Somatic hypermutation patterns in immunoglobulin variable regions are dictated by a motif-specific sequence grammar and motif position

Somatic hypermutation (SHM) of immunoglobulin variable (V) regions by activation-induced deaminase (AID) is essential for the maturation of protective antibodies. AID preferentially mutates cytosines within WRCH motifs (W=A/T, R=A/G, H=A/C/T), yet WRCH motifs show large but reproducible variations in mutation frequency, highlighting a crucial role for sequence-intrinsic mechanisms (a sequence grammar) in determining mutational outcomes and, therefore, in antibody maturation. Here, we demonstrate that the same sequence context can exert significantly varying effects on the mutability of different WRCH motifs. Furthermore, targeting of SHM to the template and non-template cytosines in palindromic AGCT motifs can be differentially regulated by sequence contexts. Additionally, we provide evidence that the location of a motif within the V region can have a significant impact on its mutability. Therefore, discrete V region mutation patterns arise from a combination of a motif-specific sequence grammar and motif position. Overall design: Examination of mutations in immunoglobulin variable region using MutPE-seq