Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates

Abstract

It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines.

Single genome retrieval of context-dependent variability in mutation rates for human germline

“…The 1-mer averaged data were used for only the k-mers that contain either C or G bases of a CpG dyad at the centre, to assign the overall substitution rate constants by the Trek mapper. This was done since none of the CpG sites in the L1 remnants passed our robustness checks (Methods), due to the targeted, epigenetic- or APOBEC-affected single-nucleotide substitutions there [12–14]. The latter effects were likely to be non-uniform with time (active targeting, , while in the viable epoch for each L1 subfamily, at both DNA and RNA levels) and may had been present in order to silence the active retrotransposons.…”

“…Conversely, the adjacent enrichment in T increases the BSP of G ( c ) and decreases that of C ( f ) bases. Note, that our data are for , thus independent from the methylation-driven increased mutation rates in CpG dyads [12–14] …”

“…The outcome in Figure S11 in Additional file 1, overlapped with the whole-genome BSP profile, shows that stable sites in the human genome, assigned by the Trek mapper to have below 1.13 byr −1 , are significantly less likely to undergo somatic mutations in cancer. Like many other disease-causing mutation sites [64], most of the sites that are highly enriched in cancer (Figure S12a in Additional file 1) are CpGs [65], which, even without accounting for the methylation driven increase [12–14] of the mutation rates, show high basal mutability [66]. However, Figure S12b, c in Additional file 1 demonstrates the discussed trend in the 7-mer cancer enrichment ratio (Methods) vs. BSP dependence even when all the CpG sites are removed from the analysis.…”

“…In the equation above, the short-range effect is captured through the term and mainly describes the totality of the intrinsic properties and sequence-dependent interactions of DNA with overall mutagenic and reparation processes in a given organism [11]. The better-studied substitution patterns at a CpG context [12–14] are separated in the term, since besides having a specific short-range dyad context, the CpG mutations underlying the substitution term also depend on a number of regional factors that alter the epigenetic targeting of the CpG sites [10, 15–18]. Many relatively recent studies provide essential insights into the variation caused by the regional effects that depend on a long-range (megabase) sequence context through general mechanisms, such as recombination and GC-biased gene conversion [1, 19–21], transcription-coupled biased genome repair [22] and instability [23], chromatin-organisation- [24] and replication-associated mutational bias [25] and inhomogeneous repair [26], differential DNA mismatch repair [27], non-allelic gene conversion [28], and male mutation bias [29].…”

Alternative roles for oxidized mCs and TETs

“…This is attributed to an increased tendency for spontaneous deamination of 5mC compared to C [54,55] and the differential recruitment of error-prone repair enzymes. Deamination of an unmethylated C or 5hmC generates U:G or 5hmU:G mismatches that are efficiently repaired by thymine and uracil DNA glyosylases, TDG and SMUG1 [11,56].…”