Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma

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 neighboring nucleotides. In humans, contrary to prior suggestions, we find that nucleotides in the close vicinity (±3 bp) of methylated cytosines mutate less frequently. Reduced mutability around methylated CpGs is also observed in cancer genomes, considering single nucleotide variants alongside tissue-of-origin-matched methylation data. In contrast, methylation is associated with increased neighborhood mutation risk in A. thaliana and rice. The difference in neighborhood mutation risk is less pronounced further away from the focal CpG and modulated by regional GC content. Our results are consistent with a model where altered risk at neighboring bases is linked to lesion formation at the focal CpG and subsequent long-patch repair. Our findings indicate that cytosine methylation has a broader mutational footprint than is commonly assumed.

The Impact of DNA Methylation Dynamics on the Mutation Rate During Human Germline Development

“…The impact of methylation on germline mutation has long been a focus topic for scientists. Interestingly, our result is different from 2 previous researches (Xia et al 2012;Kusmartsev et al 2020) which reported few correlation between methylation and mutation. These two researches applied methylome of the 1 H embryonic stem cell which is somatic instead of germline-relevant.…”

“…Methylation level at a certain site may change dramatically during early fetal development ( Guo et al 2014 , 2015 ). To illustrate the methylation dynamics across stages, we classified methylation level into three groups, highly methylated (methylation level ≥70%), unmethylated (methylation level < 20%) and methylated (methylation level in between) ( Kusmartsev et al 2020 ). We then calculated the mutation rates for different combinations of methylation level groups on a certain site in all the stages.…”

“…A good method for overcoming the limitation of the small density of germline mutation variants is to use polymorphisms on behalf of de novo mutations (Agarwal and Przeworski 2019;Kusmartsev et al 2020). In large-scale mutation datasets, polymorphisms with low frequency variants are rare, so these mutations can be regarded as neutral mutations that minimize the effects of indirect selection and biased gene conversion (Schaibley et al 1984;Rahbari et al 2016;Carlson et al 2018;Agarwal and Przeworski 2019).…”

Comparative Analysis of Plastid Genomes in the Non-photosynthetic Genus Thismia Reveals Ongoing Gene Set Reduction

“…The analysis of substitution spectra and their contexts can give insights into the possible causes that underlie changes in the genomic sequence – for example, environmental factors such as UV light, or intrinsic genome properties such as methylation ( Ossowski et al, 2010 ; Kusmartsev et al, 2020 ). We analyzed the frequencies of synonymous substitutions in different contexts in the plastid genes of Thismia species.…”

Epigenetic Regulation of Genomic Stability by Vitamin C

“…DNA hypermethylation can also promote genomic instability, by silencing the expression of DNA repair genes, or by inhibiting the recruitment of DNA repair proteins ( Toffolatti et al, 2014 ; Tsuboi et al, 2020 ). Methylated cytosines are also intrinsically more mutagenic than unmethylated cytosines ( Poulos et al, 2017 ; Kusmartsev et al, 2020 ). Balancing the activity of writers and erasers of DNA methylation ensures that epigenetic information is interpreted and inherited correctly, but also protects cells from acquiring permanent changes to the genetic code.…”