respectively. Arrows indicate the position of the nested primers used to detect Sμ-Sγ3 junctions. (B) Percentage of junctions exhibiting insertions (ins), blunt joins, or microhomologies. (C) Scatter plot representing the length in base pairs of each detected microhomology. Horizontal bars indicate the mean length of microhomology. (D) Frequency and type of mutations accumulated at the Sμ-Sγ3 junctions of WT and Mlh1^GR/GR B cells. Insertions and deletions (ins/del) were computed together. WRC:GYW and WA:TW motifs (W = A or T; R = purine; Y = pyrimidine) correspond to preferred AID and error-prone polymerase Polη hotspots, respectively. (E) Distribution of mutations around the recombination breakpoints. Mutations occurring within the same bin window of 100 bp were counted together and represented in histograms.