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

Area of Science:

• Genetics
• Genomics
• Evolutionary Biology

Background:

• Mutation rate variation is influenced by sequence context, notably at CpG sites due to cytosine methylation.
• While methylation is a known factor, flanking sequences also affect CpG mutation rates, with incomplete correlation to methylation levels.

Purpose of the Study:

• To precisely quantify CpG mutation rates and the mutagenic impact of methylation across diverse sequence contexts.
• To investigate how sequence context, methylation, and their interactions shape mutation patterns in the human genome.

Main Methods:

• Utilized a regression framework accounting for recurrent mutations to analyze human polymorphism data from the gnomAD dataset.
• Estimated mutation rates for both unmethylated and methylated CpGs within specific 4-mer and 6-mer sequence contexts.

Main Results:

• CpG mutation rate variation is determined by methylation status, flanking nucleotides, and their interactions, indicating distinct patterns for methylated and unmethylated CpGs.
• Upstream sequences, particularly adenine, substantially elevate CpG mutation rates irrespective of methylation or downstream sequences.
• Sequence context effects on CpG mutability show conservation across human, chimpanzee, and rhesus macaque, but species-specific differences, especially in methylation effects on the chimpanzee lineage, suggest recent evolutionary changes.

Conclusions:

• Sequence context and methylation are key drivers of CpG mutation rate variation, with upstream sequences playing a significant role.
• Conserved sequence features influence CpG mutability, while inter-species variations highlight recent evolutionary adaptations in DNA repair and demethylation pathways.