Methylation protects cytidines from AID-mediated deamination

Area of Science:

• Immunology
• Molecular Biology
• Epigenetics

Background:

• Somatic hypermutation (SHM), class switch recombination (CSR), and gene conversion rely on activation-induced cytidine deaminase (AID).
• The mechanism restricting AID activity to immunoglobulin genes remains unclear, despite some non-antibody genes mutating.
• AID inefficiently deaminates methyl cytidines, suggesting methylation could protect the genome from off-target AID activity.

Purpose of the Study:

• To investigate whether AID deaminates methylated CpG motifs in various sequence contexts.
• To determine if DNA methylation serves as a protective mechanism against AID activity outside immunoglobulin loci.

Main Methods:

• In vitro experiments using plasmid substrates to assess AID activity.
• Examined AID's deamination of both methylated and unmethylated CpG motifs.
• Evaluated AID's processivity on single-stranded DNA tracks.

Main Results:

• AID demonstrated processive-like activity, deaminating single-stranded DNA tracks longer than 300 nucleotides.
• Methylated CpG motifs were protected from AID-mediated deamination, unlike unmethylated CpG motifs.
• Methylation did not protect cytidines adjacent to CpG motifs, indicating context-dependent protection.

Conclusions:

• DNA methylation at CpG sites can protect against AID-mediated deamination, potentially safeguarding the genome from off-target mutations.
• These findings suggest a mechanism for restricting AID activity to immunoglobulin loci.
• AID and related cytidine deaminases may offer a faster method for identifying methylated CpG motifs compared to traditional bisulfite sequencing.