# Somatic hypermutation patterns are shaped by both motif position and sequence grammar

## TL;DR

This study shows that the mutation patterns in antibodies depend on both the position and surrounding DNA sequence of specific motifs.

## Contribution

The study reveals a motif-specific sequence grammar and positional effects that influence AID activity during somatic hypermutation.

## Key findings

- Identical sequence contexts can have varying effects on different WRCH motifs' mutagenesis.
- Molecular dynamics show that AID's interaction with DNA is modulated by motif and context.
- Relocating a motif within the variable region alters its mutability.

## Abstract

Somatic hypermutation (SHM) in variable regions of immunoglobulin genes by activation-induced deaminase (AID) is essential for the maturation of protective antibodies against pathogen and vaccine antigens. AID preferentially mutates cytosines within WRCH motifs (wherein W = A/T, R = A/G, and H = A/C/T) in single-stranded DNA, yet these motifs show large but reproducible variation in mutation frequency, suggesting a crucial role for sequences flanking the WRCH motifs (i.e., a sequence grammar) in determining mutational outcomes. However, the nature of this sequence grammar is poorly understood. Here, we demonstrate that identical sequence contexts can exert significantly varying effects on the mutagenesis of different WRCH motifs. Molecular dynamics simulations reveal that both the sequence context and the specific WRCH motif modulate AID activity by altering the mode and strength of AID’s interactions with single-stranded DNA. Repositioning a motif and its context within the variable region significantly alters its mutability. Therefore, the mutability of AID target cytosines is determined by a motif-specific sequence grammar that determines, in part, how activation-induced deaminase binds single-stranded DNA, as well as the motif position.

Somatic hypermutation of immunoglobulin variable regions, a critical process for protective antibody maturation, is characterized by position-dependent variation in the mutability of WRCH motifs. This study shows that this differential mutability depends on a motif-specific sequence grammar and the location of the motif within the variable region.

Different WRCH motifs flanked by identical sequences exhibit significantly different mutation frequencies, suggesting that not only the sequence context, but also the specific motif sequence contributes to the observed differential mutability.Molecular modelling suggests that the mode and strength of single-stranded DNA binding by activation-induced deaminase (AID) are influenced by both the central motif and its sequence context, providing a mechanistic explanation for the observed differential mutability.Relocating a motif along with its sequence context within the variable region changes its mutability.

Different WRCH motifs flanked by identical sequences exhibit significantly different mutation frequencies, suggesting that not only the sequence context, but also the specific motif sequence contributes to the observed differential mutability.

Molecular modelling suggests that the mode and strength of single-stranded DNA binding by activation-induced deaminase (AID) are influenced by both the central motif and its sequence context, providing a mechanistic explanation for the observed differential mutability.

Relocating a motif along with its sequence context within the variable region changes its mutability.

Motif sequence, context, and position within the immunoglobulin variable region determine AID-dependent mutation frequencies.