Cytosine methylation affects the mutability of neighbouring nucleotides in human, Arabidopsis, and rice

Abstract

Methylated cytosines deaminate at higher rates than unmethylated cytosines and the lesions they produce are repaired less efficiently. As a result, methylated cytosines are mutational hotspots. Here, combining rare polymorphism and base-resolution methylation data in humans, Arabidopsis thaliana, and rice (Oryza sativa), we present evidence that methylation state affects mutation dynamics not only at the focal cytosine but also at neighbouring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity ({+/-}3nt) of methylated cytosines mutate less frequently. In contrast, methylation is associated with increased neighbourhood mutation risk in A. thaliana and rice. The difference in mutation risk associated with methylation is less pronounced further away from the focal CpG, is modulated by regional GC content, and enhanced in heterochromatic regions. Our results are consistent with a model where elevated risk at neighbouring bases is linked to lesion formation at the focal cytosine and subsequent long-patch repair. Our results provide evidence that cytosine methylation has a broader mutational footprints than commonly assumed. They also illustrate that methylation is not intrinsically associated with higher mutation risk for surrounding bases, but that mutagenic effects reflect evolved species-specific and lesion-specific predispositions to elicit error-prone long-patch DNA repair.