Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.

Area of Science:

• Genomics
• Evolutionary Biology
• Molecular Biology

Background:

• DNA sequence context significantly impacts mutation rates.
• CpG dinucleotides exhibit elevated mutation rates due to cytosine methylation.
• Methylation levels alone do not fully explain mutation rate variations in different sequence contexts.

Purpose of the Study:

• To quantify CpG mutation rates and the mutagenic effect of methylation across diverse sequence contexts.
• To investigate the interplay between methylation, flanking sequences, and CpG mutation rates.
• To explore conserved and species-specific patterns of CpG mutability in primates.

Main Methods:

• Utilized human polymorphism data from the gnomAD dataset.
• Employed a regression framework accounting for recurrent mutations.
• Estimated mutation rates for unmethylated and methylated CpGs in unique 4-mer and 6-mer contexts.

Main Results:

• CpG mutation rate variation is shaped by methylation, flanking nucleotides, and their interactions.
• Upstream sequences and downstream sequences exert largely independent effects on mutation rates.
• An upstream adenine markedly increases CpG mutation rates irrespective of methylation status or downstream sequences.
• Conserved sequence features influence CpG mutability across human, chimpanzee, and rhesus macaque.
• Pronounced inter-species differences, particularly at methylated sites in chimpanzees, suggest recent evolutionary changes.

Conclusions:

• Distinct context-dependent mutation patterns exist for unmethylated and methylated cytosines.
• Intrinsic DNA sequence features contribute to conserved context effects on CpG mutation rate.
• Inter-species variations in CpG mutability may stem from recent evolutionary adaptations in DNA demethylation and repair pathways.